quaat
commented
7 years ago Hi Sigve, It seems there is a problem with your version of hdf5. You can to try to disable hdf5. I'm currently on vacation, but I'll try to reproduce this if you can give me a few days. You may want to contact Jester Friis is as he has done the Python implementation.
best, Thomas
On Jul 11, 2017 9:40 AM, "Sigve Karolius" notifications@github.com wrote:
Hello Thomas,
I am attempting to compile your software on Ubuntu 16.04 and in the process hitting a few problems with some of the options (most of them works just fine, although I have not tested the following: HSM, Porto, Python 3 and Numerics).
I have included the verbose output of the errors below, maybe you have an idea of how I can fix it (I am particularly interested in the Python and Test oprions).
-- Sigve Karolius Tests
[ 32%] Linking CXX executable storage-test-hdf5 cd /home/sigveka/Git/Porto/build/storage/test/hdf5 && /usr/bin/cmake -E cmake_link_script CMakeFiles/storage-test-hdf5.dir/link.txt --verbose=1 /usr/bin/c++ -g CMakeFiles/storage-test-hdf5.dir/hdf5test.cpp.o CMakeFiles/storage-test-hdf5.dir/hdf5strategytest.cpp.o CMakeFiles/storage-test-hdf5.dir/testentity.cpp.o CMakeFiles/storage-test-hdf5.dir/main.cpp.o CMakeFiles/storage-test-hdf5.dir/storage-test-hdf5_automoc.cpp.o -o storage-test-hdf5 -rdynamic ../../src/hdf5/libsoft-storage-hdf5.so /usr/lib/x86_64-linux-gnu/hdf5/serial/lib/libhdf5.so -lpthread -lsz -lz -ldl -lm ../../../core/src/kernel/libsoft-kernel.so /usr/local/lib/libbson-1.0.so -lpthread /home/sigveka/Qt5.6.2/5.6/gcc_64/lib/libQt5Network.so.5.6.2 /home/sigveka/Qt5.6.2/5.6/gcc_64/lib/libQt5Script.so.5.6.2 /home/sigveka/Qt5.6.2/5.6/gcc_64/lib/libQt5Concurrent.so.5.6.2 /usr/local/lib/libgtest.a /home/sigveka/Qt5.6.2/5.6/gcc_64/lib/libQt5Core.so.5.6.2 -Wl,-rpath,/home/sigveka/Git/Porto/build/storage/src/hdf5:/usr/lib/x86_64-linux-gnu/hdf5/serial/lib:/home/sigveka/Git/Porto/build/core/src/kernel:/usr/local/lib:/home/sigveka/Qt5.6.2/5.6/gcc_64/lib /usr/bin/ld: /usr/local/lib/libgtest.a(gtest-all.cc.o): undefined reference to symbol 'pthread_key_delete@@GLIBC_2.2.5' /lib/x86_64-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status storage/test/hdf5/CMakeFiles/storage-test-hdf5.dir/build.make:212: recipe for target 'storage/test/hdf5/storage-test-hdf5' failed make[2]: [storage/test/hdf5/storage-test-hdf5] Error 1 make[2]: Leaving directory '/home/sigveka/Git/Porto/build' CMakeFiles/Makefile2:583: recipe for target 'storage/test/hdf5/CMakeFiles/storage-test-hdf5.dir/all' failed make[1]: [storage/test/hdf5/CMakeFiles/storage-test-hdf5.dir/all] Error 2 make[1]: Leaving directory '/home/sigveka/Git/Porto/build' Makefile:160: recipe for target 'all' failed make: *** [all] Error 2
Python (2)
-- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- 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 -- Detecting C compile features -- Detecting C compile features - 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 -- Detecting CXX compile features -- Detecting CXX compile features - done -- Setting build type to 'Debug' as none was specified. -- Looking for pthread.h -- Looking for 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 -- Found BSON: /usr/local/lib/libbson-1.0.so;-lpthread (found version "1.3.0") -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.8.16") -- Found MONGOC: /usr/local/lib/libmongoc-1.0.so;-lpthread (found version "1.3.0") -- Using HDF5_INCLUDE_DIR: /usr/include/hdf5/serial -- Using HDF5_LIBRARIES: /usr/lib/x86_64-linux-gnu/hdf5/serial/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so -- soft-storage-mongo libs: /usr/local/lib/libmongoc-1.0.so;-lpthread;soft-kernel;/usr/local/lib/libbson-1.0.so;-lpthread;Qt5::Core;Qt5::Network;Qt5::Script;Qt5::Concurrent -- Found NLOPT: /usr/lib/x86_64-linux-gnu/libnlopt.so -- Found SWIG: /usr/bin/swig3.0 (found version "3.0.8") -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found version "2.7.12") CMake Error at foreign/python/src/softpy/CMakeLists.txt:52 (get_filename_component): get_filename_component called with incorrect number of arguments
CMake Error at foreign/python/src/softpy/CMakeLists.txt:54 (file): file RELATIVE_PATH called with incorrect number of arguments
CMake Error at foreign/python/src/softpy/CMakeLists.txt:61 (install): install FILES given no DESTINATION!
CMake Error at foreign/python/src/softpy/CMakeLists.txt:63 (install): install FILES given no DESTINATION!
-- Found Doxygen: /usr/local/bin/doxygen (found version "1.8.14") -- Configuring incomplete, errors occurred! See also "/home/sigveka/Git/Porto/build/CMakeFiles/CMakeOutput.log". See also "/home/sigveka/Git/Porto/build/CMakeFiles/CMakeError.log".
Fortran
[ 96%] Building Fortran object foreign/fortran/src/softf/CMakeFiles/softf.dir/entity-module.f90.o cd /home/sigveka/Git/Porto/build/foreign/fortran/src/softf && /usr/bin/gfortran -Dsoftf_EXPORTS -I/home/sigveka/Git/Porto/build/foreign/fortran/src/softf -I/home/sigveka/Git/Porto/foreign/fortran/src/softf -fno-f2c -O0 -g -fPIC -c /home/sigveka/Git/Porto/foreign/fortran/src/softf/entity-module.f90 -o CMakeFiles/softf.dir/entity-module.f90.o /home/sigveka/Git/Porto/foreign/fortran/src/softf/entity-module.f90:18:14:
procedure, public, pass(self) :: get_id => entity_get_id3 1Error: ‘entity_get_id3’ must be a module procedure or an external procedure with an explicit interface at (1) foreign/fortran/src/softf/CMakeFiles/softf.dir/build.make:62: recipe for target 'foreign/fortran/src/softf/CMakeFiles/softf.dir/entity-module.f90.o' failed make[2]: [foreign/fortran/src/softf/CMakeFiles/softf.dir/entity-module.f90.o] Error 1 make[2]: Leaving directory '/home/sigveka/Git/Porto/build' CMakeFiles/Makefile2:1532: recipe for target 'foreign/fortran/src/softf/CMakeFiles/softf.dir/all' failed make[1]: [foreign/fortran/src/softf/CMakeFiles/softf.dir/all] Error 2 make[1]: Leaving directory '/home/sigveka/Git/Porto/build' Makefile:149: recipe for target 'all' failed make: *** [all] Error 2
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sigveka
Hello Thomas,
I am attempting to compile your software on Ubuntu 16.04 and in the process hitting a few problems with some of the options (most of them works just fine, although I have not tested the following: HSM, Porto, Python 3 and Numerics).
I have included the verbose output of the errors below, maybe you have an idea of how I can fix it (I am particularly interested in the Python and Test oprions).
-- Sigve Karolius
Tests
Python (2)
Fortran