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I2PC / xmipp

Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy.
http://biocomputingunit.es/
GNU General Public License v3.0
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[Installation] No such file or directory: 'src/xmippCore/install/xmipp.conf' #402

Closed jianhaoc closed 2 years ago

jianhaoc commented 2 years ago

Hi, did I miss anything for installation (see below)?

$ ./xmipp compile 10 Building Dependencies ------------------------------------- cmake .. -- The C compiler identification is GNU 4.8.5 -- The CXX compiler identification is GNU 4.8.5 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Found PythonInterp: /usr/bin/python (found version "2.7.5") -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Configuring done -- Generating done -- Build files have been written to: /data2/sw/xmipp/xmipp-bundle/src/googletest/build make gtest gtest_main Scanning dependencies of target gtest [100%] Building CXX object googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o Linking CXX static library ../lib/libgtest.a [100%] Built target gtest [ 50%] Built target gtest Scanning dependencies of target gtest_main [100%] Building CXX object googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o Linking CXX static library ../lib/libgtest_main.a [100%] Built target gtest_main Compiling ------------------------------------------- Traceback (most recent call last): File "./xmipp", line 1928, in ok = compile(Nproc) File "./xmipp", line 1388, in compile return compileXmipp(Nproc) File "./xmipp", line 1432, in compileXmipp if not compileModule(Nproc,"xmippCore"): File "./xmipp", line 1316, in compileModule shutil.copyfile(CONFIG_FILE_NAME,"src/%s/install/%s" % (module, CONFIG_FILE_NAME)) File "/usr/lib64/python3.6/shutil.py", line 121, in copyfile with open(dst, 'wb') as fdst: FileNotFoundError: [Errno 2] No such file or directory: 'src/xmippCore/install/xmipp.conf'

Vilax commented 2 years ago

Dear Jian,

If you want to install Xmipp, my advice is to download the repository ( https://github.com/I2PC/xmipp) as you did. And then launch

./xmipp

without compiling. The installer will give you tips if the installation shows drawbacks. Let me know if it does not work

Best

JL Vilas

El jue, 12 ago 2021 a las 21:04, jianhaoc @.***>) escribió:

Hi, did I miss anything for installation (see below)?

$ ./xmipp compile 10 Building Dependencies ------------------------------------- cmake .. -- The C compiler identification is GNU 4.8.5 -- The CXX compiler identification is GNU 4.8.5 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Found PythonInterp: /usr/bin/python (found version "2.7.5") -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Configuring done -- Generating done -- Build files have been written to: /data2/sw/xmipp/xmipp-bundle/src/googletest/build make gtest gtest_main Scanning dependencies of target gtest [100%] Building CXX object googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o Linking CXX static library ../lib/libgtest.a [100%] Built target gtest [ 50%] Built target gtest Scanning dependencies of target gtest_main [100%] Building CXX object googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o Linking CXX static library ../lib/libgtest_main.a [100%] Built target gtest_main Compiling ------------------------------------------- Traceback (most recent call last): File "./xmipp", line 1928, in ok = compile(Nproc) File "./xmipp", line 1388, in compile return compileXmipp(Nproc) File "./xmipp", line 1432, in compileXmipp if not compileModule(Nproc,"xmippCore"): File "./xmipp", line 1316, in compileModule shutil.copyfile(CONFIG_FILE_NAME,"src/%s/install/%s" % (module, CONFIG_FILE_NAME)) File "/usr/lib64/python3.6/shutil.py", line 121, in copyfile with open(dst, 'wb') as fdst: FileNotFoundError: [Errno 2] No such file or directory: 'src/xmippCore/install/xmipp.conf'

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DStrelak commented 2 years ago

Hi @jianhaoc ,

I would like to expand on the answer from JL. The recommended compilation / installation procedure for the standalone version is:

  1. git clone https://github.com/I2PC/xmipp.git xmipp-bundle
  2. cd xmipp-bundle
  3. ./xmipp

From the log, it seems that some steps of the installation were skipped / did not execute properly. I recommend you to start from scratch by deleting your current xmipp directory and making a clean clone from github.

I would also like to recommend you to update your compiler and Python. Preferably use the newest version of your favorite c++11 compatible compiler (for example GCC 7.5) and Python 3.6 or newer.

If you use Scipion, the recommended way is to install Xmipp via Scipion's Plugin Manager:

  1. navigate to the folder with Scipion
  2. ./scipion3
  3. In the top bar, select Others -> Plugin Manager
  4. Select scipion-em-xmipp plugin (the square should be black)
  5. Press the "Play" button to install it
jianhaoc commented 2 years ago

Hi, thank you for your help. But there are still some issues (see below).

  1. how can I set up to use nvcc to compile? nvcc fatal : A single input file is required for a non-link phase when an outputfile is specified Check the NVCC, NVCC_CXXFLAGS and INCDIRFLAGS Cannot compile with NVCC, continuing without CUDA

  2. look like some files are missed. scons: building terminated because of errors.

'CTPL/ctpl_stl.h' file not found. This file belongs to CTPL dependency. Please, try 'cd src/CTPL ; git checkout -- ctpl_stl.h ; cd -' and re-compile.

Some error occurred during the compilation of 'xmipp' ('libraries/reconstruction/aalign_significant.os').

My environment is gcc-7.5.0, cuda-10.2. Before compiling, I also set up some environment variants. export CXX_CUDA=/usr/local/cuda-10.2/bin export NVCC_CXXFLAGS=/data2/sw/gcc/gcc-7.5.0/build/bin export INCDIRFLAGS=/data2/sw/gcc/gcc-7.5.0/build/include

for complete output

$ ./xmipp Configuring ----------------------------------------- gcc detected g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o /data2/sw/gcc/gcc-7.5.0/build/include OpenCV not found rm -v xmipp_test_opencv* CUDA-10.2.89 detected. Using '/usr/local/cuda-10.2/targets/x86_64-linux/lib'. 'mpirun' detected. 'mpicc' detected. 'mpicxx' detected. Java detected at: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64

Do you want to build tests [yes/NO]NO Configuration completed..... Checking configuration ------------------------------ Checking MPI configuration ... mpicxx -c -w /data2/sw/gcc/gcc-7.5.0/build/include -mtune=native -march=native -std=c++11 -O3 -I/usr/include/openmpi-x86_64 xmipp_mpi_test_main.cpp -o xmipp_mpi_test_main.o g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done mpicxx -L/opt/conda3/envs/xmipp/lib xmipp_mpi_test_main.o -o xmipp_mpi_test_main -lfftw3 -lfftw3_threads -lhdf5 -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread rm xmipp_mpi_test_main* mpirun -np 2 echo ' > This sentence should be printed 2 times if mpi runs fine.'

This sentence should be printed 2 times if mpi runs fine. This sentence should be printed 2 times if mpi runs fine. Checking Java configuration... /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/bin/javac Xmipp.java rm Xmipp.java Xmipp.class g++ -c -w -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/include/linux /data2/sw/gcc/gcc-7.5.0/build/include xmipp_jni_test.cpp -o xmipp_jni_test.o g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done rm xmipp_jni_test Checking CUDA configuration ... /usr/local/cuda-10.2/bin/nvcc -c -w /data2/sw/gcc/gcc-7.5.0/build/bin /data2/sw/gcc/gcc-7.5.0/build/include xmipp_cuda_test.cpp -o xmipp_cuda_test.o nvcc fatal : A single input file is required for a non-link phase when an outputfile is specified Check the NVCC, NVCC_CXXFLAGS and INCDIRFLAGS Cannot compile with NVCC, continuing without CUDA rm xmipp_cuda_test Getting Dependencies ------------------------------------- git clone -b master https://github.com/vit-vit/CTPL.git src/CTPL Cloning into 'src/CTPL'... Getting sources ------------------------------------- git clone -b devel https://github.com/I2PC/xmippCore.git src/xmippCore Cloning into 'src/xmippCore'... git clone -b devel https://github.com/I2PC/xmippViz.git src/xmippViz Cloning into 'src/xmippViz'... git clone -b devel https://github.com/I2PC/scipion-em-xmipp.git src/scipion-em-xmipp Cloning into 'src/scipion-em-xmipp'... Checkouting xmipp:devel ... Already up-to-date. Building Dependencies ------------------------------------- Compiling ------------------------------------------- scons -j8 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... g++ -o core/args.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/args.cpp g++ -o core/argsparser.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/argsparser.cpp g++ -o core/argsprinter.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/argsprinter.cpp g++ -o core/comment_list.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/comment_list.cpp g++ -o core/geometry.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/geometry.cpp g++ -o core/histogram.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/histogram.cpp g++ -o core/linear_system_helper.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/linear_system_helper.cpp g++ -o core/matrix1d.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/matrix1d.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/matrix2d.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/matrix2d.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_base.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/metadata_base.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_db.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/metadata_db.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_extension.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/metadata_extension.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_generator.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/metadata_generator.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_object.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/metadata_object.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_query.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/metadata_query.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_row_sql.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/metadata_row_sql.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_row_vec.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/metadata_row_vec.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_sql.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/metadata_sql.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_static.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/metadata_static.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_vec.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/metadata_vec.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/multidim_array.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/multidim_array.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/multidim_array_base.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/multidim_array_base.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/multidim_array_generic.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/multidim_array_generic.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/numerical_recipes.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/numerical_recipes.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwDM3.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/rwDM3.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwDM4.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/rwDM4.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwEM.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/rwEM.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwHDF5.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/rwHDF5.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwIMAGIC.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/rwIMAGIC.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwINF.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/rwINF.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwJPEG.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/rwJPEG.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwMRC.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/rwMRC.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwPIF.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/rwPIF.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwRAW.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/rwRAW.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwSPE.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/rwSPE.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwSPIDER.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/rwSPIDER.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwTIA.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/rwTIA.cpp g++ -o core/rwTIFF.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/rwTIFF.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/symmetries.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/symmetries.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/transformations.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/transformations.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/userSettings.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/userSettings.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_color.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_color.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_datatype.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_datatype.cpp g++ -o core/xmipp_error.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_error.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_fft.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_fft.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_fftw.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_fftw.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_filename.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_filename.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_funcs.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_funcs.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_hdf5.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_hdf5.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_image.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_image.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_image_base.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_image_base.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_image_extension.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_image_extension.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_image_generic.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_image_generic.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_log.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_log.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_memory.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_memory.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_metadata_program.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_metadata_program.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_program.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_program.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_program_sql.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_program_sql.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_strings.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_strings.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_threads.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xmipp_threads.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xvsmooth.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/xvsmooth.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done gcc -o core/sqlite3-extension-functions.os -c -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/sqlite3-extension-functions.c g++ -o core/bilib/changebasis.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/changebasis.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/convert.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/convert.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/dft.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/dft.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/dht.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/dht.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/findroot.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/findroot.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/firconvolve.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/firconvolve.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/flip.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/flip.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/fold.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/fold.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/fourierconvolve.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/fourierconvolve.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/geometry.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/geometry.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/getpoles.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/getpoles.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/getput.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/getput.cc g++ -o core/bilib/getputd.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/getputd.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/gradient.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/gradient.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/histogram.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/histogram.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/iirconvolve.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/iirconvolve.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/interpolate.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/interpolate.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/kernel.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/kernel.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/kerneldiff.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/kerneldiff.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/kerneldiff1.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/kerneldiff1.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/kerneldiff2.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/kerneldiff2.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/kernelintegrate.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/kernelintegrate.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/linearalgebra.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/linearalgebra.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/messagedisplay.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/messagedisplay.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/minmax.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/minmax.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/morphology.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/morphology.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/movingaverage.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/movingaverage.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/polynomial.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/polynomial.cc g++ -o core/bilib/positivepower.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/positivepower.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/pyramidfilters.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/pyramidfilters.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/pyramidtools.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/pyramidtools.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/round.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/round.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/swap.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/swap.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/timestamp.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/timestamp.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/traceline.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/traceline.cc g++ -o core/bilib/wavelet.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/wavelet.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/waveletfilters.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/waveletfilters.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/waveletfiltersfract.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/waveletfiltersfract.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/wavelettools.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/wavelettools.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/window.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/bilib/window.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/alglibinternal.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/alglib/alglibinternal.cpp g++ -o core/alglib/alglibmisc.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/alglib/alglibmisc.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/ap.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/alglib/ap.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/dataanalysis.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/alglib/dataanalysis.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/diffequations.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/alglib/diffequations.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/fasttransforms.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/alglib/fasttransforms.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/integration.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/alglib/integration.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/interpolation.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/alglib/interpolation.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/linalg.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/alglib/linalg.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/optimization.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/alglib/optimization.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/solvers.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/alglib/solvers.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/specialfunctions.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/alglib/specialfunctions.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/statistics.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/alglib/statistics.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/utils/sql_utils.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/utils/sql_utils.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/utils/time_utils.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include core/utils/time_utils.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o lib/libXmippCore.so -L/opt/conda3/envs/xmipp/lib -shared core/args.os core/argsparser.os core/argsprinter.os core/comment_list.os core/geometry.os core/histogram.os core/linear_system_helper.os core/matrix1d.os core/matrix2d.os core/metadata_base.os core/metadata_db.os core/metadata_extension.os core/metadata_generator.os core/metadata_object.os core/metadata_query.os core/metadata_row_sql.os core/metadata_row_vec.os core/metadata_sql.os core/metadata_static.os core/metadata_vec.os core/multidim_array.os core/multidim_array_base.os core/multidim_array_generic.os core/numerical_recipes.os core/rwDM3.os core/rwDM4.os core/rwEM.os core/rwHDF5.os core/rwIMAGIC.os core/rwINF.os core/rwJPEG.os core/rwMRC.os core/rwPIF.os core/rwRAW.os core/rwSPE.os core/rwSPIDER.os core/rwTIA.os core/rwTIFF.os core/symmetries.os core/transformations.os core/userSettings.os core/xmipp_color.os core/xmipp_datatype.os core/xmipp_error.os core/xmipp_fft.os core/xmipp_fftw.os core/xmipp_filename.os core/xmipp_funcs.os core/xmipp_hdf5.os core/xmipp_image.os core/xmipp_image_base.os core/xmipp_image_extension.os core/xmipp_image_generic.os core/xmipp_log.os core/xmipp_memory.os core/xmipp_metadata_program.os core/xmipp_program.os core/xmipp_program_sql.os core/xmipp_strings.os core/xmipp_threads.os core/xvsmooth.os core/sqlite3-extension-functions.os core/bilib/changebasis.os core/bilib/convert.os core/bilib/dft.os core/bilib/dht.os core/bilib/findroot.os core/bilib/firconvolve.os core/bilib/flip.os core/bilib/fold.os core/bilib/fourierconvolve.os core/bilib/geometry.os core/bilib/getpoles.os core/bilib/getput.os core/bilib/getputd.os core/bilib/gradient.os core/bilib/histogram.os core/bilib/iirconvolve.os core/bilib/interpolate.os core/bilib/kernel.os core/bilib/kerneldiff.os core/bilib/kerneldiff1.os core/bilib/kerneldiff2.os core/bilib/kernelintegrate.os core/bilib/linearalgebra.os core/bilib/messagedisplay.os core/bilib/minmax.os core/bilib/morphology.os core/bilib/movingaverage.os core/bilib/polynomial.os core/bilib/positivepower.os core/bilib/pyramidfilters.os core/bilib/pyramidtools.os core/bilib/round.os core/bilib/swap.os core/bilib/timestamp.os core/bilib/traceline.os core/bilib/wavelet.os core/bilib/waveletfilters.os core/bilib/waveletfiltersfract.os core/bilib/wavelettools.os core/bilib/window.os core/alglib/alglibinternal.os core/alglib/alglibmisc.os core/alglib/ap.os core/alglib/dataanalysis.os core/alglib/diffequations.os core/alglib/fasttransforms.os core/alglib/integration.os core/alglib/interpolation.os core/alglib/linalg.os core/alglib/optimization.os core/alglib/solvers.os core/alglib/specialfunctions.os core/alglib/statistics.os core/utils/sql_utils.os core/utils/time_utils.os $( -Llib -L/opt/conda3/envs/xmipp/lib $) -lfftw3 -lfftw3_threads -lhdf5 -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread gcc -o lib/xmippCore.so -L/opt/conda3/envs/xmipp/lib -shared $( -Llib -L/opt/conda3/envs/xmipp/lib $) -lpython3.8 -lXmippCore scons: done building targets. scons -j8 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... g++ -o external/condor/CNLSolver.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/CNLSolver.cpp g++ -o external/condor/CTRSSolver.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/CTRSSolver.cpp g++ -o external/condor/IntPoly.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/IntPoly.cpp g++ -o external/condor/KeepBests.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/KeepBests.cpp g++ -o external/condor/MSSolver.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/MSSolver.cpp g++ -o external/condor/Matrix.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/Matrix.cpp g++ -o external/condor/MatrixTriangle.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/MatrixTriangle.cpp g++ -o external/condor/MultInd.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/MultInd.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/ObjectiveFunction.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/ObjectiveFunction.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/Poly.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/Poly.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/QPSolver.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/QPSolver.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/UTRSSolver.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/UTRSSolver.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/Vector.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/Vector.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/VectorChar.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/VectorChar.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/VectorInt.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/VectorInt.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/parallel.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/parallel.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/tools.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/tools.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/dcel.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/dcel.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/delaunay.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/delaunay.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/graph.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/graph.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/point.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/point.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/polygon.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/polygon.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/sorting.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/sorting.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/stack.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/stack.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/triangulation.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/triangulation.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/voronoi.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/voronoi.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/ahc_classifier.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/ahc_classifier.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/analyze_cluster.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/analyze_cluster.cpp g++ -o libraries/classification/batch_som.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/batch_som.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/code_book.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/code_book.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/fcmeans.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/fcmeans.cpp g++ -o libraries/classification/fkcn.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/fkcn.cpp g++ -o libraries/classification/fuzzy_code_book.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/fuzzy_code_book.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/fuzzy_som.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/fuzzy_som.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/gaussian_kerdensom.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/gaussian_kerdensom.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/kSVD.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/kSVD.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/kerdensom.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/kerdensom.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/knn_classifier.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/knn_classifier.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/map.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/map.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/naive_bayes.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/naive_bayes.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/pca.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/pca.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/sammon.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/sammon.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/som.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/som.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/svm.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/svm.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/svm_classifier.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/svm_classifier.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/training_vector.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/training_vector.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/basic_pca.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/basic_pca.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/basis.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/basis.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/blobs.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/blobs.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/cpu.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/cpu.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/ctf.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/ctf.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/euler.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/euler.cpp g++ -o libraries/data/filters.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/filters.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/fourier_filter.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/fourier_filter.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/fourier_projection.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/fourier_projection.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/grids.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/grids.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/image_operate.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/image_operate.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/image_resize.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/image_resize.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/integration.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/integration.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/mask.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/mask.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/micrograph.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/micrograph.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/monogenic_signal.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/monogenic_signal.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/morphology.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/morphology.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/normalize.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/normalize.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/numerical_tools.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/numerical_tools.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/pdb.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/pdb.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/phantom.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/phantom.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/polar.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/polar.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/projection.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/projection.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/psf_xr.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/psf_xr.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/rotational_spectrum.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/rotational_spectrum.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/sampling.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/sampling.cpp g++ -o libraries/data/sparse_matrix2d.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/sparse_matrix2d.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/spherical_harmonics.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/spherical_harmonics.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/splines.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/splines.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/steerable.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/steerable.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/symmetries.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/symmetries.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/transform_downsample.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/transform_downsample.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/transform_geometry.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/transform_geometry.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/unitCell.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/unitCell.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/wavelet.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/wavelet.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/xmipp_image_convert.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/xmipp_image_convert.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/xmipp_image_over.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/xmipp_image_over.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/xmipp_polynomials.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/xmipp_polynomials.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/diffusionMaps.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/diffusionMaps.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/dimred_tools.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/dimred_tools.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/gplvm.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/gplvm.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/hessianLLE.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/hessianLLE.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/kernelPCA.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/kernelPCA.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/laplacianEigenmaps.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/laplacianEigenmaps.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/lltsa.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/lltsa.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/lpp.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/lpp.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/ltsa.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/ltsa.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/matrix_dimred.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/matrix_dimred.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/nca.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/nca.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/npe.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/npe.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/pca.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/pca.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/probabilisticPCA.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/probabilisticPCA.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/spe.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/spe.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/transform_dimred.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/transform_dimred.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/interface/docfile.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/interface/docfile.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/interface/frm.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/interface/frm.cpp g++ -o libraries/interface/python_utils.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/interface/python_utils.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/interface/selfile.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/interface/selfile.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/interface/spider.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/interface/spider.cpp g++ -o libraries/reconstruction/aalign_significant.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/aalign_significant.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done In file included from libraries/reconstruction/aalign_significant.cpp:26:0: libraries/reconstruction/aalign_significant.h:32:10: fatal error: CTPL/ctpl_stl.h: No such file or directory

include <CTPL/ctpl_stl.h>

^~~~~ compilation terminated. scons: *** [libraries/reconstruction/aalign_significant.os] Error 1 g++ -o libraries/reconstruction/adjust_volume_grey_levels.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/adjust_volume_grey_levels.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done scons: building terminated because of errors.

'CTPL/ctpl_stl.h' file not found. This file belongs to CTPL dependency. Please, try 'cd src/CTPL ; git checkout -- ctpl_stl.h ; cd -' and re-compile.

Some error occurred during the compilation of 'xmipp' ('libraries/reconstruction/aalign_significant.os').

jianhaoc commented 2 years ago

I also tried 'cd src/CTPL ; git checkout -- ctpl_stl.h ; cd -' and re-run ./xmipp. Look like it doesn't work (see below).

$ ./xmipp 'xmipp.conf' detected. Checking configuration ------------------------------ 'xmipp.conf' is already checked. Set VERIFIED=False to re-checked Getting Dependencies ------------------------------------- Checkouting CTPL:master ... Already up-to-date. Getting sources ------------------------------------- Checkouting xmippCore:devel ... Already up-to-date. Checkouting xmippViz:devel ... Already up-to-date. Checkouting scipion-em-xmipp:devel ... Already up-to-date. Checkouting xmipp:devel ... Already up-to-date. Building Dependencies ------------------------------------- Compiling ------------------------------------------- scons -j8 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... scons: lib/libXmippCore.so' is up to date. scons:lib/xmippCore.so' is up to date. scons: done building targets. scons -j8 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... g++ -o libraries/reconstruction/aalign_significant.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/aalign_significant.cpp g++ -o libraries/reconstruction/aextrema_finder.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/aextrema_finder.cpp g++ -o libraries/reconstruction/align2d.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/align2d.cpp g++ -o libraries/reconstruction/align_tilt_pairs.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/align_tilt_pairs.cpp g++ -o libraries/reconstruction/angular_accuracy_pca.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_accuracy_pca.cpp g++ -o libraries/reconstruction/angular_break_symmetry.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_break_symmetry.cpp g++ -o libraries/reconstruction/angular_commonline.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_commonline.cpp In file included from libraries/reconstruction/aalign_significant.cpp:26:0: libraries/reconstruction/aalign_significant.h:32:10: fatal error: CTPL/ctpl_stl.h: No such file or directory

include <CTPL/ctpl_stl.h>

      ^~~~~~~~~~~~~~~~~

compilation terminated. scons: *** [libraries/reconstruction/aalign_significant.os] Error 1 g++ -o libraries/reconstruction/angular_continuous_assign.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_continuous_assign.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done scons: building terminated because of errors.

'CTPL/ctpl_stl.h' file not found. This file belongs to CTPL dependency. Please, try 'cd src/CTPL ; git checkout -- ctpl_stl.h ; cd -' and re-compile.

Some error occurred during the compilation of 'xmipp' ('libraries/reconstruction/aalign_significant.os').

DStrelak commented 2 years ago

Hi @jianhaoc,

Did you manually modify the xmipp.conf file? It seems like you're missing -I../ in the INCDIRFLAGS. Try to add it and let me know if that helped. Ideally rename the xmipp.conf and regenerate it, it should be added automatically.

jianhaoc commented 2 years ago

Hi @DStrelak,

I didn't manually modify the xmipp.conf file. I add -I../ as you mentioned. Some issue is fixed and another issue comes out (see below). I still couldn't compile with cuda. Should I change environment variable NVCC_CXXFLAGS to the path to nvcc (/usr/local/cuda-10.2/bin)? I'm not sure what should be these variable, CXX_CUDA, NVCC_CXXFLAGS, INCDIRFLAGS. Are they should be paths to some folders in cuda or gcc?

$ more xmipp.conf [BUILD] BUILD_TESTS=False CC=gcc CCFLAGS=-std=c99 CONFIG_VERSION=da79a68646fc02c9ce2b4e7f622b5085949fd899 CUDA=False CXX=g++ CXXFLAGS=-mtune=native -march=native -std=c++11 -O3 CXX_CUDA=/usr/local/cuda-10.2/bin DEBUG=False INCDIRFLAGS=/data2/sw/gcc/gcc-7.5.0/build/include -I../ JAR=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/bin/jar JAVAC=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/bin/javac JAVA_BINDIR=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/bin JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64 JNI_CPPPATH=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/include:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/include/linux LIBDIRFLAGS=-L/opt/conda3/envs/xmipp/lib LINKERFORPROGRAMS=g++ LINKFLAGS= MATLAB=False MATLAB_DIR= MPI_CC=mpicc MPI_CXX=mpicxx MPI_CXXFLAGS=-I/usr/include/openmpi-x86_64 MPI_LINKERFORPROGRAMS=mpicxx MPI_LINKFLAGS= MPI_RUN=mpirun NVCC=/usr/local/cuda-10.2/bin/nvcc NVCC_CXXFLAGS=/data2/sw/gcc/gcc-7.5.0/build/bin NVCC_LINKFLAGS=-L/usr/local/cuda-10.2/targets/x86_64-linux/lib -L/usr/local/cuda-10.2/targets/x86_64-linux/lib/stubs OPENCV=False OPENCV3=False OPENCVSUPPORTSCUDA=False PYTHONINCFLAGS=-I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include PYTHON_LIB=python3.8 STARPU=False STARPU_HOME= STARPU_INCLUDE=/include/starpu/1.3 STARPU_LIB=/lib STARPU_LIBRARY=libstarpu-1.3 USE_DL=False VERIFIED=True

$ ./xmipp 'xmipp.conf' detected. Checking configuration ------------------------------ 'xmipp.conf' is already checked. Set VERIFIED=False to re-checked Getting Dependencies ------------------------------------- Checkouting CTPL:master ... Already up-to-date. Getting sources ------------------------------------- Checkouting xmippCore:devel ... Already up-to-date. Checkouting xmippViz:devel ... Already up-to-date. Checkouting scipion-em-xmipp:devel ... Already up-to-date. Checkouting xmipp:devel ... Already up-to-date. Building Dependencies ------------------------------------- Compiling ------------------------------------------- scons -j8 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... g++ -o core/args.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/args.cpp g++ -o core/argsparser.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/argsparser.cpp g++ -o core/argsprinter.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/argsprinter.cpp g++ -o core/comment_list.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/comment_list.cpp g++ -o core/geometry.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/geometry.cpp g++ -o core/histogram.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/histogram.cpp g++ -o core/linear_system_helper.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/linear_system_helper.cpp g++ -o core/matrix1d.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/matrix1d.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/matrix2d.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/matrix2d.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_base.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/metadata_base.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_db.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/metadata_db.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_extension.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/metadata_extension.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_generator.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/metadata_generator.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_object.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/metadata_object.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_query.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/metadata_query.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_row_sql.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/metadata_row_sql.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_row_vec.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/metadata_row_vec.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_sql.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/metadata_sql.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_static.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/metadata_static.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/metadata_vec.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/metadata_vec.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/multidim_array.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/multidim_array.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/multidim_array_base.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/multidim_array_base.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/multidim_array_generic.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/multidim_array_generic.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/numerical_recipes.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/numerical_recipes.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwDM3.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/rwDM3.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwDM4.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/rwDM4.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwEM.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/rwEM.cpp g++ -o core/rwHDF5.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/rwHDF5.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwIMAGIC.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/rwIMAGIC.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwINF.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/rwINF.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwJPEG.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/rwJPEG.cpp g++ -o core/rwMRC.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/rwMRC.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwPIF.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/rwPIF.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwRAW.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/rwRAW.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwSPE.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/rwSPE.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwSPIDER.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/rwSPIDER.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwTIA.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/rwTIA.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/rwTIFF.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/rwTIFF.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/symmetries.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/symmetries.cpp g++ -o core/transformations.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/transformations.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/userSettings.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/userSettings.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_color.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_color.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_datatype.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_datatype.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_error.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_error.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_fft.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_fft.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_fftw.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_fftw.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_filename.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_filename.cpp g++ -o core/xmipp_funcs.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_funcs.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_hdf5.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_hdf5.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_image.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_image.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_image_base.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_image_base.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_image_extension.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_image_extension.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_image_generic.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_image_generic.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_log.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_log.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_memory.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_memory.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_metadata_program.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_metadata_program.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_program.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_program.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_program_sql.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_program_sql.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_strings.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_strings.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xmipp_threads.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xmipp_threads.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/xvsmooth.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/xvsmooth.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/changebasis.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/changebasis.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/convert.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/convert.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/dft.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/dft.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/dht.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/dht.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/findroot.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/findroot.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/firconvolve.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/firconvolve.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/flip.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/flip.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/fold.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/fold.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/fourierconvolve.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/fourierconvolve.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/geometry.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/geometry.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/getpoles.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/getpoles.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/getput.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/getput.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/getputd.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/getputd.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/gradient.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/gradient.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/histogram.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/histogram.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/iirconvolve.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/iirconvolve.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/interpolate.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/interpolate.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/kernel.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/kernel.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/kerneldiff.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/kerneldiff.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/kerneldiff1.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/kerneldiff1.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/kerneldiff2.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/kerneldiff2.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/kernelintegrate.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/kernelintegrate.cc g++ -o core/bilib/linearalgebra.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/linearalgebra.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/messagedisplay.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/messagedisplay.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/minmax.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/minmax.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/morphology.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/morphology.cc g++ -o core/bilib/movingaverage.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/movingaverage.cc g++ -o core/bilib/polynomial.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/polynomial.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/positivepower.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/positivepower.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/pyramidfilters.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/pyramidfilters.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/pyramidtools.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/pyramidtools.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/round.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/round.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/swap.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/swap.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/timestamp.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/timestamp.cc g++ -o core/bilib/traceline.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/traceline.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/wavelet.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/wavelet.cc g++ -o core/bilib/waveletfilters.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/waveletfilters.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/waveletfiltersfract.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/waveletfiltersfract.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/wavelettools.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/wavelettools.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/bilib/window.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/bilib/window.cc g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/alglibinternal.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/alglib/alglibinternal.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/alglibmisc.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/alglib/alglibmisc.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/ap.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/alglib/ap.cpp g++ -o core/alglib/dataanalysis.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/alglib/dataanalysis.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/diffequations.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/alglib/diffequations.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/fasttransforms.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/alglib/fasttransforms.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/integration.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/alglib/integration.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/interpolation.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/alglib/interpolation.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/linalg.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/alglib/linalg.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/optimization.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/alglib/optimization.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/solvers.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/alglib/solvers.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/specialfunctions.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/alglib/specialfunctions.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/alglib/statistics.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/alglib/statistics.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/utils/sql_utils.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/utils/sql_utils.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o core/utils/time_utils.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src core/utils/time_utils.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done scons: lib/libXmippCore.so' is up to date. scons:lib/xmippCore.so' is up to date. scons: done building targets. scons -j8 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... g++ -o external/condor/CNLSolver.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/CNLSolver.cpp g++ -o external/condor/CTRSSolver.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/CTRSSolver.cpp g++ -o external/condor/IntPoly.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/IntPoly.cpp g++ -o external/condor/KeepBests.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/KeepBests.cpp g++ -o external/condor/MSSolver.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/MSSolver.cpp g++ -o external/condor/Matrix.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/Matrix.cpp g++ -o external/condor/MatrixTriangle.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/MatrixTriangle.cpp g++ -o external/condor/MultInd.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/MultInd.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/ObjectiveFunction.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/ObjectiveFunction.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/Poly.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/Poly.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/QPSolver.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/QPSolver.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/UTRSSolver.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/UTRSSolver.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/Vector.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/Vector.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/VectorChar.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/VectorChar.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/VectorInt.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/VectorInt.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/parallel.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/parallel.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/condor/tools.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/condor/tools.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/dcel.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/dcel.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/delaunay.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/delaunay.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/graph.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/graph.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/point.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/point.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/polygon.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/polygon.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/sorting.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/sorting.cpp g++ -o external/delaunay/stack.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/stack.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/triangulation.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/triangulation.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/delaunay/voronoi.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/delaunay/voronoi.cpp g++ -o libraries/classification/ahc_classifier.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/ahc_classifier.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/analyze_cluster.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/analyze_cluster.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/batch_som.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/batch_som.cpp g++ -o libraries/classification/code_book.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/code_book.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/fcmeans.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/fcmeans.cpp g++ -o libraries/classification/fkcn.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/fkcn.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/fuzzy_code_book.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/fuzzy_code_book.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/fuzzy_som.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/fuzzy_som.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/gaussian_kerdensom.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/gaussian_kerdensom.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/kSVD.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/kSVD.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/kerdensom.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/kerdensom.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/knn_classifier.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/knn_classifier.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/map.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/map.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/naive_bayes.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/naive_bayes.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/pca.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/pca.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/sammon.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/sammon.cpp g++ -o libraries/classification/som.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/som.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/svm.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/svm.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/svm_classifier.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/svm_classifier.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/classification/training_vector.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/classification/training_vector.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/basic_pca.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/basic_pca.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/basis.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/basis.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/blobs.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/blobs.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/cpu.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/cpu.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/ctf.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/ctf.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/euler.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/euler.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/filters.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/filters.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/fourier_filter.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/fourier_filter.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/fourier_projection.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/fourier_projection.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/grids.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/grids.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/image_operate.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/image_operate.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/image_resize.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/image_resize.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/integration.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/integration.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/mask.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/mask.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/micrograph.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/micrograph.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/monogenic_signal.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/monogenic_signal.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/morphology.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/morphology.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/normalize.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/normalize.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/numerical_tools.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/numerical_tools.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/pdb.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/pdb.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/phantom.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/phantom.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/polar.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/polar.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/projection.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/projection.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/psf_xr.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/psf_xr.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/rotational_spectrum.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/rotational_spectrum.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/sampling.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/sampling.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/sparse_matrix2d.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/sparse_matrix2d.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/spherical_harmonics.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/spherical_harmonics.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/splines.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/splines.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/steerable.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/steerable.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/symmetries.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/symmetries.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/transform_downsample.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/transform_downsample.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/transform_geometry.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/transform_geometry.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/unitCell.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/unitCell.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/wavelet.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/wavelet.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/xmipp_image_convert.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/xmipp_image_convert.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/xmipp_image_over.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/xmipp_image_over.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/data/xmipp_polynomials.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/data/xmipp_polynomials.cpp g++ -o libraries/dimred/diffusionMaps.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/diffusionMaps.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/dimred_tools.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/dimred_tools.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/gplvm.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/gplvm.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/hessianLLE.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/hessianLLE.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/kernelPCA.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/kernelPCA.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/laplacianEigenmaps.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/laplacianEigenmaps.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/lltsa.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/lltsa.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/lpp.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/lpp.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/ltsa.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/ltsa.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/matrix_dimred.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/matrix_dimred.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/nca.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/nca.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/npe.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/npe.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/pca.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/pca.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/probabilisticPCA.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/probabilisticPCA.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/spe.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/spe.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/dimred/transform_dimred.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/dimred/transform_dimred.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/interface/docfile.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/interface/docfile.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/interface/frm.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/interface/frm.cpp g++ -o libraries/interface/python_utils.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/interface/python_utils.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/interface/selfile.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/interface/selfile.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/interface/spider.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/interface/spider.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/aalign_significant.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/aalign_significant.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/adjust_volume_grey_levels.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/adjust_volume_grey_levels.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/aextrema_finder.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/aextrema_finder.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/align2d.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/align2d.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/align_tilt_pairs.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/align_tilt_pairs.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/angular_accuracy_pca.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_accuracy_pca.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/angular_break_symmetry.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_break_symmetry.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/angular_commonline.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_commonline.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/angular_continuous_assign.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_continuous_assign.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/angular_continuous_assign2.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_continuous_assign2.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/angular_discrete_assign.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_discrete_assign.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/angular_distance.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_distance.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/angular_distribution_show.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_distribution_show.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/angular_estimate_tilt_axis.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_estimate_tilt_axis.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/angular_neighbourhood.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_neighbourhood.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/angular_project_library.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_project_library.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/angular_projection_matching.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_projection_matching.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/angular_rotate.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_rotate.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/angular_sph_alignment.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/angular_sph_alignment.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/arotation_estimator.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/arotation_estimator.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/art_crystal.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/art_crystal.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/art_xray.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/art_xray.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ashift_corr_estimator.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ashift_corr_estimator.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ashift_estimator.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ashift_estimator.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/base_art_recons.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/base_art_recons.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/basic_art.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/basic_art.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/bspline_geo_transformer.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/bspline_geo_transformer.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/bspline_helper.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/bspline_helper.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/classify_compare_classes.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/classify_compare_classes.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/classify_evaluate_classes.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/classify_evaluate_classes.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/classify_extract_features.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/classify_extract_features.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/classify_first_split.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/classify_first_split.cpp g++ -o libraries/reconstruction/classify_first_split3.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/classify_first_split3.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/classify_kerdensom.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/classify_kerdensom.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/classify_kmeans_2d.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/classify_kmeans_2d.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/classify_significant.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/classify_significant.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/common_lines.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/common_lines.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/coordinates_noisy_zones_filter.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/coordinates_noisy_zones_filter.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/correlation_computer.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/correlation_computer.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ctf_correct_idr.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ctf_correct_idr.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ctf_correct_phase.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ctf_correct_phase.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ctf_correct_wiener2d.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ctf_correct_wiener2d.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ctf_correct_wiener3d.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ctf_correct_wiener3d.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ctf_create_ctfdat.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ctf_create_ctfdat.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ctf_enhance_psd.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ctf_enhance_psd.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ctf_estimate_from_micrograph.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ctf_estimate_from_micrograph.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ctf_estimate_from_psd.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ctf_estimate_from_psd.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ctf_estimate_from_psd_base.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ctf_estimate_from_psd_base.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ctf_estimate_from_psd_fast.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ctf_estimate_from_psd_fast.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ctf_estimate_psd_with_arma.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ctf_estimate_psd_with_arma.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ctf_group.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ctf_group.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ctf_phase_flip.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ctf_phase_flip.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ctf_show.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ctf_show.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ctf_sort_psds.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ctf_sort_psds.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/denoise.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/denoise.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/directions.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/directions.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/eq_system_solver.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/eq_system_solver.cpp g++ -o libraries/reconstruction/evaluate_coordinates.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/evaluate_coordinates.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/extract_subset.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/extract_subset.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/fftwT.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/fftwT.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/flexible_alignment.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/flexible_alignment.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/fringe_processing.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/fringe_processing.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/idr_xray_tomo.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/idr_xray_tomo.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/image_assignment_tilt_pair.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/image_assignment_tilt_pair.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/image_eliminate_byEnergy.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/image_eliminate_byEnergy.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/image_eliminate_empty_particles.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/image_eliminate_empty_particles.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/image_find_center.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/image_find_center.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/image_header.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/image_header.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/image_histogram.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/image_histogram.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/image_odd_even.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/image_odd_even.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/image_rotational_pca.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/image_rotational_pca.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/image_rotational_spectra.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/image_rotational_spectra.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/image_separate_objects.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/image_separate_objects.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/image_sort_by_statistics.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/image_sort_by_statistics.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/image_statistics.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/image_statistics.cpp g++ -o libraries/reconstruction/image_vectorize.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/image_vectorize.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/iterative_alignment_estimator.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/iterative_alignment_estimator.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/mean_shift.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/mean_shift.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/metadata_convert_to_spider.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/metadata_convert_to_spider.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/metadata_histogram.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/metadata_histogram.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/metadata_split.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/metadata_split.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/metadata_split_3D.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/metadata_split_3D.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/metadata_utilities.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/metadata_utilities.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/metadata_xml.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/metadata_xml.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/micrograph_automatic_picking2.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/micrograph_automatic_picking2.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/micrograph_scissor.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/micrograph_scissor.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ml2d.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ml2d.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ml_align2d.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ml_align2d.cpp g++ -o libraries/reconstruction/ml_refine3d.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ml_refine3d.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/ml_tomo.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/ml_tomo.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/mlf_align2d.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/mlf_align2d.cpp g++ -o libraries/reconstruction/movie_alignment_correlation.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/movie_alignment_correlation.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/movie_alignment_correlation_base.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/movie_alignment_correlation_base.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/movie_estimate_gain.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/movie_estimate_gain.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/movie_filter_dose.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/movie_filter_dose.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/multireference_aligneability.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/multireference_aligneability.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/nma_alignment.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/nma_alignment.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/nma_alignment_vol.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/nma_alignment_vol.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/pdb_analysis.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/pdb_analysis.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/pdb_construct_dictionary.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/pdb_construct_dictionary.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/pdb_label_from_volume.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/pdb_label_from_volume.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/pdb_nma_deform.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/pdb_nma_deform.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/pdb_reduce_pseudoatoms.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/pdb_reduce_pseudoatoms.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/pdb_restore_with_dictionary.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/pdb_restore_with_dictionary.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/phantom_movie.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/phantom_movie.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/phantom_simulate_microscope.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/phantom_simulate_microscope.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/phantom_transform.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/phantom_transform.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/polar_rotation_estimator.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/polar_rotation_estimator.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/precompute_sampling.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/precompute_sampling.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/program_extension.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/program_extension.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/program_filter.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/program_filter.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/program_image_residuals.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/program_image_residuals.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/program_image_ssnr.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/program_image_ssnr.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/project.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/project.cpp g++ -o libraries/reconstruction/project_crystal.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/project_crystal.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/project_real_shears.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/project_real_shears.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/project_tomography.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/project_tomography.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/project_xray.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/project_xray.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/psd_estimator.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/psd_estimator.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/radon.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/radon.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/recons_misc.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/recons_misc.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/reconstruct_ADMM.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/reconstruct_ADMM.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/reconstruct_art.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/reconstruct_art.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/reconstruct_art_pseudo.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/reconstruct_art_pseudo.cpp g++ -o libraries/reconstruction/reconstruct_art_xray.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/reconstruct_art_xray.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/reconstruct_fourier.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/reconstruct_fourier.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/reconstruct_fourier_accel.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/reconstruct_fourier_accel.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/reconstruct_significant.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/reconstruct_significant.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/reconstruct_wbp.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/reconstruct_wbp.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/refinement.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/refinement.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/resolution_directional.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/resolution_directional.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/resolution_fsc.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/resolution_fsc.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/resolution_fso.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/resolution_fso.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/resolution_ibw.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/resolution_ibw.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/resolution_localfilter.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/resolution_localfilter.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/resolution_monogenic_signal.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/resolution_monogenic_signal.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/resolution_monotomo.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/resolution_monotomo.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/resolution_pdb_bfactor.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/resolution_pdb_bfactor.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/resolution_ssnr.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/resolution_ssnr.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/score_micrograph.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/score_micrograph.cpp g++ -o libraries/reconstruction/shift_corr_estimator.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/shift_corr_estimator.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/single_extrema_finder.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/single_extrema_finder.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/symmetrize.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/symmetrize.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/threshold.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/threshold.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/tomo_align_dual_tilt_series.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/tomo_align_dual_tilt_series.cpp g++ -o libraries/reconstruction/tomo_align_refinement.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/tomo_align_refinement.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/tomo_align_tilt_series.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/tomo_align_tilt_series.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/tomo_detect_missing_wedge.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/tomo_detect_missing_wedge.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/tomo_extract_subvolume.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/tomo_extract_subvolume.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/tomo_map_back.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/tomo_map_back.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/tomo_remove_fluctuations.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/tomo_remove_fluctuations.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/transform_add_noise.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/transform_add_noise.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/transform_adjust_image_grey_levels.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/transform_adjust_image_grey_levels.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/transform_center_image.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/transform_center_image.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/transform_morphology.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/transform_morphology.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/transform_range_adjust.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/transform_range_adjust.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/transform_window.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/transform_window.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/validation_nontilt.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/validation_nontilt.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/validation_tilt_pairs.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/validation_tilt_pairs.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_align_prog.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_align_prog.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_correct_bfactor.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_correct_bfactor.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_deform_sph.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_deform_sph.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_enhance_contrast.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_enhance_contrast.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_find_symmetry.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_find_symmetry.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_from_pdb.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_from_pdb.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_halves_restoration.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_halves_restoration.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_initial_simulated_annealing.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_initial_simulated_annealing.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_local_sharpening.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_local_sharpening.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_pca.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_pca.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_reslice.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_reslice.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_segment.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_segment.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_structure_factor.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_structure_factor.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_subtraction.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_subtraction.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_to_pseudoatoms.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_to_pseudoatoms.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_to_web.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_to_web.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volume_validate_pca.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volume_validate_pca.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/volumeset_align.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/volumeset_align.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/xray_import.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/xray_import.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o libraries/reconstruction/xray_psf_create.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/reconstruction/xray_psf_create.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/SpharmonicKit27/FFTcode.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/FFTcode.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/SpharmonicKit27/FST_semi_memo.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/FST_semi_memo.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/SpharmonicKit27/MathFace.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/MathFace.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/SpharmonicKit27/OURmods.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/OURmods.cpp g++ -o external/sh_alignment/SpharmonicKit27/OURperms.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/OURperms.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/SpharmonicKit27/cospmls.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/cospmls.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/SpharmonicKit27/csecond.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/csecond.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/SpharmonicKit27/fft_grids.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/fft_grids.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/SpharmonicKit27/indextables.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/indextables.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/SpharmonicKit27/naive_synthesis.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/naive_synthesis.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/SpharmonicKit27/newFCT.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/newFCT.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/SpharmonicKit27/oddweights.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/oddweights.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/SpharmonicKit27/primitive.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/primitive.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/SpharmonicKit27/primitive_FST.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/primitive_FST.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/SpharmonicKit27/seminaive.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/seminaive.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/SpharmonicKit27/weights.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/SpharmonicKit27/weights.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/frm.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/frm.cpp g++ -o external/sh_alignment/frm_wrap.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/frm_wrap.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/lib_err.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/lib_err.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/lib_eul.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/lib_eul.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/lib_pio.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/lib_pio.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/lib_pwk.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/lib_pwk.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/lib_std.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/lib_std.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o external/sh_alignment/lib_tim.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/lib_tim.cpp g++ -o external/sh_alignment/lib_vec.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/lib_vec.cpp g++ -o external/sh_alignment/lib_vio.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/lib_vio.cpp g++ -o external/sh_alignment/lib_vwk.os -c -mtune=native -march=native -std=c++11 -O3 /data2/sw/gcc/gcc-7.5.0/build/include -I../ -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore external/sh_alignment/lib_vwk.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o applications/programs/angular_accuracy_pca/angular_accuracy_pca_main.o -c -mtune=native -march=native -std=c++11 -O3 -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src applications/programs/angular_accuracy_pca/angular_accuracy_pca_main.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o applications/programs/angular_break_symmetry/angular_break_symmetry_main.o -c -mtune=native -march=native -std=c++11 -O3 -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src applications/programs/angular_break_symmetry/angular_break_symmetry_main.cpp g++ -o applications/programs/angular_commonline/angular_commonline_main.o -c -mtune=native -march=native -std=c++11 -O3 -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src applications/programs/angular_commonline/angular_commonline_main.cpp g++ -o applications/programs/angular_continuous_assign/angular_continuous_assign_main.o -c -mtune=native -march=native -std=c++11 -O3 -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src applications/programs/angular_continuous_assign/angular_continuous_assign_main.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o applications/programs/angular_continuous_assign2/angular_continuous_assign_main2.o -c -mtune=native -march=native -std=c++11 -O3 -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src applications/programs/angular_continuous_assign2/angular_continuous_assign_main2.cpp g++ -o applications/programs/angular_discrete_assign/angular_discrete_assign_main.o -c -mtune=native -march=native -std=c++11 -O3 -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src applications/programs/angular_discrete_assign/angular_discrete_assign_main.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o lib/_swig_frm.so -L/opt/conda3/envs/xmipp/lib -shared external/sh_alignment/SpharmonicKit27/FFTcode.os external/sh_alignment/SpharmonicKit27/FST_semi_memo.os external/sh_alignment/SpharmonicKit27/MathFace.os external/sh_alignment/SpharmonicKit27/OURmods.os external/sh_alignment/SpharmonicKit27/OURperms.os external/sh_alignment/SpharmonicKit27/cospmls.os external/sh_alignment/SpharmonicKit27/csecond.os external/sh_alignment/SpharmonicKit27/fft_grids.os external/sh_alignment/SpharmonicKit27/indextables.os external/sh_alignment/SpharmonicKit27/naive_synthesis.os external/sh_alignment/SpharmonicKit27/newFCT.os external/sh_alignment/SpharmonicKit27/oddweights.os external/sh_alignment/SpharmonicKit27/primitive.os external/sh_alignment/SpharmonicKit27/primitive_FST.os external/sh_alignment/SpharmonicKit27/seminaive.os external/sh_alignment/SpharmonicKit27/weights.os external/sh_alignment/frm.os external/sh_alignment/frm_wrap.os external/sh_alignment/lib_err.os external/sh_alignment/lib_eul.os external/sh_alignment/lib_pio.os external/sh_alignment/lib_pwk.os external/sh_alignment/lib_std.os external/sh_alignment/lib_tim.os external/sh_alignment/lib_vec.os external/sh_alignment/lib_vio.os external/sh_alignment/lib_vwk.os $( -L/data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib -Llib -L/opt/conda3/envs/xmipp/lib $) -lfftw3 -lfftw3_threads g++ -o applications/programs/angular_distance/angular_distance_main.o -c -mtune=native -march=native -std=c++11 -O3 -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src applications/programs/angular_distance/angular_distance_main.cpp g++ -o applications/programs/angular_distribution_show/angular_distribution_show_main.o -c -mtune=native -march=native -std=c++11 -O3 -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src applications/programs/angular_distribution_show/angular_distribution_show_main.cpp g++ -o applications/programs/angular_estimate_tilt_axis/angular_estimate_tilt_axis_main.o -c -mtune=native -march=native -std=c++11 -O3 -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src applications/programs/angular_estimate_tilt_axis/angular_estimate_tilt_axis_main.cpp g++: warning: /data2/sw/gcc/gcc-7.5.0/build/include: linker input file unused because linking not done g++ -o lib/libXmipp.so -L/opt/conda3/envs/xmipp/lib -shared external/condor/CNLSolver.os external/condor/CTRSSolver.os external/condor/IntPoly.os external/condor/KeepBests.os external/condor/MSSolver.os external/condor/Matrix.os external/condor/MatrixTriangle.os external/condor/MultInd.os external/condor/ObjectiveFunction.os external/condor/Poly.os external/condor/QPSolver.os external/condor/UTRSSolver.os external/condor/Vector.os external/condor/VectorChar.os external/condor/VectorInt.os external/condor/parallel.os external/condor/tools.os external/delaunay/dcel.os external/delaunay/delaunay.os external/delaunay/graph.os external/delaunay/point.os external/delaunay/polygon.os external/delaunay/sorting.os external/delaunay/stack.os external/delaunay/triangulation.os external/delaunay/voronoi.os libraries/classification/ahc_classifier.os libraries/classification/analyze_cluster.os libraries/classification/batch_som.os libraries/classification/code_book.os libraries/classification/fcmeans.os libraries/classification/fkcn.os libraries/classification/fuzzy_code_book.os libraries/classification/fuzzy_som.os libraries/classification/gaussian_kerdensom.os libraries/classification/kSVD.os libraries/classification/kerdensom.os libraries/classification/knn_classifier.os libraries/classification/map.os libraries/classification/naive_bayes.os libraries/classification/pca.os libraries/classification/sammon.os libraries/classification/som.os libraries/classification/svm.os libraries/classification/svm_classifier.os libraries/classification/training_vector.os libraries/data/basic_pca.os libraries/data/basis.os libraries/data/blobs.os libraries/data/cpu.os libraries/data/ctf.os libraries/data/euler.os libraries/data/filters.os libraries/data/fourier_filter.os libraries/data/fourier_projection.os libraries/data/grids.os libraries/data/image_operate.os libraries/data/image_resize.os libraries/data/integration.os libraries/data/mask.os libraries/data/micrograph.os libraries/data/monogenic_signal.os libraries/data/morphology.os libraries/data/normalize.os libraries/data/numerical_tools.os libraries/data/pdb.os libraries/data/phantom.os libraries/data/polar.os libraries/data/projection.os libraries/data/psf_xr.os libraries/data/rotational_spectrum.os libraries/data/sampling.os libraries/data/sparse_matrix2d.os libraries/data/spherical_harmonics.os libraries/data/splines.os libraries/data/steerable.os libraries/data/symmetries.os libraries/data/transform_downsample.os libraries/data/transform_geometry.os libraries/data/unitCell.os libraries/data/wavelet.os libraries/data/xmipp_image_convert.os libraries/data/xmipp_image_over.os libraries/data/xmipp_polynomials.os libraries/dimred/diffusionMaps.os libraries/dimred/dimred_tools.os libraries/dimred/gplvm.os libraries/dimred/hessianLLE.os libraries/dimred/kernelPCA.os libraries/dimred/laplacianEigenmaps.os libraries/dimred/lltsa.os libraries/dimred/lpp.os libraries/dimred/ltsa.os libraries/dimred/matrix_dimred.os libraries/dimred/nca.os libraries/dimred/npe.os libraries/dimred/pca.os libraries/dimred/probabilisticPCA.os libraries/dimred/spe.os libraries/dimred/transform_dimred.os libraries/interface/docfile.os libraries/interface/frm.os libraries/interface/python_utils.os libraries/interface/selfile.os libraries/interface/spider.os libraries/reconstruction/aalign_significant.os libraries/reconstruction/adjust_volume_grey_levels.os libraries/reconstruction/aextrema_finder.os libraries/reconstruction/align2d.os libraries/reconstruction/align_tilt_pairs.os libraries/reconstruction/angular_accuracy_pca.os libraries/reconstruction/angular_break_symmetry.os libraries/reconstruction/angular_commonline.os libraries/reconstruction/angular_continuous_assign.os libraries/reconstruction/angular_continuous_assign2.os libraries/reconstruction/angular_discrete_assign.os libraries/reconstruction/angular_distance.os libraries/reconstruction/angular_distribution_show.os libraries/reconstruction/angular_estimate_tilt_axis.os libraries/reconstruction/angular_neighbourhood.os libraries/reconstruction/angular_project_library.os libraries/reconstruction/angular_projection_matching.os libraries/reconstruction/angular_rotate.os libraries/reconstruction/angular_sph_alignment.os libraries/reconstruction/arotation_estimator.os libraries/reconstruction/art_crystal.os libraries/reconstruction/art_xray.os libraries/reconstruction/ashift_corr_estimator.os libraries/reconstruction/ashift_estimator.os libraries/reconstruction/base_art_recons.os libraries/reconstruction/basic_art.os libraries/reconstruction/bspline_geo_transformer.os libraries/reconstruction/bspline_helper.os libraries/reconstruction/classify_compare_classes.os libraries/reconstruction/classify_evaluate_classes.os libraries/reconstruction/classify_extract_features.os libraries/reconstruction/classify_first_split.os libraries/reconstruction/classify_first_split3.os libraries/reconstruction/classify_kerdensom.os libraries/reconstruction/classify_kmeans_2d.os libraries/reconstruction/classify_significant.os libraries/reconstruction/common_lines.os libraries/reconstruction/coordinates_noisy_zones_filter.os libraries/reconstruction/correlation_computer.os libraries/reconstruction/ctf_correct_idr.os libraries/reconstruction/ctf_correct_phase.os libraries/reconstruction/ctf_correct_wiener2d.os libraries/reconstruction/ctf_correct_wiener3d.os libraries/reconstruction/ctf_create_ctfdat.os libraries/reconstruction/ctf_enhance_psd.os libraries/reconstruction/ctf_estimate_from_micrograph.os libraries/reconstruction/ctf_estimate_from_psd.os libraries/reconstruction/ctf_estimate_from_psd_base.os libraries/reconstruction/ctf_estimate_from_psd_fast.os libraries/reconstruction/ctf_estimate_psd_with_arma.os libraries/reconstruction/ctf_group.os libraries/reconstruction/ctf_phase_flip.os libraries/reconstruction/ctf_show.os libraries/reconstruction/ctf_sort_psds.os libraries/reconstruction/denoise.os libraries/reconstruction/directions.os libraries/reconstruction/eq_system_solver.os libraries/reconstruction/evaluate_coordinates.os libraries/reconstruction/extract_subset.os libraries/reconstruction/fftwT.os libraries/reconstruction/flexible_alignment.os libraries/reconstruction/fringe_processing.os libraries/reconstruction/idr_xray_tomo.os libraries/reconstruction/image_assignment_tilt_pair.os libraries/reconstruction/image_eliminate_byEnergy.os libraries/reconstruction/image_eliminate_empty_particles.os libraries/reconstruction/image_find_center.os libraries/reconstruction/image_header.os libraries/reconstruction/image_histogram.os libraries/reconstruction/image_odd_even.os libraries/reconstruction/image_rotational_pca.os libraries/reconstruction/image_rotational_spectra.os libraries/reconstruction/image_separate_objects.os libraries/reconstruction/image_sort_by_statistics.os libraries/reconstruction/image_statistics.os libraries/reconstruction/image_vectorize.os libraries/reconstruction/iterative_alignment_estimator.os libraries/reconstruction/mean_shift.os libraries/reconstruction/metadata_convert_to_spider.os libraries/reconstruction/metadata_histogram.os libraries/reconstruction/metadata_split.os libraries/reconstruction/metadata_split_3D.os libraries/reconstruction/metadata_utilities.os libraries/reconstruction/metadata_xml.os libraries/reconstruction/micrograph_automatic_picking2.os libraries/reconstruction/micrograph_scissor.os libraries/reconstruction/ml2d.os libraries/reconstruction/ml_align2d.os libraries/reconstruction/ml_refine3d.os libraries/reconstruction/ml_tomo.os libraries/reconstruction/mlf_align2d.os libraries/reconstruction/movie_alignment_correlation.os libraries/reconstruction/movie_alignment_correlation_base.os libraries/reconstruction/movie_estimate_gain.os libraries/reconstruction/movie_filter_dose.os libraries/reconstruction/multireference_aligneability.os libraries/reconstruction/nma_alignment.os libraries/reconstruction/nma_alignment_vol.os libraries/reconstruction/pdb_analysis.os libraries/reconstruction/pdb_construct_dictionary.os libraries/reconstruction/pdb_label_from_volume.os libraries/reconstruction/pdb_nma_deform.os libraries/reconstruction/pdb_reduce_pseudoatoms.os libraries/reconstruction/pdb_restore_with_dictionary.os libraries/reconstruction/phantom_movie.os libraries/reconstruction/phantom_simulate_microscope.os libraries/reconstruction/phantom_transform.os libraries/reconstruction/polar_rotation_estimator.os libraries/reconstruction/precompute_sampling.os libraries/reconstruction/program_extension.os libraries/reconstruction/program_filter.os libraries/reconstruction/program_image_residuals.os libraries/reconstruction/program_image_ssnr.os libraries/reconstruction/project.os libraries/reconstruction/project_crystal.os libraries/reconstruction/project_real_shears.os libraries/reconstruction/project_tomography.os libraries/reconstruction/project_xray.os libraries/reconstruction/psd_estimator.os libraries/reconstruction/radon.os libraries/reconstruction/recons_misc.os libraries/reconstruction/reconstruct_ADMM.os libraries/reconstruction/reconstruct_art.os libraries/reconstruction/reconstruct_art_pseudo.os libraries/reconstruction/reconstruct_art_xray.os libraries/reconstruction/reconstruct_fourier.os libraries/reconstruction/reconstruct_fourier_accel.os libraries/reconstruction/reconstruct_significant.os libraries/reconstruction/reconstruct_wbp.os libraries/reconstruction/refinement.os libraries/reconstruction/resolution_directional.os libraries/reconstruction/resolution_fsc.os libraries/reconstruction/resolution_fso.os libraries/reconstruction/resolution_ibw.os libraries/reconstruction/resolution_localfilter.os libraries/reconstruction/resolution_monogenic_signal.os libraries/reconstruction/resolution_monotomo.os libraries/reconstruction/resolution_pdb_bfactor.os libraries/reconstruction/resolution_ssnr.os libraries/reconstruction/score_micrograph.os libraries/reconstruction/shift_corr_estimator.os libraries/reconstruction/single_extrema_finder.os libraries/reconstruction/symmetrize.os libraries/reconstruction/threshold.os libraries/reconstruction/tomo_align_dual_tilt_series.os libraries/reconstruction/tomo_align_refinement.os libraries/reconstruction/tomo_align_tilt_series.os libraries/reconstruction/tomo_detect_missing_wedge.os libraries/reconstruction/tomo_extract_subvolume.os libraries/reconstruction/tomo_map_back.os libraries/reconstruction/tomo_remove_fluctuations.os libraries/reconstruction/transform_add_noise.os libraries/reconstruction/transform_adjust_image_grey_levels.os libraries/reconstruction/transform_center_image.os libraries/reconstruction/transform_morphology.os libraries/reconstruction/transform_range_adjust.os libraries/reconstruction/transform_window.os libraries/reconstruction/validation_nontilt.os libraries/reconstruction/validation_tilt_pairs.os libraries/reconstruction/volume_align_prog.os libraries/reconstruction/volume_correct_bfactor.os libraries/reconstruction/volume_deform_sph.os libraries/reconstruction/volume_enhance_contrast.os libraries/reconstruction/volume_find_symmetry.os libraries/reconstruction/volume_from_pdb.os libraries/reconstruction/volume_halves_restoration.os libraries/reconstruction/volume_initial_simulated_annealing.os libraries/reconstruction/volume_local_sharpening.os libraries/reconstruction/volume_pca.os libraries/reconstruction/volume_reslice.os libraries/reconstruction/volume_segment.os libraries/reconstruction/volume_structure_factor.os libraries/reconstruction/volume_subtraction.os libraries/reconstruction/volume_to_pseudoatoms.os libraries/reconstruction/volume_to_web.os libraries/reconstruction/volume_validate_pca.os libraries/reconstruction/volumeset_align.os libraries/reconstruction/xray_import.os libraries/reconstruction/xray_psf_create.os $( -L/data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib -Llib -L/opt/conda3/envs/xmipp/lib $) -lpthread -lpython3.8 -lfftw3f -lfftw3f_threads g++ -o applications/programs/angular_neighbourhood/angular_neighbourhood_main.o -c -mtune=native -march=native -std=c++11 -O3 -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src applications/programs/angular_neighbourhood/angular_neighbourhood_main.cpp g++ -o applications/programs/angular_project_library/angular_project_library_main.o -c -mtune=native -march=native -std=c++11 -O3 -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src applications/programs/angular_project_library/angular_project_library_main.cpp g++ -o applications/programs/angular_projection_matching/angular_projection_matching_main.o -c -mtune=native -march=native -std=c++11 -O3 -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src applications/programs/angular_projection_matching/angular_projection_matching_main.cpp g++ -o applications/programs/angular_rotate/angular_rotate_main.o -c -mtune=native -march=native -std=c++11 -O3 -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src applications/programs/angular_rotate/angular_rotate_main.cpp g++ -o applications/programs/angular_sph_alignment/angular_sph_alignment_main.o -c -mtune=native -march=native -std=c++11 -O3 -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/gcc/gcc-7.5.0/build/include -I/data2/sw/xmipp/xmipp-bundle/src applications/programs/angular_sph_alignment/angular_sph_alignment_main.cpp g++ -o bin/xmipp_angular_break_symmetry applications/programs/angular_break_symmetry/angular_break_symmetry_main.o -L/data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib -Llib -Llib -L/opt/conda3/envs/xmipp/lib -L/usr/local/cuda-10.2/lib64 -L/data2/sw/gcc/gcc-7.5.0/build/lib64 -L/data2/sw/r31_20210418/external/fltk/lib -L/opt/pymol/lib64 -L/opt/pymol/lib64 -L/opt/IMOD/lib -L/opt/pymol/lib64 -L/opt/pymol/lib64 -L/opt/IMOD/lib -L/opt/pymol/lib64 -L/usr/lib64/openmpi/lib -L/opt/relion-3.1-b/lib -L/opt/pymol/lib64 -L/opt/IMOD/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpython3.8 -lpthread -lXmippCore lib/libXmipp.so: undefined reference to non-virtual thunk to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' lib/libXmipp.so: undefined reference toH5::H5File::throwException(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' /data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const' collect2: error: ld returned 1 exit status scons: *** [bin/xmipp_angular_break_symmetry] Error 1 scons: building terminated because of errors.

Some error occurred during the compilation of 'xmipp' ('bin/xmipp_angular_break_symmetry').

DStrelak commented 2 years ago

Hi @jianhaoc Your config file is completely broken and I don't know how it can be in this shape without manual modification. Discard it and generate it again. The easiest way is to rename it and run again the xmipp script via ./xmipp.

dmaluenda commented 2 years ago

Hi,

If the problem persists after redoing the config file as @DStrelak said, please send us the output for the command printenv. Xmipp uses the values found in the environment. Then if, for some reason, your environment contains INCDIRFLAGS=something, Xmipp will prepend that something to the include flag. [check this: https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)#c-configuration]

Cheers,

jianhaoc commented 2 years ago

Hi @dmaluenda ,

Yes, after deleted xmipp.conf and ran ./xmipp again, there is still the same issue. Below is the output of printenv.

$ printenv CCP4I_TCLTK=/data2/sw/ccp4-20210317/ccp4-7.1/bin CCP4_HELPDIR=/data2/sw/ccp4-20210317/ccp4-7.1/help/ MPI_INCLUDE=/usr/include/openmpi-x86_64 MANPATH=/data2/sw/ccp4-20210317/ccp4-7.1/share/man:/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man RELION_ALLOW_CHANGE_MINIMUM_DEDICATED=0 XDG_SESSION_ID=80 IMOD_DIR=/opt/IMOD HOSTNAME=zhanglab SSL_CERT_FILE=/data2/sw/ccp4-20210317/ccp4-7.1/etc/ssl/cacert.pem CHTML=/data2/sw/ccp4-20210317/ccp4-7.1/html LIBTBX_TMPVAL= SELINUX_ROLE_REQUESTED= NVCC_CXXFLAGS=/data2/sw/gcc/gcc-7.5.0/build/bin GFORTRAN_UNBUFFERED_PRECONNECTED=Y TERM=xterm-256color SHELL=/bin/bash IMOD_QTLIBDIR=/opt/IMOD/qtlib HISTSIZE=1000 SSH_CLIENT=137.53.221.139 32791 22 CONDA_SHLVL=2 RELION_WARNING_LOCAL_MPI=12 CONDA_PROMPT_MODIFIER=(xmipp) SELINUX_USE_CURRENT_RANGE= RELION_MOTIONCOR2_EXECUTABLE=/opt/bin/MotionCor2 QTDIR=/usr/lib64/qt-3.3 OLDPWD=/data2/sw/xmipp QTINC=/usr/lib64/qt-3.3/include CCP4=/data2/sw/ccp4-20210317/ccp4-7.1 PHENIX=/data2/sw/phenix-1.19-4092/phenix-1.19-4092 SSH_TTY=/dev/pts/3 CLIB=/data2/sw/ccp4-20210317/ccp4-7.1/lib QT_GRAPHICSSYSTEM_CHECKED=1 MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi CUDA_HOME=/usr/local/cuda-11.4 USER=spuser CEXAM=/data2/sw/ccp4-20210317/ccp4-7.1/examples LD_LIBRARY_PATH=/opt/pymol/lib64:/usr/lib64/openmpi/lib:/opt/relion-3.1-b/lib:/usr/local/cuda-11.4/lib64:/opt/pymol/lib64:/opt/IMOD/lib: LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:.tar=38;5;9:.tgz=38;5;9:.arc=38;5;9:.arj=38;5;9:.taz=38;5;9:.lha=38;5;9:.lz4=38;5;9:.lzh=38;5;9:.lzma=38;5;9:.tlz=38;5;9:.txz=38;5;9:.tzo=38;5;9:.t7z=38;5;9:.zip=38;5;9:.z=38;5;9:.Z=38;5;9:.dz=38;5;9:.gz=38;5;9:.lrz=38;5;9:.lz=38;5;9:.lzo=38;5;9:.xz=38;5;9:.bz2=38;5;9:.bz=38;5;9:.tbz=38;5;9:.tbz2=38;5;9:.tz=38;5;9:.deb=38;5;9:.rpm=38;5;9:.jar=38;5;9:.war=38;5;9:.ear=38;5;9:.sar=38;5;9:.rar=38;5;9:.alz=38;5;9:.ace=38;5;9:.zoo=38;5;9:.cpio=38;5;9:.7z=38;5;9:.rz=38;5;9:.cab=38;5;9:.jpg=38;5;13:.jpeg=38;5;13:.gif=38;5;13:.bmp=38;5;13:.pbm=38;5;13:.pgm=38;5;13:.ppm=38;5;13:.tga=38;5;13:.xbm=38;5;13:.xpm=38;5;13:.tif=38;5;13:.tiff=38;5;13:.png=38;5;13:.svg=38;5;13:.svgz=38;5;13:.mng=38;5;13:.pcx=38;5;13:.mov=38;5;13:.mpg=38;5;13:.mpeg=38;5;13:.m2v=38;5;13:.mkv=38;5;13:.webm=38;5;13:.ogm=38;5;13:.mp4=38;5;13:.m4v=38;5;13:.mp4v=38;5;13:.vob=38;5;13:.qt=38;5;13:.nuv=38;5;13:.wmv=38;5;13:.asf=38;5;13:.rm=38;5;13:.rmvb=38;5;13:.flc=38;5;13:.avi=38;5;13:.fli=38;5;13:.flv=38;5;13:.gl=38;5;13:.dl=38;5;13:.xcf=38;5;13:.xwd=38;5;13:.yuv=38;5;13:.cgm=38;5;13:.emf=38;5;13:.axv=38;5;13:.anx=38;5;13:.ogv=38;5;13:.ogx=38;5;13:.aac=38;5;45:.au=38;5;45:.flac=38;5;45:.mid=38;5;45:.midi=38;5;45:.mka=38;5;45:.mp3=38;5;45:.mpc=38;5;45:.ogg=38;5;45:.ra=38;5;45:.wav=38;5;45:.axa=38;5;45:.oga=38;5;45:.spx=38;5;45:.xspf=38;5;45: CONDA_EXE=/opt/conda3/bin/conda BALBES_ROOT=/data2/sw/ccp4-20210317/ccp4-7.1/BALBES RELION_UNBLUR_EXECUTABLE=/opt/bin/unblur_openmp_7_17_15.exe INCDIRFLAGS=/data2/sw/gcc/gcc-7.5.0/build/include RELION_MINIMUM_DEDICATED=32 CCP4I_TOP=/data2/sw/ccp4-20210317/ccp4-7.1/share/ccp4i MPI_LIB=/usr/lib64/openmpi/lib CXX_CUDA=/usr/local/cuda-10.2/bin _CE_CONDA= CONDA_PREFIX_1=/opt/conda3 LIBTBX_BUILD= MAIL=/var/spool/mail/spuser PATH=/opt/conda3/envs/xmipp/bin:/opt/conda3/condabin:/data/sw/UCSFchimera20210201/bin:/data2/sw/ccp4-20210317/ccp4-7.1/etc:/data2/sw/ccp4-20210317/ccp4-7.1/bin:/data/sw/ccpem-20201204/bin:/data2/sw/phenix-1.19-4092/phenix-1.19-4092/build/bin:/opt/cryosparc2/cryosparc2_master/bin:/opt/pymol/bin:/usr/lib64/openmpi/bin:/opt/relion-3.1-b/bin:/usr/local/cuda-11.4/bin:/usr/lib64/qt-3.3/bin:/opt/IMOD/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/spuser/.local/bin:/home/spuser/bin MPI_BIN=/usr/lib64/openmpi/bin IMOD_PLUGIN_DIR=/opt/IMOD/lib/imodplug CONDA_PREFIX=/opt/conda3/envs/xmipp MPI_COMPILER=openmpi-x86_64 CCP4_OPEN=UNKNOWN PWD=/data2/sw/xmipp/xmipp-bundle LMFILES=/opt/sp/modulefiles/cuda/11.4:/opt/sp/modulefiles/relion/3.1:/etc/modulefiles/mpi/openmpi-x86_64 CETC=/data2/sw/ccp4-20210317/ccp4-7.1/etc RELION_RESMAP_EXECUTABLE=/opt/bin/ResMap IMOD_JAVADIR=/usr/local/java LANG=en_US.UTF-8 MODULEPATH=/opt/sp/modulefiles:/usr/share/Modules/modulefiles:/etc/modulefiles LOADEDMODULES=cuda/11.4:relion/3.1:mpi/openmpi-x86_64 KDEDIRS=/usr CLIBD_MON=/data2/sw/ccp4-20210317/ccp4-7.1/lib/data/monomers/ CCP4_SCR=/tmp/spuser FOR_DISABLE_STACK_TRACE=1 SELINUX_LEVEL_REQUESTED= _CE_M= PHENIX_VERSION=1.19-4092 RELION_CTFFIND_EXECUTABLE=/opt/bin/ctffind SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass HISTCONTROL=ignoredups MPI_SYSCONFIG=/etc/openmpi-x86_64 SHLVL=1 HOME=/home/spuser LIBTBX_OPATH= MPI_SUFFIX=_openmpi CRANK=/data2/sw/ccp4-20210317/ccp4-7.1/share/ccp4i/crank MPI_MAN=/usr/share/man/openmpi-x86_64 RELION_SUMMOVIE_EXECUTABLE=/opt/bin/sum_movie_openmp_7_17_15.exe CONDA_PYTHON_EXE=/opt/conda3/bin/python PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi LOGNAME=spuser CLIBD=/data2/sw/ccp4-20210317/ccp4-7.1/lib/data QTLIB=/usr/lib64/qt-3.3/lib XDG_DATA_DIRS=/home/spuser/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share SSH_CONNECTION=137.53.221.139 32791 10.149.48.12 22 CBIN=/data2/sw/ccp4-20210317/ccp4-7.1/bin MPI_HOME=/usr/lib64/openmpi MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64 MODULESHOME=/usr/share/Modules CONDA_DEFAULT_ENV=xmipp CINCL=/data2/sw/ccp4-20210317/ccp4-7.1/include CCP4_MASTER=/data2/sw/ccp4-20210317 RELION_GCTF_EXECUTABLE=/opt/bin/Gctf LESSOPEN=||/usr/bin/lesspipe.sh %s IMOD_CALIB_DIR=/usr/local/ImodCalib MMCIFDIC=/data2/sw/ccp4-20210317/ccp4-7.1/lib/ccp4/cif_mmdic.lib RELION_PDFVIEWER_EXECUTABLEe=evince XDG_RUNTIME_DIR=/run/user/1000 QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $` } _=/usr/bin/printenv

dmaluenda commented 2 years ago

Ok. I see the following colliding variables:

NVCC_CXXFLAGS=/data2/sw/gcc/gcc-7.5.0/build/bin
INCDIRFLAGS=/data2/sw/gcc/gcc-7.5.0/build/include
CXX_CUDA=/usr/local/cuda-10.2/bin

they are directories while the first two should be flags (i.e. a serial of path with a minus something prefix) and the last should a compiler path. I don't know where they are defined.

You can fristly try to restart your terminal and check if they still there. If they still there, I suggest to unset them by

unset NVCC_CXXFLAGS INCDIRFLAGS CXX_CUDA

then, again, delete/move the xmipp.conf file and run ./xmipp.

After a succesful installation, I recommend you to restart the terminal rescue the original configuration, Xmip should work anyway.

dmaluenda commented 2 years ago

I've just checked the whole thread and now I've realized you set that variables because you want to force using gcc-7.5.0 and cuda-10.2. Right?

Then I suggest you to restart the terminal and just set the following

export CXX=/data2/sw/gcc/gcc-7.5.0/build/bin/gcc  # it must be a C++ compiler path
export CUDA_CXX=/data2/sw/gcc/gcc-7.5.0/build/bin/gcc  # it must be a C++ compiler path to be used for cuda code
export NVCC=/usr/local/cuda-10.2/bin/nvcc  # it must be a cuda compiler

the rest should be done automatically. Moreover, if those compilers are accessible from the PATH (i.e. you can call them just by gcc or nvcc in the terminal), do not set anything. Xmipp will automatically do it.

jianhaoc commented 2 years ago

Hi @dmaluenda ,

I started a new terminal and tried again as following.

$ echo $NVCC_CXXFLAGS

$ echo $INCDIRFLAGS

$ echo $CXX_CUDA

$ rm -rf xmipp.conf $ which gcc /data2/sw/gcc/gcc-7.5.0/build/bin/gcc $ gcc --version gcc (GCC) 7.5.0 Copyright (C) 2017 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. $ which nvcc /usr/local/cuda-10.2/bin/nvcc

$ nvcc --version nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2019 NVIDIA Corporation Built on Wed_Oct_23_19:24:38_PDT_2019 Cuda compilation tools, release 10.2, V10.2.89

$ ./xmipp Configuring ----------------------------------------- gcc detected /data2/sw/gcc/gcc-7.5.0/build/bin/gcc -c -w xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/opt/conda3/envs/xmipp/include OpenCV not found rm -v xmipp_test_opencv* Checking for compatible GCC to be used with your CUDA No valid compiler found. Skipping CUDA compilation. To manually set the compiler, export CXX_CUDA=/path/to/requested_compiler' and run again 'xmipp config'. 'mpirun' detected. 'mpicc' detected. 'mpicxx' detected. Java detected at: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64

Do you want to build tests [yes/NO]NO Configuration completed..... Checking configuration ------------------------------ Checking MPI configuration ... mpicxx -c -w -I../ -I/opt/conda3/envs/xmipp/include -I/usr/include/openmpi-x86_64 xmipp_mpi_test_main.cpp -o xmipp_mpi_test_main.o mpicxx -L/opt/conda3/envs/xmipp/lib xmipp_mpi_test_main.o -o xmipp_mpi_test_main -lfftw3 -lfftw3_threads -lhdf5 -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread rm xmipp_mpi_test_main* mpirun -np 2 echo ' > This sentence should be printed 2 times if mpi runs fine.'

This sentence should be printed 2 times if mpi runs fine. This sentence should be printed 2 times if mpi runs fine. Checking Java configuration... /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/bin/javac Xmipp.java rm Xmipp.java Xmipp.class /data2/sw/gcc/gcc-7.5.0/build/bin/gcc -c -w -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/include/linux -I../ -I/opt/conda3/envs/xmipp/include xmipp_jni_test.cpp -o xmipp_jni_test.o rm xmipp_jni_test* Getting Dependencies ------------------------------------- Checkouting CTPL:master ... Already up-to-date. Getting sources ------------------------------------- Checkouting xmippCore:devel ... Already up-to-date. Checkouting xmippViz:devel ... Already up-to-date. Checkouting scipion-em-xmipp:devel ... Already up-to-date. Checkouting xmipp:devel ... Already up-to-date. Building Dependencies ------------------------------------- Compiling ------------------------------------------- scons -j8 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... gcc -o core/sqlite3-extension-functions.os -c -fPIC -I/data2/sw/xmipp/xmipp-bundle/src -I/opt/conda3/envs/xmipp/include core/sqlite3-extension-functions.c /data2/sw/gcc/gcc-7.5.0/build/bin/gcc -o lib/libXmippCore.so -L/opt/conda3/envs/xmipp/lib -shared core/args.os core/argsparser.os core/argsprinter.os core/comment_list.os core/geometry.os core/histogram.os core/linear_system_helper.os core/matrix1d.os core/matrix2d.os core/metadata_base.os core/metadata_db.os core/metadata_extension.os core/metadata_generator.os core/metadata_object.os core/metadata_query.os core/metadata_row_sql.os core/metadata_row_vec.os core/metadata_sql.os core/metadata_static.os core/metadata_vec.os core/multidim_array.os core/multidim_array_base.os core/multidim_array_generic.os core/numerical_recipes.os core/rwDM3.os core/rwDM4.os core/rwEM.os core/rwHDF5.os core/rwIMAGIC.os core/rwINF.os core/rwJPEG.os core/rwMRC.os core/rwPIF.os core/rwRAW.os core/rwSPE.os core/rwSPIDER.os core/rwTIA.os core/rwTIFF.os core/symmetries.os core/transformations.os core/userSettings.os core/xmipp_color.os core/xmipp_datatype.os core/xmipp_error.os core/xmipp_fft.os core/xmipp_fftw.os core/xmipp_filename.os core/xmipp_funcs.os core/xmipp_hdf5.os core/xmipp_image.os core/xmipp_image_base.os core/xmipp_image_extension.os core/xmipp_image_generic.os core/xmipp_log.os core/xmipp_memory.os core/xmipp_metadata_program.os core/xmipp_program.os core/xmipp_program_sql.os core/xmipp_strings.os core/xmipp_threads.os core/xvsmooth.os core/sqlite3-extension-functions.os core/bilib/changebasis.os core/bilib/convert.os core/bilib/dft.os core/bilib/dht.os core/bilib/findroot.os core/bilib/firconvolve.os core/bilib/flip.os core/bilib/fold.os core/bilib/fourierconvolve.os core/bilib/geometry.os core/bilib/getpoles.os core/bilib/getput.os core/bilib/getputd.os core/bilib/gradient.os core/bilib/histogram.os core/bilib/iirconvolve.os core/bilib/interpolate.os core/bilib/kernel.os core/bilib/kerneldiff.os core/bilib/kerneldiff1.os core/bilib/kerneldiff2.os core/bilib/kernelintegrate.os core/bilib/linearalgebra.os core/bilib/messagedisplay.os core/bilib/minmax.os core/bilib/morphology.os core/bilib/movingaverage.os core/bilib/polynomial.os core/bilib/positivepower.os core/bilib/pyramidfilters.os core/bilib/pyramidtools.os core/bilib/round.os core/bilib/swap.os core/bilib/timestamp.os core/bilib/traceline.os core/bilib/wavelet.os core/bilib/waveletfilters.os core/bilib/waveletfiltersfract.os core/bilib/wavelettools.os core/bilib/window.os core/alglib/alglibinternal.os core/alglib/alglibmisc.os core/alglib/ap.os core/alglib/dataanalysis.os core/alglib/diffequations.os core/alglib/fasttransforms.os core/alglib/integration.os core/alglib/interpolation.os core/alglib/linalg.os core/alglib/optimization.os core/alglib/solvers.os core/alglib/specialfunctions.os core/alglib/statistics.os core/utils/sql_utils.os core/utils/time_utils.os $( -Llib -L/opt/conda3/envs/xmipp/lib $) -lfftw3 -lfftw3_threads -lhdf5 -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread gcc -o lib/xmippCore.so -L/opt/conda3/envs/xmipp/lib -shared $( -Llib -L/opt/conda3/envs/xmipp/lib $) -lpython3.8 -lXmippCore scons: done building targets. scons -j8 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... scons: lib/libXmipp.so' is up to date. scons:lib/_swig_frm.so' is up to date. mpicxx -o libraries/parallel/mpi_angular_accuracy_pca.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_angular_accuracy_pca.cpp mpicxx -o libraries/parallel/mpi_angular_class_average.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_angular_class_average.cpp mpicxx -o libraries/parallel/mpi_angular_continuous_assign.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_angular_continuous_assign.cpp mpicxx -o libraries/parallel/mpi_angular_project_library.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_angular_project_library.cpp mpicxx -o libraries/parallel/mpi_angular_projection_matching.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_angular_projection_matching.cpp mpicxx -o libraries/parallel/mpi_angular_sph_alignment.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_angular_sph_alignment.cpp mpicxx -o libraries/parallel/mpi_classify_CL2D.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_classify_CL2D.cpp mpicxx -o libraries/parallel/mpi_classify_CL2D_core_analysis.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_classify_CL2D_core_analysis.cpp mpicxx -o libraries/parallel/mpi_classify_CLTomo_prog.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_classify_CLTomo_prog.cpp mpicxx -o libraries/parallel/mpi_classify_FTTRI.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_classify_FTTRI.cpp mpicxx -o libraries/parallel/mpi_image_rotational_pca.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_image_rotational_pca.cpp mpicxx -o libraries/parallel/mpi_image_sort.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_image_sort.cpp mpicxx -o libraries/parallel/mpi_ml_align2d.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_ml_align2d.cpp mpicxx -o libraries/parallel/mpi_multireference_aligneability.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_multireference_aligneability.cpp mpicxx -o libraries/parallel/mpi_nma_alignment.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_nma_alignment.cpp mpicxx -o libraries/parallel/mpi_nma_alignment_vol.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_nma_alignment_vol.cpp mpicxx -o libraries/parallel/mpi_performance_test.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_performance_test.cpp mpicxx -o libraries/parallel/mpi_project_XR.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_project_XR.cpp mpicxx -o libraries/parallel/mpi_reconstruct_admm.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_reconstruct_admm.cpp mpicxx -o libraries/parallel/mpi_reconstruct_art.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_reconstruct_art.cpp mpicxx -o libraries/parallel/mpi_reconstruct_fourier.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_reconstruct_fourier.cpp mpicxx -o libraries/parallel/mpi_reconstruct_fourier_accel.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_reconstruct_fourier_accel.cpp mpicxx -o libraries/parallel/mpi_reconstruct_significant.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_reconstruct_significant.cpp mpicxx -o libraries/parallel/mpi_reconstruct_wbp.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_reconstruct_wbp.cpp mpicxx -o libraries/parallel/mpi_run.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_run.cpp mpicxx -o libraries/parallel/mpi_transform_adjust_image_grey_levels.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_transform_adjust_image_grey_levels.cpp mpicxx -o libraries/parallel/mpi_validation_nontilt.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_validation_nontilt.cpp mpicxx -o libraries/parallel/mpi_volumeset_align.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/mpi_volumeset_align.cpp mpicxx -o libraries/parallel/xmipp_mpi.os -c -I/usr/include/openmpi-x86_64 -I../ -I/opt/conda3/envs/xmipp/include -fPIC -I/opt/conda3/envs/xmipp/include/python3.8 -I/opt/conda3/envs/xmipp/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore libraries/parallel/xmipp_mpi.cpp /data2/sw/gcc/gcc-7.5.0/build/bin/gcc -o applications/programs/angular_accuracy_pca/angular_accuracy_pca_main.o -c -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/xmipp/xmipp-bundle/src -I/opt/conda3/envs/xmipp/include applications/programs/angular_accuracy_pca/angular_accuracy_pca_main.cpp /data2/sw/gcc/gcc-7.5.0/build/bin/gcc -o applications/programs/angular_break_symmetry/angular_break_symmetry_main.o -c -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/xmipp/xmipp-bundle/src -I/opt/conda3/envs/xmipp/include applications/programs/angular_break_symmetry/angular_break_symmetry_main.cpp /data2/sw/gcc/gcc-7.5.0/build/bin/gcc -o applications/programs/angular_commonline/angular_commonline_main.o -c -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/xmipp/xmipp-bundle/src -I/opt/conda3/envs/xmipp/include applications/programs/angular_commonline/angular_commonline_main.cpp /data2/sw/gcc/gcc-7.5.0/build/bin/gcc -o applications/programs/angular_continuous_assign/angular_continuous_assign_main.o -c -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/xmipp/xmipp-bundle/src -I/opt/conda3/envs/xmipp/include applications/programs/angular_continuous_assign/angular_continuous_assign_main.cpp /data2/sw/gcc/gcc-7.5.0/build/bin/gcc -o applications/programs/angular_continuous_assign2/angular_continuous_assign_main2.o -c -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/xmipp/xmipp-bundle/src -I/opt/conda3/envs/xmipp/include applications/programs/angular_continuous_assign2/angular_continuous_assign_main2.cpp /data2/sw/gcc/gcc-7.5.0/build/bin/gcc -o applications/programs/angular_discrete_assign/angular_discrete_assign_main.o -c -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/xmipp/xmipp-bundle/src -I/opt/conda3/envs/xmipp/include applications/programs/angular_discrete_assign/angular_discrete_assign_main.cpp /data2/sw/gcc/gcc-7.5.0/build/bin/gcc -o applications/programs/angular_distance/angular_distance_main.o -c -Iexternal -Ilibraries -I/data2/sw/xmipp/xmipp-bundle/src/xmippCore -I/data2/sw/xmipp/xmipp-bundle/src -I/opt/conda3/envs/xmipp/include applications/programs/angular_distance/angular_distance_main.cpp mpicxx -o lib/libXmippParallel.so -L/opt/conda3/envs/xmipp/lib -shared libraries/parallel/mpi_angular_accuracy_pca.os libraries/parallel/mpi_angular_class_average.os libraries/parallel/mpi_angular_continuous_assign.os libraries/parallel/mpi_angular_project_library.os libraries/parallel/mpi_angular_projection_matching.os libraries/parallel/mpi_angular_sph_alignment.os libraries/parallel/mpi_classify_CL2D.os libraries/parallel/mpi_classify_CL2D_core_analysis.os libraries/parallel/mpi_classify_CLTomo_prog.os libraries/parallel/mpi_classify_FTTRI.os libraries/parallel/mpi_image_rotational_pca.os libraries/parallel/mpi_image_sort.os libraries/parallel/mpi_ml_align2d.os libraries/parallel/mpi_multireference_aligneability.os libraries/parallel/mpi_nma_alignment.os libraries/parallel/mpi_nma_alignment_vol.os libraries/parallel/mpi_performance_test.os libraries/parallel/mpi_project_XR.os libraries/parallel/mpi_reconstruct_admm.os libraries/parallel/mpi_reconstruct_art.os libraries/parallel/mpi_reconstruct_fourier.os libraries/parallel/mpi_reconstruct_fourier_accel.os libraries/parallel/mpi_reconstruct_significant.os libraries/parallel/mpi_reconstruct_wbp.os libraries/parallel/mpi_run.os libraries/parallel/mpi_transform_adjust_image_grey_levels.os libraries/parallel/mpi_validation_nontilt.os libraries/parallel/mpi_volumeset_align.os libraries/parallel/xmipp_mpi.os $( -L/data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib -Llib -L/opt/conda3/envs/xmipp/lib $) -lXmipp -lpython3.8 g++ -o bin/xmipp_angular_accuracy_pca applications/programs/angular_accuracy_pca/angular_accuracy_pca_main.o -L/data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib -Llib -Llib -L/opt/conda3/envs/xmipp/lib -L/usr/local/cuda-10.2/lib64 -L/data2/sw/gcc/gcc-7.5.0/build/lib64 -L/opt/pymol/lib64 -L/usr/lib64/openmpi/lib -L/opt/relion-3.1-b/lib -L/opt/pymol/lib64 -L/opt/IMOD/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpython3.8 -lpthread -lXmippCore g++ -o bin/xmipp_angular_break_symmetry applications/programs/angular_break_symmetry/angular_break_symmetry_main.o -L/data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib -Llib -Llib -L/opt/conda3/envs/xmipp/lib -L/usr/local/cuda-10.2/lib64 -L/data2/sw/gcc/gcc-7.5.0/build/lib64 -L/opt/pymol/lib64 -L/usr/lib64/openmpi/lib -L/opt/relion-3.1-b/lib -L/opt/pymol/lib64 -L/opt/IMOD/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpython3.8 -lpthread -lXmippCore lib/libXmipp.so: undefined reference to non-virtual thunk to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' lib/libXmipp.so: undefined reference toH5::H5File::throwException(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' /data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib/libXmippCore.so: undefined reference to H5::H5Location::getFileName[abi:cxx11]() const' collect2: error: ld returned 1 exit status scons: *** [bin/xmipp_angular_accuracy_pca] Error 1 lib/libXmipp.so: undefined reference tonon-virtual thunk to H5::H5File::throwException(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' lib/libXmipp.so: undefined reference to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' /data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib/libXmippCore.so: undefined reference toH5::H5Location::getFileName[abi:cxx11]() const' collect2: error: ld returned 1 exit status scons: *** [bin/xmipp_angular_break_symmetry] Error 1 scons: building terminated because of errors.

Some error occurred during the compilation of 'xmipp' ('bin/xmipp_angular_break_symmetry').

It doesn't work yet.

Then I set up as @dmaluenda mentioned.

$ export CXX=/data2/sw/gcc/gcc-7.5.0/build/bin/gcc # it must be a C++ compiler path $ export CXX_CUDA=/data2/sw/gcc/gcc-7.5.0/build/bin/gcc # it must be a C++ compiler path to be used for cuda code, CUDA_CXX is a typo? $ export NVCC=/usr/local/cuda-10.2/bin/nvcc # it must be a cuda compiler $ rm -rf xmipp.conf $ ./xmipp Configuring ----------------------------------------- gcc detected /data2/sw/gcc/gcc-7.5.0/build/bin/gcc -c -w xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/opt/conda3/envs/xmipp/include OpenCV not found rm -v xmipp_test_opencv* Using '/usr/local/cuda-10.2/targets/x86_64-linux/lib'. 'mpirun' detected. 'mpicc' detected. 'mpicxx' detected. Java detected at: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64

Do you want to build tests [yes/NO]NO Configuration completed..... Checking configuration ------------------------------ Checking MPI configuration ... mpicxx -c -w -I../ -I/opt/conda3/envs/xmipp/include -I/usr/include/openmpi-x86_64 xmipp_mpi_test_main.cpp -o xmipp_mpi_test_main.o mpicxx -L/opt/conda3/envs/xmipp/lib xmipp_mpi_test_main.o -o xmipp_mpi_test_main -lfftw3 -lfftw3_threads -lhdf5 -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread rm xmipp_mpi_test_main* mpirun -np 2 echo ' > This sentence should be printed 2 times if mpi runs fine.'

This sentence should be printed 2 times if mpi runs fine. This sentence should be printed 2 times if mpi runs fine. Checking Java configuration... /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/bin/javac Xmipp.java rm Xmipp.java Xmipp.class /data2/sw/gcc/gcc-7.5.0/build/bin/gcc -c -w -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/include/linux -I../ -I/opt/conda3/envs/xmipp/include xmipp_jni_test.cpp -o xmipp_jni_test.o rm xmipp_jni_test Checking CUDA configuration ... /usr/local/cuda-10.2/bin/nvcc -c -w --x cu -D_FORCE_INLINES -Xcompiler -fPIC -ccbin /data2/sw/gcc/gcc-7.5.0/build/bin/gcc -std=c++11 --expt-extended-lambda -gencode=arch=compute_35,code=compute_35 -gencode=arch=compute_50,code=compute_50 -gencode=arch=compute_60,code=compute_60 -gencode=arch=compute_61,code=compute_61 -I../ -I/opt/conda3/envs/xmipp/include xmipp_cuda_test.cpp -o xmipp_cuda_test.o /usr/local/cuda-10.2/bin/nvcc -L/usr/local/cuda-10.2/targets/x86_64-linux/lib -L/usr/local/cuda-10.2/targets/x86_64-linux/lib/stubs xmipp_cuda_test.o -o xmipp_cuda_test -lcudart -lcufft /data2/sw/gcc/gcc-7.5.0/build/bin/gcc -L/usr/local/cuda-10.2/targets/x86_64-linux/lib -L/usr/local/cuda-10.2/targets/x86_64-linux/lib/stubs xmipp_cuda_test.o -o xmipp_cuda_test -lcudart -lcufft rm xmipp_cuda_test Getting Dependencies ------------------------------------- Checkouting cuFFTAdvisor:master ... Already up-to-date. Checkouting CTPL:master ... Already up-to-date. Getting sources ------------------------------------- Checkouting xmippCore:devel ... Already up-to-date. Checkouting xmippViz:devel ... Already up-to-date. Checkouting scipion-em-xmipp:devel ... Already up-to-date. Checkouting xmipp:devel ... Already up-to-date. Building Dependencies ------------------------------------- make all mkdir -p build/ nvcc --cudart static -shared -link -Wno-deprecated-gpu-targets -o build/libcuFFTAdvisor.so obj/benchmarkResult.o obj/transform.o obj/advisor.o obj/validator.o obj/cudaAsserts.o obj/transformGenerator.o obj/benchmarker.o obj/generalTransform.o obj/main.o obj/sizeOptimizer.o obj/inputParser.o mkdir -p build/ nvcc -o build/cuFFTAdvisor obj/benchmarkResult.o obj/transform.o obj/advisor.o obj/validator.o obj/cudaAsserts.o obj/transformGenerator.o obj/benchmarker.o obj/generalTransform.o obj/main.o obj/sizeOptimizer.o obj/inputParser.o -lcufft -Wno-deprecated-gpu-targets cp src/cuFFTAdvisor/build/libcuFFTAdvisor.so src/xmipp/lib/ Compiling ------------------------------------------- scons -j8 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... scons: lib/libXmippCore.so' is up to date. scons:lib/xmippCore.so' is up to date. scons: done building targets. scons -j8 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... scons: lib/libXmipp.so' is up to date. scons:lib/_swig_frm.so' is up to date. ar rc lib/libXmippCuda.a libraries/reconstruction_cuda/cuda_all.o libraries/reconstruction_cuda/cuda_bspline_geo_transformer.o libraries/reconstruction_cuda/cuda_cdf.o libraries/reconstruction_cuda/cuda_correlation_computer.o libraries/reconstruction_cuda/cuda_fft.o libraries/reconstruction_cuda/cuda_gpu_correlation.o libraries/reconstruction_cuda/cuda_gpu_geo_shift_transformer.o libraries/reconstruction_cuda/cuda_gpu_geo_transformer.o libraries/reconstruction_cuda/cuda_gpu_movie_alignment_correlation.o libraries/reconstruction_cuda/cuda_gpu_reconstruct_fourier.o libraries/reconstruction_cuda/cuda_rot_polar_estimator.o libraries/reconstruction_cuda/cuda_shift_corr_estimator.o libraries/reconstruction_cuda/cuda_single_extrema_finder.o libraries/reconstruction_cuda/cuda_volume_halves_restorator.o libraries/reconstruction_cuda/cuda_volume_restoration_kernels.o libraries/reconstruction_cuda/cuda_xmipp_utils.o libraries/reconstruction_cuda/gpu.o ranlib lib/libXmippCuda.a scons: lib/libXmippParallel.so' is up to date. g++ -o bin/xmipp_angular_accuracy_pca applications/programs/angular_accuracy_pca/angular_accuracy_pca_main.o -L/data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib -Llib -Llib -L/opt/conda3/envs/xmipp/lib -L/usr/local/cuda-10.2/lib64 -L/data2/sw/gcc/gcc-7.5.0/build/lib64 -L/opt/pymol/lib64 -L/usr/lib64/openmpi/lib -L/opt/relion-3.1-b/lib -L/opt/pymol/lib64 -L/opt/IMOD/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpython3.8 -lpthread -lXmippCore g++ -o bin/xmipp_angular_break_symmetry applications/programs/angular_break_symmetry/angular_break_symmetry_main.o -L/data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib -Llib -Llib -L/opt/conda3/envs/xmipp/lib -L/usr/local/cuda-10.2/lib64 -L/data2/sw/gcc/gcc-7.5.0/build/lib64 -L/opt/pymol/lib64 -L/usr/lib64/openmpi/lib -L/opt/relion-3.1-b/lib -L/opt/pymol/lib64 -L/opt/IMOD/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpython3.8 -lpthread -lXmippCore g++ -o bin/xmipp_angular_commonline applications/programs/angular_commonline/angular_commonline_main.o -L/data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib -Llib -Llib -L/opt/conda3/envs/xmipp/lib -L/usr/local/cuda-10.2/lib64 -L/data2/sw/gcc/gcc-7.5.0/build/lib64 -L/opt/pymol/lib64 -L/usr/lib64/openmpi/lib -L/opt/relion-3.1-b/lib -L/opt/pymol/lib64 -L/opt/IMOD/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpython3.8 -lpthread -lXmippCore g++ -o bin/xmipp_angular_continuous_assign applications/programs/angular_continuous_assign/angular_continuous_assign_main.o -L/data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib -Llib -Llib -L/opt/conda3/envs/xmipp/lib -L/usr/local/cuda-10.2/lib64 -L/data2/sw/gcc/gcc-7.5.0/build/lib64 -L/opt/pymol/lib64 -L/usr/lib64/openmpi/lib -L/opt/relion-3.1-b/lib -L/opt/pymol/lib64 -L/opt/IMOD/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpython3.8 -lpthread -lXmippCore g++ -o bin/xmipp_angular_continuous_assign2 applications/programs/angular_continuous_assign2/angular_continuous_assign_main2.o -L/data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib -Llib -Llib -L/opt/conda3/envs/xmipp/lib -L/usr/local/cuda-10.2/lib64 -L/data2/sw/gcc/gcc-7.5.0/build/lib64 -L/opt/pymol/lib64 -L/usr/lib64/openmpi/lib -L/opt/relion-3.1-b/lib -L/opt/pymol/lib64 -L/opt/IMOD/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpython3.8 -lpthread -lXmippCore g++ -o bin/xmipp_angular_discrete_assign applications/programs/angular_discrete_assign/angular_discrete_assign_main.o -L/data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib -Llib -Llib -L/opt/conda3/envs/xmipp/lib -L/usr/local/cuda-10.2/lib64 -L/data2/sw/gcc/gcc-7.5.0/build/lib64 -L/opt/pymol/lib64 -L/usr/lib64/openmpi/lib -L/opt/relion-3.1-b/lib -L/opt/pymol/lib64 -L/opt/IMOD/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpython3.8 -lpthread -lXmippCore g++ -o bin/xmipp_angular_distance applications/programs/angular_distance/angular_distance_main.o -L/data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib -Llib -Llib -L/opt/conda3/envs/xmipp/lib -L/usr/local/cuda-10.2/lib64 -L/data2/sw/gcc/gcc-7.5.0/build/lib64 -L/opt/pymol/lib64 -L/usr/lib64/openmpi/lib -L/opt/relion-3.1-b/lib -L/opt/pymol/lib64 -L/opt/IMOD/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpython3.8 -lpthread -lXmippCore /data2/sw/gcc/gcc-7.5.0/build/bin/gcc -o lib/libXmippInterfaceCuda.so -L/usr/local/cuda-10.2/targets/x86_64-linux/lib -L/usr/local/cuda-10.2/targets/x86_64-linux/lib/stubs -L/opt/conda3/envs/xmipp/lib -shared libraries/reconstruction_adapt_cuda/align_significant_gpu.os libraries/reconstruction_adapt_cuda/movie_alignment_correlation_gpu.os libraries/reconstruction_adapt_cuda/reconstruct_fourier_gpu.os libraries/reconstruction_adapt_cuda/volume_halves_restoration_gpu.os libraries/reconstruction_adapt_cuda/xmipp_gpu_correlation.os libraries/reconstruction_adapt_cuda/xmipp_gpu_utils.os $( -L/data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib -Llib -L/opt/conda3/envs/xmipp/lib $) -lXmipp -lXmippCore -lXmippCuda -lcudart -lcufft -lnvidia-ml -lcuFFTAdvisor lib/libXmipp.so: undefined reference tonon-virtual thunk to H5::H5File::throwException(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' lib/libXmipp.so: undefined reference to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' /data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib/libXmippCore.so: undefined reference toH5::H5Location::getFileName[abi:cxx11]() const' collect2: error: ld returned 1 exit status scons: [bin/xmipp_angular_accuracy_pca] Error 1 lib/libXmipp.so: undefined reference to non-virtual thunk to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' lib/libXmipp.so: undefined reference toH5::H5File::throwException(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' /data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const' collect2: error: ld returned 1 exit status scons: [bin/xmipp_angular_break_symmetry] Error 1 lib/libXmipp.so: undefined reference to non-virtual thunk to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' lib/libXmipp.so: undefined reference toH5::H5File::throwException(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' /data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib/libXmippCore.so: undefined reference to H5::H5Location::getFileName[abi:cxx11]() const' collect2: error: ld returned 1 exit status scons: *** [bin/xmipp_angular_commonline] Error 1 lib/libXmipp.so: undefined reference tonon-virtual thunk to H5::H5File::throwException(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' lib/libXmipp.so: undefined reference to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' /data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib/libXmippCore.so: undefined reference toH5::H5Location::getFileName[abi:cxx11]() const' collect2: error: ld returned 1 exit status scons: [bin/xmipp_angular_continuous_assign] Error 1 lib/libXmipp.so: undefined reference to non-virtual thunk to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' lib/libXmipp.so: undefined reference toH5::H5File::throwException(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' /data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const' collect2: error: ld returned 1 exit status scons: [bin/xmipp_angular_discrete_assign] Error 1 lib/libXmipp.so: undefined reference to non-virtual thunk to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' lib/libXmipp.so: undefined reference toH5::H5File::throwException(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' /data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib/libXmippCore.so: undefined reference to H5::H5Location::getFileName[abi:cxx11]() const' collect2: error: ld returned 1 exit status scons: *** [bin/xmipp_angular_continuous_assign2] Error 1 lib/libXmipp.so: undefined reference tonon-virtual thunk to H5::H5File::throwException(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' lib/libXmipp.so: undefined reference to H5::H5File::throwException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' /data2/sw/xmipp/xmipp-bundle/src/xmippCore/lib/libXmippCore.so: undefined reference toH5::H5Location::getFileName[abi:cxx11]() const' collect2: error: ld returned 1 exit status scons: *** [bin/xmipp_angular_distance] Error 1 scons: building terminated because of errors.

Some error occurred during the compilation of 'xmipp' ('bin/xmipp_angular_distance').

There is still the same error.

DStrelak commented 2 years ago

Hi @jianhaoc you have to install hdf5 libraries. For Ubuntu, you can do that via sudo apt-get install -y libhdf5-dev For Centos, sudo yum -y install hdf5-devel (see https://github.com/I2PC/xmipp/issues/322#issuecomment-675205994 for more details) In both cases, make sure there is no hdf5 library installed via conda (conda list | grep hdf5 and conda remove .... the hdf5 package). After that, restart the terminal, remove existing xmipp.conf and try again.

jianhaoc commented 2 years ago

Hi @DStrelak ,

I tried to install hdf5-devel, but it has been installed.

$ sudo yum -y install hdf5-devel [sudo] password for spuser: Loaded plugins: fastestmirror, langpacks, nvidia Loading mirror speeds from cached hostfile epel/x86_64/metalink | 15 kB 00:00:00

I also tried as described in https://github.com/I2PC/xmipp/issues/322#issuecomment-673964596

$ ./xmipp git checkout release-20.07 (cd src/xmippCore; git checkout release-20.07) error: pathspec 'release-20.07' did not match any file(s) known to git. (cd src/xmipp; git checkout release-20.07) error: pathspec 'release-20.07' did not match any file(s) known to git. (cd src/xmippViz; git checkout release-20.07) error: pathspec 'release-20.07' did not match any file(s) known to git. (cd src/scipion-em-xmipp; git checkout release-20.07) error: pathspec 'release-20.07' did not match any file(s) known to git.

It also doesn't work.

jianhaoc commented 2 years ago

My OS is centOS7 as the same environment described in https://github.com/I2PC/xmipp/issues/322#issuecomment-673964596

DStrelak commented 2 years ago

Hi @jianhaoc did you make sure that your conda virtual environment does not have any hdf5 package installed?

jianhaoc commented 2 years ago

Hi @DStrelak ,

Yes, as you mentioned previously, I ran $ conda list | grep hdf5 and nothing is in the output.

DStrelak commented 2 years ago

Hi @jianhaoc then please contact your system admin. The problem you have is that the header files of the hdf5 are not compatible with the shared libraries of the hdf5. In other words, you have two versions of the same library which are not compatible. Tell him / her to check the include paths for compilation (INCDIRFLAGS in xmipp.conf + standard paths), and LD_LIBRARY_PATH.

jianhaoc commented 2 years ago

Hi @DStrelak ,

Xmipp is to be installed on my own workstation. I didn't find anything strange when checking the environment variables. Should I re-install hdf5-devel and which version is recommended?

$ printenv | grep inc MPI_INCLUDE=/usr/include/openmpi-x86_64 QTINC=/usr/lib64/qt-3.3/include CINCL=/data2/sw/ccp4-20210317/ccp4-7.1/include RELION_PDFVIEWER_EXECUTABLEe=evince $ printenv | grep INC MPI_INCLUDE=/usr/include/openmpi-x86_64 QTINC=/usr/lib64/qt-3.3/include CINCL=/data2/sw/ccp4-20210317/ccp4-7.1/include $ echo $PATH /usr/local/cuda-10.2/bin:/data2/sw/gcc/gcc-7.5.0/build/bin:/opt/conda3/envs/xmipp/bin:/opt/conda3/condabin:/data/sw/UCSFchimera20210201/bin:/data2/sw/ccp4-20210317/ccp4-7.1/etc:/data2/sw/ccp4-20210317/ccp4-7.1/bin:/data/sw/ccpem-20201204/bin:/data2/sw/phenix-1.19-4092/phenix-1.19-4092/build/bin:/opt/cryosparc2/cryosparc2_master/bin:/opt/pymol/bin:/usr/lib64/openmpi/bin:/opt/relion-3.1-b/bin:/usr/lib64/qt-3.3/bin:/opt/IMOD/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/spuser/.local/bin:/home/spuser/bin $ echo $LD_LIBRARY_PATH /usr/local/cuda-10.2/lib64:/data2/sw/gcc/gcc-7.5.0/build/lib64:/opt/pymol/lib64:/usr/lib64/openmpi/lib:/opt/relion-3.1-b/lib:/opt/pymol/lib64:/opt/IMOD/lib:

$ cat xmipp.conf | grep INCDIRFLAGS INCDIRFLAGS=-I../ -I/opt/conda3/envs/xmipp/include

$ printenv | grep lib IMOD_QTLIBDIR=/opt/IMOD/qtlib LIBRARY_PATH=/data2/sw/gcc/gcc-7.5.0/build/lib64: QTDIR=/usr/lib64/qt-3.3 QTINC=/usr/lib64/qt-3.3/include CLIB=/data2/sw/ccp4-20210317/ccp4-7.1/lib MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi LD_LIBRARY_PATH=/usr/local/cuda-10.2/lib64:/data2/sw/gcc/gcc-7.5.0/build/lib64:/opt/pymol/lib64:/usr/lib64/openmpi/lib:/opt/relion-3.1-b/lib:/opt/pymol/lib64:/opt/IMOD/lib: MPI_LIB=/usr/lib64/openmpi/lib PATH=/usr/local/cuda-10.2/bin:/data2/sw/gcc/gcc-7.5.0/build/bin:/opt/conda3/envs/xmipp/bin:/opt/conda3/condabin:/data/sw/UCSFchimera20210201/bin:/data2/sw/ccp4-20210317/ccp4-7.1/etc:/data2/sw/ccp4-20210317/ccp4-7.1/bin:/data/sw/ccpem-20201204/bin:/data2/sw/phenix-1.19-4092/phenix-1.19-4092/build/bin:/opt/cryosparc2/cryosparc2_master/bin:/opt/pymol/bin:/usr/lib64/openmpi/bin:/opt/relion-3.1-b/bin:/usr/lib64/qt-3.3/bin:/opt/IMOD/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/spuser/.local/bin:/home/spuser/bin MPI_BIN=/usr/lib64/openmpi/bin IMOD_PLUGIN_DIR=/opt/IMOD/lib/imodplug CLIBD_MON=/data2/sw/ccp4-20210317/ccp4-7.1/lib/data/monomers/ SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi CLIBD=/data2/sw/ccp4-20210317/ccp4-7.1/lib/data QTLIB=/usr/lib64/qt-3.3/lib XDG_DATA_DIRS=/home/spuser/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share MPI_HOME=/usr/lib64/openmpi MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64 IMOD_CALIB_DIR=/usr/local/ImodCalib MMCIFDIC=/data2/sw/ccp4-20210317/ccp4-7.1/lib/ccp4/cif_mmdic.lib QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins

$ printenv | grep LIB LIBTBX_TMPVAL= IMOD_QTLIBDIR=/opt/IMOD/qtlib LIBRARY_PATH=/data2/sw/gcc/gcc-7.5.0/build/lib64: CLIB=/data2/sw/ccp4-20210317/ccp4-7.1/lib LD_LIBRARY_PATH=/usr/local/cuda-10.2/lib64:/data2/sw/gcc/gcc-7.5.0/build/lib64:/opt/pymol/lib64:/usr/lib64/openmpi/lib:/opt/relion-3.1-b/lib:/opt/pymol/lib64:/opt/IMOD/lib: MPI_LIB=/usr/lib64/openmpi/lib LIBTBX_BUILD= CLIBD_MON=/data2/sw/ccp4-20210317/ccp4-7.1/lib/data/monomers/ LIBTBX_OPATH= CLIBD=/data2/sw/ccp4-20210317/ccp4-7.1/lib/data QTLIB=/usr/lib64/qt-3.3/lib IMOD_CALIB_DIR=/usr/local/ImodCalib

$ printenv CCP4I_TCLTK=/data2/sw/ccp4-20210317/ccp4-7.1/bin CCP4_HELPDIR=/data2/sw/ccp4-20210317/ccp4-7.1/help/ MPI_INCLUDE=/usr/include/openmpi-x86_64 MANPATH=/data2/sw/ccp4-20210317/ccp4-7.1/share/man:/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man RELION_ALLOW_CHANGE_MINIMUM_DEDICATED=0 XDG_SESSION_ID=268 IMOD_DIR=/opt/IMOD HOSTNAME=zhanglab SSL_CERT_FILE=/data2/sw/ccp4-20210317/ccp4-7.1/etc/ssl/cacert.pem CHTML=/data2/sw/ccp4-20210317/ccp4-7.1/html LIBTBX_TMPVAL= SELINUX_ROLE_REQUESTED= GFORTRAN_UNBUFFERED_PRECONNECTED=Y TERM=xterm-256color SHELL=/bin/bash IMOD_QTLIBDIR=/opt/IMOD/qtlib HISTSIZE=1000 SSH_CLIENT=137.53.221.139 56172 22 LIBRARY_PATH=/data2/sw/gcc/gcc-7.5.0/build/lib64: CONDA_SHLVL=2 RELION_WARNING_LOCAL_MPI=12 CONDA_PROMPT_MODIFIER=(xmipp) SELINUX_USE_CURRENT_RANGE= RELION_MOTIONCOR2_EXECUTABLE=/opt/bin/MotionCor2 QTDIR=/usr/lib64/qt-3.3 OLDPWD=/data2/sw/xmipp QTINC=/usr/lib64/qt-3.3/include CCP4=/data2/sw/ccp4-20210317/ccp4-7.1 PHENIX=/data2/sw/phenix-1.19-4092/phenix-1.19-4092 SSH_TTY=/dev/pts/3 CLIB=/data2/sw/ccp4-20210317/ccp4-7.1/lib QT_GRAPHICSSYSTEM_CHECKED=1 CUDA_HOME=/usr/local/cuda-10.2 MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi USER=spuser CEXAM=/data2/sw/ccp4-20210317/ccp4-7.1/examples LD_LIBRARY_PATH=/usr/local/cuda-10.2/lib64:/data2/sw/gcc/gcc-7.5.0/build/lib64:/opt/pymol/lib64:/usr/lib64/openmpi/lib:/opt/relion-3.1-b/lib:/opt/pymol/lib64:/opt/IMOD/lib: LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:.tar=38;5;9:.tgz=38;5;9:.arc=38;5;9:.arj=38;5;9:.taz=38;5;9:.lha=38;5;9:.lz4=38;5;9:.lzh=38;5;9:.lzma=38;5;9:.tlz=38;5;9:.txz=38;5;9:.tzo=38;5;9:.t7z=38;5;9:.zip=38;5;9:.z=38;5;9:.Z=38;5;9:.dz=38;5;9:.gz=38;5;9:.lrz=38;5;9:.lz=38;5;9:.lzo=38;5;9:.xz=38;5;9:.bz2=38;5;9:.bz=38;5;9:.tbz=38;5;9:.tbz2=38;5;9:.tz=38;5;9:.deb=38;5;9:.rpm=38;5;9:.jar=38;5;9:.war=38;5;9:.ear=38;5;9:.sar=38;5;9:.rar=38;5;9:.alz=38;5;9:.ace=38;5;9:.zoo=38;5;9:.cpio=38;5;9:.7z=38;5;9:.rz=38;5;9:.cab=38;5;9:.jpg=38;5;13:.jpeg=38;5;13:.gif=38;5;13:.bmp=38;5;13:.pbm=38;5;13:.pgm=38;5;13:.ppm=38;5;13:.tga=38;5;13:.xbm=38;5;13:.xpm=38;5;13:.tif=38;5;13:.tiff=38;5;13:.png=38;5;13:.svg=38;5;13:.svgz=38;5;13:.mng=38;5;13:.pcx=38;5;13:.mov=38;5;13:.mpg=38;5;13:.mpeg=38;5;13:.m2v=38;5;13:.mkv=38;5;13:.webm=38;5;13:.ogm=38;5;13:.mp4=38;5;13:.m4v=38;5;13:.mp4v=38;5;13:.vob=38;5;13:.qt=38;5;13:.nuv=38;5;13:.wmv=38;5;13:.asf=38;5;13:.rm=38;5;13:.rmvb=38;5;13:.flc=38;5;13:.avi=38;5;13:.fli=38;5;13:.flv=38;5;13:.gl=38;5;13:.dl=38;5;13:.xcf=38;5;13:.xwd=38;5;13:.yuv=38;5;13:.cgm=38;5;13:.emf=38;5;13:.axv=38;5;13:.anx=38;5;13:.ogv=38;5;13:.ogx=38;5;13:.aac=38;5;45:.au=38;5;45:.flac=38;5;45:.mid=38;5;45:.midi=38;5;45:.mka=38;5;45:.mp3=38;5;45:.mpc=38;5;45:.ogg=38;5;45:.ra=38;5;45:.wav=38;5;45:.axa=38;5;45:.oga=38;5;45:.spx=38;5;45:.xspf=38;5;45: CONDA_EXE=/opt/conda3/bin/conda BALBES_ROOT=/data2/sw/ccp4-20210317/ccp4-7.1/BALBES RELION_UNBLUR_EXECUTABLE=/opt/bin/unblur_openmp_7_17_15.exe RELION_MINIMUM_DEDICATED=32 dgcc750=/data2/sw/gcc/gcc-7.5.0/build CCP4I_TOP=/data2/sw/ccp4-20210317/ccp4-7.1/share/ccp4i MPI_LIB=/usr/lib64/openmpi/lib _CE_CONDA= CONDA_PREFIX_1=/opt/conda3 LIBTBX_BUILD= MAIL=/var/spool/mail/spuser PATH=/usr/local/cuda-10.2/bin:/data2/sw/gcc/gcc-7.5.0/build/bin:/opt/conda3/envs/xmipp/bin:/opt/conda3/condabin:/data/sw/UCSFchimera20210201/bin:/data2/sw/ccp4-20210317/ccp4-7.1/etc:/data2/sw/ccp4-20210317/ccp4-7.1/bin:/data/sw/ccpem-20201204/bin:/data2/sw/phenix-1.19-4092/phenix-1.19-4092/build/bin:/opt/cryosparc2/cryosparc2_master/bin:/opt/pymol/bin:/usr/lib64/openmpi/bin:/opt/relion-3.1-b/bin:/usr/lib64/qt-3.3/bin:/opt/IMOD/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/spuser/.local/bin:/home/spuser/bin MPI_BIN=/usr/lib64/openmpi/bin CUDA_CXX=/data2/sw/gcc/gcc-7.5.0/build/bin/gcc IMOD_PLUGIN_DIR=/opt/IMOD/lib/imodplug CONDA_PREFIX=/opt/conda3/envs/xmipp MPI_COMPILER=openmpi-x86_64 CCP4_OPEN=UNKNOWN PWD=/data2/sw/xmipp/xmipp-bundle LMFILES=/opt/sp/modulefiles/relion/3.1:/etc/modulefiles/mpi/openmpi-x86_64:/opt/sp/modulefiles/cuda/10.2 CETC=/data2/sw/ccp4-20210317/ccp4-7.1/etc RELION_RESMAP_EXECUTABLE=/opt/bin/ResMap IMOD_JAVADIR=/usr/local/java LANG=en_US.UTF-8 MODULEPATH=/opt/sp/modulefiles:/usr/share/Modules/modulefiles:/etc/modulefiles LOADEDMODULES=relion/3.1:mpi/openmpi-x86_64:cuda/10.2 KDEDIRS=/usr CLIBD_MON=/data2/sw/ccp4-20210317/ccp4-7.1/lib/data/monomers/ CCP4_SCR=/tmp/spuser FOR_DISABLE_STACK_TRACE=1 SELINUX_LEVEL_REQUESTED= CXX=/data2/sw/gcc/gcc-7.5.0/build/bin/gcc _CE_M= PHENIX_VERSION=1.19-4092 RELION_CTFFIND_EXECUTABLE=/opt/bin/ctffind SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass HISTCONTROL=ignoredups MPI_SYSCONFIG=/etc/openmpi-x86_64 SHLVL=1 HOME=/home/spuser LIBTBX_OPATH= MPI_SUFFIX=_openmpi CRANK=/data2/sw/ccp4-20210317/ccp4-7.1/share/ccp4i/crank MPI_MAN=/usr/share/man/openmpi-x86_64 RELION_SUMMOVIE_EXECUTABLE=/opt/bin/sum_movie_openmp_7_17_15.exe CONDA_PYTHON_EXE=/opt/conda3/bin/python PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi LOGNAME=spuser CLIBD=/data2/sw/ccp4-20210317/ccp4-7.1/lib/data QTLIB=/usr/lib64/qt-3.3/lib XDG_DATA_DIRS=/home/spuser/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share SSH_CONNECTION=137.53.221.139 56172 10.149.48.12 22 NVCC=/usr/local/cuda-10.2/bin/nvcc CBIN=/data2/sw/ccp4-20210317/ccp4-7.1/bin MPI_HOME=/usr/lib64/openmpi MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64 MODULESHOME=/usr/share/Modules CONDA_DEFAULT_ENV=xmipp CINCL=/data2/sw/ccp4-20210317/ccp4-7.1/include CCP4_MASTER=/data2/sw/ccp4-20210317 RELION_GCTF_EXECUTABLE=/opt/bin/Gctf LESSOPEN=||/usr/bin/lesspipe.sh %s IMOD_CALIB_DIR=/usr/local/ImodCalib MMCIFDIC=/data2/sw/ccp4-20210317/ccp4-7.1/lib/ccp4/cif_mmdic.lib RELION_PDFVIEWER_EXECUTABLEe=evince XDG_RUNTIME_DIR=/run/user/1000 QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $` } _=/usr/bin/printenv

DStrelak commented 2 years ago

Hi, the problem is not with the values of the variables. The problem is that in one of the folders listed in LD_LIBRARY_PATH or LIBDIRFLAGS of the xmipp.conf there is a libhdf5.so library, which is not compatible with the header file used during the compilation (i.e. one found in either standard paths or listed in INCDIRFLAGS in xmipp.conf). You can look for them by installing mlocate: sudo yum install mlocate ; sudo updatedb And then locate hdf5.so. Ideally, you would see just a few locations. On my machine, I see this:

/home/david/miniconda3/envs/xmipp_DLTK_v0.3/lib/libhdf5.so
/home/david/miniconda3/envs/xmipp_DLTK_v0.3/lib/libhdf5.so.101
/home/david/miniconda3/envs/xmipp_DLTK_v0.3/lib/libhdf5.so.101.1.0
/home/david/miniconda3/envs/xmipp_MicCleaner/lib/libhdf5.so
/home/david/miniconda3/envs/xmipp_MicCleaner/lib/libhdf5.so.103
/home/david/miniconda3/envs/xmipp_MicCleaner/lib/libhdf5.so.103.2.0
/home/david/miniconda3/envs/xmipp_deepEMhancer/lib/libhdf5.so
/home/david/miniconda3/envs/xmipp_deepEMhancer/lib/libhdf5.so.103
/home/david/miniconda3/envs/xmipp_deepEMhancer/lib/libhdf5.so.103.2.0
/home/david/miniconda3/pkgs/hdf5-1.10.2-hba1933b_1/lib/libhdf5.so
/home/david/miniconda3/pkgs/hdf5-1.10.2-hba1933b_1/lib/libhdf5.so.101
/home/david/miniconda3/pkgs/hdf5-1.10.2-hba1933b_1/lib/libhdf5.so.101.1.0
/home/david/miniconda3/pkgs/hdf5-1.10.6-hb1b8bf9_0/lib/libhdf5.so
/home/david/miniconda3/pkgs/hdf5-1.10.6-hb1b8bf9_0/lib/libhdf5.so.103
/home/david/miniconda3/pkgs/hdf5-1.10.6-hb1b8bf9_0/lib/libhdf5.so.103.2.0
/home/david/miniconda3/pkgs/hdf5-1.12.0-hc3cf35f_0/lib/libhdf5.so
/home/david/miniconda3/pkgs/hdf5-1.12.0-hc3cf35f_0/lib/libhdf5.so.200
/home/david/miniconda3/pkgs/hdf5-1.12.0-hc3cf35f_0/lib/libhdf5.so.200.0.0
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so
/usr/local/MATLAB/R2018b/bin/glnxa64/libhdf5.so.8
/usr/local/MATLAB/R2018b/bin/glnxa64/libhdf5.so.8.0.1
/usr/local/MATLAB/R2018b/bin/glnxa64/libitkhdf5.so.1

Notice that conda locations are from different environments than the one I use for Scipion. The Matlab location is not standard path. Therefor, during linking phase, the /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so will be used by default. That is correct, as my INCDIRFLAGS also contains -I/usr/include/hdf5/serial, which holds headers compatible with that shared library (both were installed via sudo apt install libhdf5-dev

$ locate hdf5.h
/home/david/miniconda3/envs/opencv2/include/opencv2/flann/hdf5.h
/home/david/miniconda3/envs/xmipp_DLTK_v0.3/include/hdf5.h
/home/david/miniconda3/envs/xmipp_DLTK_v0.3/include/opencv2/flann/hdf5.h
/home/david/miniconda3/envs/xmipp_DLTK_v0.3/include/opencv2/hdf/hdf5.hpp
/home/david/miniconda3/envs/xmipp_MicCleaner/include/hdf5.h
/home/david/miniconda3/envs/xmipp_deepEMhancer/include/hdf5.h
/home/david/miniconda3/pkgs/hdf5-1.10.2-hba1933b_1/include/hdf5.h
/home/david/miniconda3/pkgs/hdf5-1.10.6-hb1b8bf9_0/include/hdf5.h
/home/david/miniconda3/pkgs/hdf5-1.12.0-hc3cf35f_0/include/hdf5.h
/home/david/miniconda3/pkgs/libopencv-3.4.2-hb342d67_1/include/opencv2/flann/hdf5.h
/home/david/miniconda3/pkgs/libopencv-3.4.2-hb342d67_1/include/opencv2/hdf/hdf5.hpp
/home/david/miniconda3/pkgs/opencv-2.4.11-nppy27_0/include/opencv2/flann/hdf5.h
/usr/include/hdf5/serial/hdf5.h
/usr/local/MATLAB/R2018b/help/matlab/hdf5.html
/usr/local/MATLAB/R2018b/help/matlab/ref/h5f.is_hdf5.html
/usr/local/MATLAB/R2018b/toolbox/vision/builtins/src/ocv/include/flann/hdf5.h
/usr/local/MATLAB/R2018b/toolbox/vision/builtins/src/ocvcg/opencv/include/opencv2/flann/hdf5.h

Again, notice that hdf5.h is either in conda environment NOT used for Scipion, or not in the default path (MATLAB).

DStrelak commented 2 years ago

Closed by helpint user to install Xmipp