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FileNotFoundError during compilation (/ScannerBit/lib/plugin_libraries.list) #1

Closed fzeiser closed 4 years ago

fzeiser commented 4 years ago

trying to follow the steps fro compilation

mkdir build
cd build
cmake ..
make -j N scanners   # N er antall prosesser som make for bruke
cmake ..
make -j N

but failing during cmake in the build directory with following error message

(myenv) fabiobz@fabiobz-tp1 ~/Desktop/Masterthesis/misc/gambit_np/build $ [master] cmake ..
-- Build type is set to None 
-- Found PythonInterp: /home/fabiobz/miniconda3/envs/myenv/bin/python3 (found suitable version "3.7.3", minimum required is "3") 
   Using Python interpreter version 3.7.3 for build.
   Using Python libraries version 3.5.2 for Python backend support.
   NOTE: You are using different Python versions for the interpreter and the libraries!
   In principle this should be fine, as the interpreter is only used for building GAMBIT, and the
   libraries are only used for providing support for Python backends at runtime.  However, if you
   have matching versions installed, you can make this message go away by trying the following
   (making sure to clean out your build directory in between any such changes):
   1. invoke cmake as cmake -DFORCE_PYTHON2=True .. (or similar)
   2. invoke cmake as cmake -DFORCE_PYTHON3=True .. (or similar)
   3. set the following variables when invoking cmake:
     PYTHON_LIBRARY
     PYTHON_INCLUDE_DIR
     PYTHON_INCLUDE_DIR2 (you might be able to get away without setting this one)
     PYTHON_EXECUTABLE   (you might be able to get away without setting this one)

-- pybind11 v2.4.3
   Found pybind11 2.4.3 at /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/contrib/pybind11.
-- Found Python module yaml.
-- Found Python module os.
-- Found Python module re.
-- Found Python module datetime.
-- Found Python module sys.
-- Found Python module getopt.
-- Found Python module shutil.
-- Found Python module itertools.
   Axel utility not found.  Backend downloads would be faster if you installed axel.
-- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) (Required is at least version "3.1.0")
-- Eigen not found
-- OpenMP found successfully
   Missing library libuuid required for WSTP. Mathematica will be disabled.
-- Werror is disabled
 X MPI is disabled. Executables will not be parallelised with MPI. Please use -DWITH_MPI=ON to enable MPI.
-- A library with LAPACK API found.
   Using the following LAPACK libraries: /home/fabiobz/miniconda3/envs/myenv/lib/libmkl_rt.so /home/fabiobz/miniconda3/envs/myenv/lib/libmkl_gf_lp64.so /home/fabiobz/miniconda3/envs/myenv/lib/libmkl_gnu_thread.so /home/fabiobz/miniconda3/envs/myenv/lib/libmkl_core.so /home/fabiobz/miniconda3/envs/myenv/lib/libgomp.so -lm -ldl
 X ROOT support is deactivated. Set -DWITH_ROOT=ON to activate ROOT support in GAMBIT.
   Disabling GreAT and RestFrames support in GAMBIT configuration.
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5 libraries: /home/fabiobz/miniconda3/envs/myenv/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/fabiobz/miniconda3/envs/myenv/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- Found SQLite3 libraries: /usr/lib/x86_64-linux-gnu/libsqlite3.so
fatal: No names found, cannot describe anything.
   GAMBIT version not detected via git.  Reverting to cmake/tarball_info.cmake.
-- Updating GAMBIT scanner cmake and related files
   Existing ScannerBit/include/gambit/ScannerBit/priors_rollcall.hpp is identical to candidate; leaving it untouched
   Updated ScannerBit/CMakeLists.txt
Traceback (most recent call last):
  File "/home/fabiobz/miniconda3/envs/myenv/lib/python3.7/shutil.py", line 563, in move
    os.rename(src, real_dst)
FileNotFoundError: [Errno 2] No such file or directory: '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/ScannerBit_lib_plugin_libraries.list.candidate' -> './ScannerBit/lib/plugin_libraries.list'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/scripts/scanner+_harvester.py", line 961, in <module>
    main(sys.argv[1:])
  File "/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/scripts/scanner+_harvester.py", line 831, in main
    update_only_if_different(cmake, candidate)
  File "./Utils/scripts/harvesting_tools.py", line 583, in update_only_if_different
    shutil.move(candidate,existing)
  File "/home/fabiobz/miniconda3/envs/myenv/lib/python3.7/shutil.py", line 577, in move
    copy_function(src, real_dst)
  File "/home/fabiobz/miniconda3/envs/myenv/lib/python3.7/shutil.py", line 263, in copy2
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/home/fabiobz/miniconda3/envs/myenv/lib/python3.7/shutil.py", line 121, in copyfile
    with open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory: './ScannerBit/lib/plugin_libraries.list'
CMake Error at cmake/utilities.cmake:71 (message):
  Cmake failed because a GAMBIT python script failed.  Culprit:
  /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/scripts/scanner+_harvester.py
Call Stack (most recent call first):
  CMakeLists.txt:479 (check_result)

-- Configuring incomplete, errors occurred!
See also "/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/CMakeFiles/CMakeOutput.log".
See also "/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/CMakeFiles/CMakeError.log".
fzeiser commented 4 years ago

I also wonder whether I should set some special flags, because of this part. I'm not quite sure what the backend support is though :/.

   Using Python interpreter version 3.7.3 for build.
   Using Python libraries version 3.5.2 for Python backend support.
fzeiser commented 4 years ago

@anderkve Any ideas on this?

fzeiser commented 4 years ago

Btw, the file ScannerBit_lib_plugin_libraries.list.candidate exists in build

anderkve commented 4 years ago

@fzeiser I think the problem is that I forgot to commit the empty ScannerBit/lib folder. I just pushed a fix, so you can try again.

About the backend support: A "backend" is an external package connected to GAMBIT at runtime (compiled shared library or a python code). Our nuclear physics code will be regarded by GAMBIT as a "python backend". So the message you get means that our code will be run with Python 3.5.2, unless you set the Python library flags in cmake to point to your Python 3.7.3 installation.

On my system I have 

PYTHON_EXECUTABLE=/usr/bin/python3
PYTHON_INCLUDE_DIR=/usr/include/python3.7m
PYTHON_LIBRARY/usr/lib/x86_64-linux-gnu/libpython3.7m.so

You can pass these as flags to cmake using the -D option: cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PYTHON_INCLUDE_DIR=/usr/include/python3.7m -D PYTHON_LIBRARY/usr/lib/x86_64-linux-gnu/libpython3.7m.so ..

fzeiser commented 4 years ago

So I tried recompiling with these settings (mostly writing them down to remember ;P)

export PYTHON_EXECUTABLE=/home/fabiobz/miniconda3/envs/myenv/bin/python3.7
export PYTHON_INCLUDE_DIR=/home/fabiobz/miniconda3/envs/myenv/include/python3.7m
export PYTHON_LIBRARY=/home/fabiobz/miniconda3/envs/myenv/lib/libpython3.7m.so

cmake -D PYTHON_EXECUTABLE=$PYTHON_EXECUTABLE -D PYTHON_INCLUDE_DIR=$PYTHON_INCLUDE_DIR -D PYTHON_LIBRARY=$PYTHON_LIBRARY ..

and now I get a new error:

cmake -D PYTHON_EXECUTABLE=$PYTHON_EXECUTABLE -D PYTHON_INCLUDE_DIR=$PYTHON_I
NCLUDE_DIR -D PYTHON_LIBRARY=$PYTHON_LIBRARY ..
-- Build type is set to None 
-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- The Fortran compiler identification is GNU 5.4.0
-- Check for working C compiler: /home/fabiobz/miniconda3/envs/myenv/bin/x86_64-conda_cos6-linux-gnu-cc
-- Check for working C compiler: /home/fabiobz/miniconda3/envs/myenv/bin/x86_64-conda_cos6-linux-gnu-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: /home/fabiobz/miniconda3/envs/myenv/bin/x86_64-conda_cos6-linux-gnu-c++
-- Check for working CXX compiler: /home/fabiobz/miniconda3/envs/myenv/bin/x86_64-conda_cos6-linux-gnu-c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- Found PythonInterp: /home/fabiobz/miniconda3/envs/myenv/bin/python3.7 (found suitable version "3.7.3", minimum required is "3") 
-- Found PythonLibs: /home/fabiobz/miniconda3/envs/myenv/lib/libpython3.7m.so (found suitable version "3.7.3", minimum required is "3") 
   Using Python interpreter version 3.7.3 for build.
   Using Python libraries version 3.7.3 for Python backend support.
-- Found PythonInterp: /home/fabiobz/miniconda3/envs/myenv/bin/python3.7 (found version "3.7.3") 
-- Found PythonLibs: /home/fabiobz/miniconda3/envs/myenv/lib/libpython3.7m.so
-- Performing Test HAS_CPP14_FLAG
-- Performing Test HAS_CPP14_FLAG - Success
-- pybind11 v2.4.3
   Found pybind11 2.4.3 at /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/contrib/pybind11.
-- Found Python module yaml.
-- Found Python module os.
-- Found Python module re.
-- Found Python module datetime.
-- Found Python module sys.
-- Found Python module getopt.
-- Found Python module shutil.
-- Found Python module itertools.
   Axel utility not found.  Backend downloads would be faster if you installed axel.
-- Performing Test COMPILER_SUPPORTS_CXX17
-- Performing Test COMPILER_SUPPORTS_CXX17 - Success
-- Found Boost: /usr/include (found suitable version "1.58.0", minimum required is "1.41")  
-- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) (Required is at least version "3.1.0")
-- Eigen not found
-- OpenMP found successfully
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") 
-- Checking for module 'gsl >= 1.15'
--   Found gsl , version 2.1
-- Found GSL: ;/usr/lib/x86_64-linux-gnu/libgsl.so;/usr/lib/x86_64-linux-gnu/libgslcblas.so;/usr/lib/x86_64-linux-gnu/libm.so  
   Missing library libuuid required for WSTP. Mathematica will be disabled.
-- Found LibDL: /usr/lib/x86_64-linux-gnu/libdl.so  
-- Werror is disabled
-- Performing Test CXX_SUPPORTS_all
-- Performing Test CXX_SUPPORTS_all - Success
-- Performing Test CXX_SUPPORTS_extra
-- Performing Test CXX_SUPPORTS_extra - Success
-- Performing Test CXX_SUPPORTS_no-misleading-indentation
-- Performing Test CXX_SUPPORTS_no-misleading-indentation - Success
 X MPI is disabled. Executables will not be parallelised with MPI. Please use -DWITH_MPI=ON to enable MPI.
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - not found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- Found BLAS: /home/fabiobz/miniconda3/envs/myenv/lib/libmkl_gf_lp64.so;/home/fabiobz/miniconda3/envs/myenv/lib/libmkl_gnu_thread.so;/home/fabiobz/miniconda3/envs/myenv/lib/libmkl_core.so;/home/fabiobz/miniconda3/envs/myenv/lib/libgomp.so;-lm;-ldl  
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
   Using the following LAPACK libraries: /home/fabiobz/miniconda3/envs/myenv/lib/libmkl_rt.so /home/fabiobz/miniconda3/envs/myenv/lib/libmkl_gf_lp64.so /home/fabiobz/miniconda3/envs/myenv/lib/libmkl_gnu_thread.so /home/fabiobz/miniconda3/envs/myenv/lib/libmkl_core.so /home/fabiobz/miniconda3/envs/myenv/lib/libgomp.so -lm -ldl
 X ROOT support is deactivated. Set -DWITH_ROOT=ON to activate ROOT support in GAMBIT.
   Disabling GreAT and RestFrames support in GAMBIT configuration.
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5 libraries: /home/fabiobz/miniconda3/envs/myenv/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/fabiobz/miniconda3/envs/myenv/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so  
-- Found SQLite3 libraries: /usr/lib/x86_64-linux-gnu/libsqlite3.so
-- Found Git: /usr/bin/git (found version "2.25.2") 
fatal: No names found, cannot describe anything.
   GAMBIT version not detected via git.  Reverting to cmake/tarball_info.cmake.
-- Updating GAMBIT scanner cmake and related files
   Existing ScannerBit/include/gambit/ScannerBit/priors_rollcall.hpp is identical to candidate; leaving it untouched
   Updated ScannerBit/CMakeLists.txt
   Existing ScannerBit/lib/plugin_libraries.list is identical to candidate; leaving it untouched
   Existing scratch/build_time/scanbit_reqd_entries.yaml is identical to candidate; leaving it untouched
   Existing scratch/build_time/scanbit_flags.yaml is identical to candidate; leaving it untouched
   Created /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/linkedout.cmake
-- Updating GAMBIT scanner cmake and related files - done.
-- Updating GAMBIT with config data
-- Looking for include file link.h
-- Looking for include file link.h - found
   Found graphviz. Model and module function hierarchy plots will be enabled.
   Configured /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/cmake/include/gambit/cmake/cmake_variables.hpp
-- Updating GAMBIT with config data - done.
-- Generated particle_database.cpp from particle_database.yaml.
-- Updating GAMBIT module, model, backend, and printer CMake files.
   Existing ExampleBit_B/CMakeLists.txt is identical to candidate; leaving it untouched
   Existing OMBit/CMakeLists.txt is identical to candidate; leaving it untouched
   Existing ExampleBit_A/CMakeLists.txt is identical to candidate; leaving it untouched
   Existing Backends/CMakeLists.txt is identical to candidate; leaving it untouched
   Existing Models/CMakeLists.txt is identical to candidate; leaving it untouched
   Existing Printers/CMakeLists.txt is identical to candidate; leaving it untouched
-- Updating GAMBIT module, backend, and printer CMake files - done.
 X Excluding great 1.0.0 from GAMBIT configuration.
 X Excluding great 1.0.0 from ScannerBit configuration.
-- Did not find scanner library diver for diver_1.0.0. Disabling scanners that depend on this.
-- Did not find scanner library diver for diver_1.0.2. Disabling scanners that depend on this.
-- Did not find scanner library diver for diver_1.0.4. Disabling scanners that depend on this.
-- Did not find scanner library great for great. Disabling scanners that depend on this.
-- Did not find scanner header fparser.hh. Disabling scanners that depend on this.
-- Did not find scanner header TGreatManager.h. Disabling scanners that depend on this.
-- Did not find scanner header TGreatModel.h. Disabling scanners that depend on this.
-- Did not find scanner header TGreatMCMCAlgorithmCovariance.h. Disabling scanners that depend on this.
-- Did not find scanner library nest3 for multinest_3.10. Disabling scanners that depend on this.
-- Did not find scanner library nest3 for multinest_3.11. Disabling scanners that depend on this.
-- Did not find scanner library chord for polychord. Disabling scanners that depend on this.
-- Configuring done
CMake Error at cmake/utilities.cmake:178 (add_library):
  Cannot find source file:

    include/gambit/Elements/types_rollcall.hpp

  Tried extensions .c .C .c++ .cc .cpp .cxx .cu .m .M .mm .h .hh .h++ .hm
  .hpp .hxx .in .txx
Call Stack (most recent call first):
  Elements/CMakeLists.txt:67 (add_gambit_library)

CMake Error at cmake/utilities.cmake:178 (add_library):
  No SOURCES given to target: Elements
Call Stack (most recent call first):
  Elements/CMakeLists.txt:67 (add_gambit_library)

CMake Generate step failed.  Build files cannot be regenerated correctly.
anderkve commented 4 years ago

Hmm, must be more files I forgot to commit in the initial commit. I'll do some tests and let you know when it's ready for you to try again.

anderkve commented 4 years ago

Yes, the file Elements/include/gambit/Elements/types_rollcall.hpp and a couple of other _rollcall.hpp files were missing in my initial commit. We auto-generate quite a few _rollcall.hpp files, in addition to the regular ones, so I guess these files were caught by some .gitignore rule made to ignore the auto-generated ones.

I have added the missing files now and tested that a fresh clone of the repo builds OK for me.

fzeiser commented 4 years ago

I get an error in the last make statement, but I assume that it's related to me not having boost.

/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_utils.hpp:34:10: fatal error: boost/iterator/zip_iterator.hpp: No such file or directory
 #include <boost/iterator/zip_iterator.hpp>

I'll install it and try again (although I would have thought that cmake should complain, shouldn't it)?

anderkve commented 4 years ago

Hmm, that's strange, since your cmake output claims it has found boost: -- Found Boost: /usr/include (found suitable version "1.58.0", minimum required is "1.41")

I'll have a look myself and see if I spot anything funny.

fzeiser commented 4 years ago

Yep, checked it also, I must have installed it some time ago then ;P

fzeiser commented 4 years ago

here is the full traceback

(myenv) fabiobz@fabiobz-tp1 ~/Desktop/Masterthesis/misc/gambit_np/build $ [master] make -j 3
Scanning dependencies of target backend_harvest
Scanning dependencies of target model_harvest
Scanning dependencies of target yaml-cpp
[  0%] Generating backends_harvested
[  0%] Generating models_harvested
[  0%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o
[  0%] Built target backend_harvest
[  1%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o
[  1%] Built target model_harvest
[  1%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o
[  1%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o
Scanning dependencies of target gambit_preload
[  3%] Building CXX object CMakeFiles/gambit_preload.dir/contrib/preload/gambit_preload.cpp.o
[  3%] Linking CXX shared library contrib/libgambit_preload.so
[  3%] Built target gambit_preload
[  4%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o
[  4%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o
Scanning dependencies of target FarrayTest
[  4%] Building Fortran object Backends/CMakeFiles/FarrayTest.dir/examples/libFarrayTest.f90.o
[  4%] Linking Fortran shared library ../../Backends/examples/libFarrayTest.so
[  4%] Built target FarrayTest
Scanning dependencies of target first
[  6%] Building CXX object Backends/CMakeFiles/first.dir/examples/libfirst.cpp.o
[  6%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o
[  6%] Linking CXX shared library ../../Backends/examples/libfirst.so
[  6%] Built target first
Scanning dependencies of target fortran
[  6%] Building Fortran object Backends/CMakeFiles/fortran.dir/examples/libfortran.f90.o
[  8%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o
[  9%] Linking Fortran shared library ../../Backends/examples/libfortran.so
[  9%] Built target fortran
[  9%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o
[  9%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o
Scanning dependencies of target module_harvest
[  9%] Generating modules_harvested
   Created Elements/include/gambit/Elements/module_types_rollcall.hpp
Harvesting types from headers...
   Created Backends/include/gambit/Backends/backend_functor_types.hpp
   Created Elements/include/gambit/Elements/module_functor_types.hpp
[  9%] Built target module_harvest
[ 11%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o
[ 11%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/node.cpp.o
[ 11%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o
[ 13%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o
[ 13%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o
Scanning dependencies of target printer_harvest
[ 14%] Generating printers_harvested
   Created Printers/include/gambit/Printers/printer_rollcall.hpp
[ 14%] Built target printer_harvest
[ 14%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/null.cpp.o
[ 16%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o
[ 16%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o
[ 16%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o
[ 18%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o
[ 18%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o
[ 18%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o
[ 19%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o
[ 19%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o
[ 19%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o
[ 21%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o
[ 21%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o
[ 21%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o
[ 22%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/contrib/graphbuilder.cpp.o
[ 22%] Building CXX object contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/src/contrib/graphbuilderadapter.cpp.o
[ 24%] Linking CXX static library ../../../contrib/yaml-cpp-0.6.2/libyaml-cpp.a
[ 24%] Built target yaml-cpp
Scanning dependencies of target scanner_postprocessor_2.0.0
Scanning dependencies of target scanner_polychord
Scanning dependencies of target scanner_twalk
[ 26%] Building CXX object ScannerBit/CMakeFiles/scanner_twalk.dir/src/scanners/twalk/twalk.cpp.o
[ 26%] Building CXX object ScannerBit/CMakeFiles/scanner_polychord.dir/src/scanners/polychord/polychord.cpp.o
[ 27%] Building CXX object ScannerBit/CMakeFiles/scanner_postprocessor_2.0.0.dir/src/scanners/postprocessor_2.0.0/postprocessor.cpp.o
In file included from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/plugin_interface.hpp:31:0,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/twalk/twalk.cpp:25:
/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_utils.hpp:34:10: fatal error: boost/iterator/zip_iterator.hpp: No such file or directory
 #include <boost/iterator/zip_iterator.hpp>
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
ScannerBit/CMakeFiles/scanner_twalk.dir/build.make:62: recipe for target 'ScannerBit/CMakeFiles/scanner_twalk.dir/src/scanners/twalk/twalk.cpp.o' failed
make[2]: *** [ScannerBit/CMakeFiles/scanner_twalk.dir/src/scanners/twalk/twalk.cpp.o] Error 1
CMakeFiles/Makefile2:3529: recipe for target 'ScannerBit/CMakeFiles/scanner_twalk.dir/all' failed
make[1]: *** [ScannerBit/CMakeFiles/scanner_twalk.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 27%] Building CXX object ScannerBit/CMakeFiles/scanner_postprocessor_2.0.0.dir/src/scanners/postprocessor_2.0.0/postprocessor_object.cpp.o
In file included from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_plugin.hpp:29:0,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:31:
/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_utils.hpp:34:10: fatal error: boost/iterator/zip_iterator.hpp: No such file or directory
 #include <boost/iterator/zip_iterator.hpp>
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
ScannerBit/CMakeFiles/scanner_polychord.dir/build.make:62: recipe for target 'ScannerBit/CMakeFiles/scanner_polychord.dir/src/scanners/polychord/polychord.cpp.o' failed
make[2]: *** [ScannerBit/CMakeFiles/scanner_polychord.dir/src/scanners/polychord/polychord.cpp.o] Error 1
CMakeFiles/Makefile2:3812: recipe for target 'ScannerBit/CMakeFiles/scanner_polychord.dir/all' failed
make[1]: *** [ScannerBit/CMakeFiles/scanner_polychord.dir/all] Error 2
In file included from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/Utils/include/gambit/Utils/util_macros.hpp:22:0,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/Utils/include/gambit/Utils/standalone_error_handlers.hpp:21,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/Utils/include/gambit/Utils/util_types.hpp:52,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/Utils/include/gambit/Utils/util_functions.hpp:31,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/postprocessor_2.0.0/postprocessor.cpp:43:
/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/Utils/include/gambit/Utils/boost_fallbacks.hpp:52:10: fatal error: boost/version.hpp: No such file or directory
 #include <boost/version.hpp>
          ^~~~~~~~~~~~~~~~~~~
compilation terminated.
ScannerBit/CMakeFiles/scanner_postprocessor_2.0.0.dir/build.make:62: recipe for target 'ScannerBit/CMakeFiles/scanner_postprocessor_2.0.0.dir/src/scanners/postprocessor_2.0.0/postprocessor.cpp.o' failed
make[2]: *** [ScannerBit/CMakeFiles/scanner_postprocessor_2.0.0.dir/src/scanners/postprocessor_2.0.0/postprocessor.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
In file included from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_plugin.hpp:29:0,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanners/postprocessor_2.0.0/postprocessor.hpp:18,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/postprocessor_2.0.0/postprocessor_object.cpp:19:
/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_utils.hpp:34:10: fatal error: boost/iterator/zip_iterator.hpp: No such file or directory
 #include <boost/iterator/zip_iterator.hpp>
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
ScannerBit/CMakeFiles/scanner_postprocessor_2.0.0.dir/build.make:75: recipe for target 'ScannerBit/CMakeFiles/scanner_postprocessor_2.0.0.dir/src/scanners/postprocessor_2.0.0/postprocessor_object.cpp.o' failed
make[2]: *** [ScannerBit/CMakeFiles/scanner_postprocessor_2.0.0.dir/src/scanners/postprocessor_2.0.0/postprocessor_object.cpp.o] Error 1
CMakeFiles/Makefile2:3560: recipe for target 'ScannerBit/CMakeFiles/scanner_postprocessor_2.0.0.dir/all' failed
make[1]: *** [ScannerBit/CMakeFiles/scanner_postprocessor_2.0.0.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2

whereas the cmake output was

cmake ..
-- Build type is set to None 
   Using Python interpreter version 3.7.3 for build.
   Using Python libraries version 3.7.3 for Python backend support.
-- pybind11 v2.4.3
   Found pybind11 2.4.3 at /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/contrib/pybind11.
-- Found Python module yaml.
-- Found Python module os.
-- Found Python module re.
-- Found Python module datetime.
-- Found Python module sys.
-- Found Python module getopt.
-- Found Python module shutil.
-- Found Python module itertools.
   Axel utility not found.  Backend downloads would be faster if you installed axel.
-- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) (Required is at least version "3.1.0")
-- Eigen not found
-- OpenMP found successfully
   Missing library libuuid required for WSTP. Mathematica will be disabled.
-- Werror is disabled
 X MPI is disabled. Executables will not be parallelised with MPI. Please use -DWITH_MPI=ON to enable MPI.
-- A library with LAPACK API found.
   Using the following LAPACK libraries: /home/fabiobz/miniconda3/envs/myenv/lib/libmkl_rt.so /home/fabiobz/miniconda3/envs/myenv/lib/libmkl_gf_lp64.so /home/fabiobz/miniconda3/envs/myenv/lib/libmkl_gnu_thread.so /home/fabiobz/miniconda3/envs/myenv/lib/libmkl_core.so /home/fabiobz/miniconda3/envs/myenv/lib/libgomp.so -lm -ldl
 X ROOT support is deactivated. Set -DWITH_ROOT=ON to activate ROOT support in GAMBIT.
   Disabling GreAT and RestFrames support in GAMBIT configuration.
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5 libraries: /home/fabiobz/miniconda3/envs/myenv/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/fabiobz/miniconda3/envs/myenv/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- Found SQLite3 libraries: /usr/lib/x86_64-linux-gnu/libsqlite3.so
fatal: No names found, cannot describe anything.
   GAMBIT version not detected via git.  Reverting to cmake/tarball_info.cmake.
-- Updating GAMBIT scanner cmake and related files
   Found library ./ScannerBit/installed/diver/1.0.4/lib/libdiver.so needed for ScannerBit plugin diver v1.0.4
   Found library ./ScannerBit/installed/multinest/3.11/libnest3.so needed for ScannerBit plugin multinest v3.11.0
   Found library ./ScannerBit/installed/polychord/1.16/lib/libchord.so needed for ScannerBit plugin polychord v1.16.0
   Existing ScannerBit/include/gambit/ScannerBit/priors_rollcall.hpp is identical to candidate; leaving it untouched
   Updated ScannerBit/CMakeLists.txt
   Existing ScannerBit/lib/plugin_libraries.list is identical to candidate; leaving it untouched
   Updated scratch/build_time/scanbit_reqd_entries.yaml
   Existing scratch/build_time/scanbit_flags.yaml is identical to candidate; leaving it untouched
   Existing /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/linkedout.cmake is identical to candidate; leaving it untouched
-- Updating GAMBIT scanner cmake and related files - done.
-- Updating GAMBIT with config data
   Found graphviz. Model and module function hierarchy plots will be enabled.
   Configured /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/cmake/include/gambit/cmake/cmake_variables.hpp
-- Updating GAMBIT with config data - done.
-- Generated particle_database.cpp from particle_database.yaml.
-- Updating GAMBIT module, model, backend, and printer CMake files.
   Existing ExampleBit_B/CMakeLists.txt is identical to candidate; leaving it untouched
   Existing OMBit/CMakeLists.txt is identical to candidate; leaving it untouched
   Existing ExampleBit_A/CMakeLists.txt is identical to candidate; leaving it untouched
   Existing Backends/CMakeLists.txt is identical to candidate; leaving it untouched
   Existing Models/CMakeLists.txt is identical to candidate; leaving it untouched
   Existing Printers/CMakeLists.txt is identical to candidate; leaving it untouched
-- Updating GAMBIT module, backend, and printer CMake files - done.
 X Excluding great 1.0.0 from GAMBIT configuration.
 X Excluding great 1.0.0 from ScannerBit configuration.
-- Did not find scanner library diver for diver_1.0.0. Disabling scanners that depend on this.
-- Did not find scanner library diver for diver_1.0.2. Disabling scanners that depend on this.
-- Did not find scanner library great for great. Disabling scanners that depend on this.
-- Did not find scanner header TGreatModel.h. Disabling scanners that depend on this.
-- Did not find scanner header fparser.hh. Disabling scanners that depend on this.
-- Did not find scanner header TGreatManager.h. Disabling scanners that depend on this.
-- Did not find scanner header TGreatMCMCAlgorithmCovariance.h. Disabling scanners that depend on this.
-- Did not find scanner library nest3 for multinest_3.10. Disabling scanners that depend on this.
-- Configuring done
-- Generating done
-- Build files have been written to: /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build
anderkve commented 4 years ago

And you actually have the file /usr/include/boost/iterator/zip_iterator.hpp on your system?

fzeiser commented 4 years ago

Yes

anderkve commented 4 years ago

I wonder if it could be related to the fact that you're using some kind of virtual environment (myenv)?

Could you send the content of build/CMakeCache.txt?

You may also want to retry from scratch, i.e. from an empty build directory.

fzeiser commented 4 years ago

Did you restart you computer? :smile:

fzeiser commented 4 years ago

here you go: CMakeCache.txt

I was building it in a fresh dir already, but just to make sure, removed everything and this is the Cache from when I was compiling once again

fzeiser commented 4 years ago

I'm in the same environment able to build and run a very simple script including boost

#include <iostream>
#include <boost/array.hpp>

using namespace std;
int main(){
  boost::array<int, 4> arr = {{1,2,3,4}};
  cout << "hi" << arr[0];
  return 0;
}

g++ -o out test.cpp

anderkve commented 4 years ago

Strange... Never encountered this before.

Could you try running make again as this VERBOSE=1 make -j 1 and send the output? Then we'll see exactly the build command that is failing.

(I have a Zoom-meeting start now, so will get back to this later.)

fzeiser commented 4 years ago 
$ VERBOSE=1 make -j 1
/opt/cmake-3.15.3-Linux-x86_64/bin/cmake -S/home/fabiobz/Desktop/Masterthesis/misc/gambit_np -B/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build --check-build-system CMakeFiles/Makefile.cmake 0
/opt/cmake-3.15.3-Linux-x86_64/bin/cmake -E cmake_progress_start /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/CMakeFiles /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
make -f contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/build.make contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/depend
make[2]: Entering directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
cd /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build && /opt/cmake-3.15.3-Linux-x86_64/bin/cmake -E cmake_depends "Unix Makefiles" /home/fabiobz/Desktop/Masterthesis/misc/gambit_np /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/contrib/yaml-cpp-0.6.2 /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/contrib/yaml-cpp-0.6.2 /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
make -f contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/build.make contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/build
make[2]: Entering directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
make[2]: Nothing to be done for 'contrib/yaml-cpp-0.6.2/CMakeFiles/yaml-cpp.dir/build'.
make[2]: Leaving directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
[ 18%] Built target yaml-cpp
make -f CMakeFiles/backend_harvest.dir/build.make CMakeFiles/backend_harvest.dir/depend
make[2]: Entering directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
cd /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build && /opt/cmake-3.15.3-Linux-x86_64/bin/cmake -E cmake_depends "Unix Makefiles" /home/fabiobz/Desktop/Masterthesis/misc/gambit_np /home/fabiobz/Desktop/Masterthesis/misc/gambit_np /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/CMakeFiles/backend_harvest.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
make -f CMakeFiles/backend_harvest.dir/build.make CMakeFiles/backend_harvest.dir/build
make[2]: Entering directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
make[2]: Nothing to be done for 'CMakeFiles/backend_harvest.dir/build'.
make[2]: Leaving directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
[ 18%] Built target backend_harvest
make -f CMakeFiles/module_harvest.dir/build.make CMakeFiles/module_harvest.dir/depend
make[2]: Entering directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
cd /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build && /opt/cmake-3.15.3-Linux-x86_64/bin/cmake -E cmake_depends "Unix Makefiles" /home/fabiobz/Desktop/Masterthesis/misc/gambit_np /home/fabiobz/Desktop/Masterthesis/misc/gambit_np /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/CMakeFiles/module_harvest.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
make -f CMakeFiles/module_harvest.dir/build.make CMakeFiles/module_harvest.dir/build
make[2]: Entering directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
make[2]: Nothing to be done for 'CMakeFiles/module_harvest.dir/build'.
make[2]: Leaving directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
[ 18%] Built target module_harvest
make -f CMakeFiles/printer_harvest.dir/build.make CMakeFiles/printer_harvest.dir/depend
make[2]: Entering directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
cd /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build && /opt/cmake-3.15.3-Linux-x86_64/bin/cmake -E cmake_depends "Unix Makefiles" /home/fabiobz/Desktop/Masterthesis/misc/gambit_np /home/fabiobz/Desktop/Masterthesis/misc/gambit_np /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/CMakeFiles/printer_harvest.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
make -f CMakeFiles/printer_harvest.dir/build.make CMakeFiles/printer_harvest.dir/build
make[2]: Entering directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
make[2]: Nothing to be done for 'CMakeFiles/printer_harvest.dir/build'.
make[2]: Leaving directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
[ 19%] Built target printer_harvest
make -f CMakeFiles/model_harvest.dir/build.make CMakeFiles/model_harvest.dir/depend
make[2]: Entering directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
cd /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build && /opt/cmake-3.15.3-Linux-x86_64/bin/cmake -E cmake_depends "Unix Makefiles" /home/fabiobz/Desktop/Masterthesis/misc/gambit_np /home/fabiobz/Desktop/Masterthesis/misc/gambit_np /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/CMakeFiles/model_harvest.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
make -f CMakeFiles/model_harvest.dir/build.make CMakeFiles/model_harvest.dir/build
make[2]: Entering directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
make[2]: Nothing to be done for 'CMakeFiles/model_harvest.dir/build'.
make[2]: Leaving directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
[ 19%] Built target model_harvest
make -f ScannerBit/CMakeFiles/scanner_polychord.dir/build.make ScannerBit/CMakeFiles/scanner_polychord.dir/depend
make[2]: Entering directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
cd /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build && /opt/cmake-3.15.3-Linux-x86_64/bin/cmake -E cmake_depends "Unix Makefiles" /home/fabiobz/Desktop/Masterthesis/misc/gambit_np /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/ScannerBit /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/ScannerBit/CMakeFiles/scanner_polychord.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
make -f ScannerBit/CMakeFiles/scanner_polychord.dir/build.make ScannerBit/CMakeFiles/scanner_polychord.dir/build
make[2]: Entering directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
[ 19%] Building CXX object ScannerBit/CMakeFiles/scanner_polychord.dir/src/scanners/polychord/polychord.cpp.o
cd /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/ScannerBit && /home/fabiobz/miniconda3/envs/myenv/bin/x86_64-conda_cos6-linux-gnu-c++  -DYAML_CPP_DLL -Dscanner_polychord_EXPORTS -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build/cmake -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/Printers/include -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/Core/include -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/Logs/include -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/Utils/include -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/Elements/include -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/Models/include -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/cmake/include -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/Backends/include -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ExampleBit_A/include -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ExampleBit_B/include -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/OMBit/include -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/contrib/mkpath/include -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/contrib/yaml-cpp-0.6.2/include -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit -I/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanners/polychord  -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/fabiobz/miniconda3/envs/myenv/include -fPIC -std=c++17 -fopenmp -Wall -Wextra -Wno-misleading-indentation -fPIC -fvisibility=default -fvisibility-inlines-hidden   -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/fabiobz/miniconda3/envs/myenv/include -fPIC -std=c++17 -fopenmp -Wall -Wextra -Wno-misleading-indentation -o CMakeFiles/scanner_polychord.dir/src/scanners/polychord/polychord.cpp.o -c /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp
In file included from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_plugin.hpp:29:0,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:31:
/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_utils.hpp:34:10: fatal error: boost/iterator/zip_iterator.hpp: No such file or directory
 #include <boost/iterator/zip_iterator.hpp>
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
ScannerBit/CMakeFiles/scanner_polychord.dir/build.make:62: recipe for target 'ScannerBit/CMakeFiles/scanner_polychord.dir/src/scanners/polychord/polychord.cpp.o' failed
make[2]: *** [ScannerBit/CMakeFiles/scanner_polychord.dir/src/scanners/polychord/polychord.cpp.o] Error 1
make[2]: Leaving directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
CMakeFiles/Makefile2:3812: recipe for target 'ScannerBit/CMakeFiles/scanner_polychord.dir/all' failed
make[1]: *** [ScannerBit/CMakeFiles/scanner_polychord.dir/all] Error 2
make[1]: Leaving directory '/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/build'
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2
fzeiser commented 4 years ago

There is no immediate hurry, I still need to finish working on the OMpy article and I have some other stuff. But thank you so much for helping me here!

fzeiser commented 4 years ago

Strange. Actually it helps to explicitly include -I /usr/include/ (where boost is located), but then I get the next error. I can try to check more whether it's due to the conda environment I'm using.

In file included from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/sysroot/usr/include/math.h:71:0,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:45,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:23:
/usr/include/bits/mathcalls.h:63:16: error: expected constructor, destructor, or type conversion before '(' token
 __MATHCALL_VEC (cos,, (_Mdouble_ __x));
                ^
/usr/include/bits/mathcalls.h:65:16: error: expected constructor, destructor, or type conversion before '(' token
 __MATHCALL_VEC (sin,, (_Mdouble_ __x));
                ^
/usr/include/bits/mathcalls.h:81:22: error: 'sincos' has not been declared
 __MATHDECL_VEC (void,sincos,,
                      ^~~~~~
/usr/include/bits/mathcalls.h:81:29: error: expected identifier before ',' token
 __MATHDECL_VEC (void,sincos,,
                             ^
/usr/include/bits/mathcalls.h:82:3: error: expected identifier before '(' token
   (_Mdouble_ __x, _Mdouble_ *__sinx, _Mdouble_ *__cosx));
   ^
/usr/include/bits/mathcalls.h:82:57: error: expected constructor, destructor, or type conversion before ';' token
   (_Mdouble_ __x, _Mdouble_ *__sinx, _Mdouble_ *__cosx));
                                                         ^
/usr/include/bits/mathcalls.h:100:16: error: expected constructor, destructor, or type conversion before '(' token
 __MATHCALL_VEC (exp,, (_Mdouble_ __x));
                ^
/usr/include/bits/mathcalls.h:109:16: error: expected constructor, destructor, or type conversion before '(' token
 __MATHCALL_VEC (log,, (_Mdouble_ __x));
                ^
/usr/include/bits/mathcalls.h:153:16: error: expected constructor, destructor, or type conversion before '(' token
 __MATHCALL_VEC (pow,, (_Mdouble_ __x, _Mdouble_ __y));
                ^
In file included from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/sysroot/usr/include/math.h:94:0,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:45,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:23:
/usr/include/bits/mathcalls.h:63:16: error: expected constructor, destructor, or type conversion before '(' token
 __MATHCALL_VEC (cos,, (_Mdouble_ __x));
                ^
/usr/include/bits/mathcalls.h:65:16: error: expected constructor, destructor, or type conversion before '(' token
 __MATHCALL_VEC (sin,, (_Mdouble_ __x));
                ^
/usr/include/bits/mathcalls.h:81:22: error: 'sincos' has not been declared
 __MATHDECL_VEC (void,sincos,,
                      ^~~~~~
/usr/include/bits/mathcalls.h:81:29: error: expected identifier before ',' token
 __MATHDECL_VEC (void,sincos,,
                             ^
/usr/include/bits/mathcalls.h:82:3: error: expected identifier before '(' token
   (_Mdouble_ __x, _Mdouble_ *__sinx, _Mdouble_ *__cosx));
   ^
/usr/include/bits/mathcalls.h:82:57: error: expected constructor, destructor, or type conversion before ';' token
   (_Mdouble_ __x, _Mdouble_ *__sinx, _Mdouble_ *__cosx));
                                                         ^
/usr/include/bits/mathcalls.h:100:16: error: expected constructor, destructor, or type conversion before '(' token
 __MATHCALL_VEC (exp,, (_Mdouble_ __x));
                ^
/usr/include/bits/mathcalls.h:109:16: error: expected constructor, destructor, or type conversion before '(' token
 __MATHCALL_VEC (log,, (_Mdouble_ __x));
                ^
/usr/include/bits/mathcalls.h:153:16: error: expected constructor, destructor, or type conversion before '(' token
 __MATHCALL_VEC (pow,, (_Mdouble_ __x, _Mdouble_ __y));
                ^
In file included from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/sysroot/usr/include/math.h:141:0,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:45,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:23:
/usr/include/bits/mathcalls.h:63:16: error: expected constructor, destructor, or type conversion before '(' token
 __MATHCALL_VEC (cos,, (_Mdouble_ __x));
                ^
/usr/include/bits/mathcalls.h:65:16: error: expected constructor, destructor, or type conversion before '(' token
 __MATHCALL_VEC (sin,, (_Mdouble_ __x));
                ^
/usr/include/bits/mathcalls.h:81:22: error: 'sincos' has not been declared
 __MATHDECL_VEC (void,sincos,,
                      ^~~~~~
/usr/include/bits/mathcalls.h:81:29: error: expected identifier before ',' token
 __MATHDECL_VEC (void,sincos,,
                             ^
/usr/include/bits/mathcalls.h:82:3: error: expected identifier before '(' token
   (_Mdouble_ __x, _Mdouble_ *__sinx, _Mdouble_ *__cosx));
   ^
/usr/include/bits/mathcalls.h:82:57: error: expected constructor, destructor, or type conversion before ';' token
   (_Mdouble_ __x, _Mdouble_ *__sinx, _Mdouble_ *__cosx));
                                                         ^
/usr/include/bits/mathcalls.h:100:16: error: expected constructor, destructor, or type conversion before '(' token
 __MATHCALL_VEC (exp,, (_Mdouble_ __x));
                ^
/usr/include/bits/mathcalls.h:109:16: error: expected constructor, destructor, or type conversion before '(' token
 __MATHCALL_VEC (log,, (_Mdouble_ __x));
                ^
/usr/include/bits/mathcalls.h:153:16: error: expected constructor, destructor, or type conversion before '(' token
 __MATHCALL_VEC (pow,, (_Mdouble_ __x, _Mdouble_ __y));
                ^
In file included from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:23:0:
/home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:180:11: error: '::cos' has not been declared
   using ::cos;
           ^~~
/home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:218:11: error: '::exp' has not been declared
   using ::exp;
           ^~~
/home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:334:11: error: '::log' has not been declared
   using ::log;
           ^~~
/home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:384:11: error: '::pow' has not been declared
   using ::pow;
           ^~~
/home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:421:11: error: '::sin' has not been declared
   using ::sin;
           ^~~
In file included from /usr/include/boost/bind/mem_fn.hpp:25:0,
                 from /usr/include/boost/mem_fn.hpp:22,
                 from /usr/include/boost/function/detail/prologue.hpp:18,
                 from /usr/include/boost/function.hpp:24,
                 from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /usr/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /usr/include/boost/algorithm/string/iter_find.hpp:27,
                 from /usr/include/boost/algorithm/string/split.hpp:16,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/Utils/include/gambit/Utils/util_functions.hpp:34,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/plugin_loader.hpp:40,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/plugin_defs.hpp:39,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_plugin.hpp:30,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:31:
/usr/include/boost/get_pointer.hpp:27:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:28:
/home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /usr/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /usr/include/boost/shared_ptr.hpp:17,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/factory_defs.hpp:29,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_plugin.hpp:32,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:31:
/usr/include/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:28:
/home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/factory_defs.hpp:29,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_plugin.hpp:32,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:31:
/usr/include/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:28:
/home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/factory_defs.hpp:29,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_plugin.hpp:32,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:31:
/usr/include/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:28:
/home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/factory_defs.hpp:29,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_plugin.hpp:32,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:31:
/usr/include/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:28:
/home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/factory_defs.hpp:29,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_plugin.hpp:32,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:31:
/usr/include/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:28:
/home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/factory_defs.hpp:29,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_plugin.hpp:32,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:31:
/usr/include/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:28:
/home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/factory_defs.hpp:29,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/include/gambit/ScannerBit/scanner_plugin.hpp:32,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:31:
/usr/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
/usr/include/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
                 from /home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
                 from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:28:
/home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp: In function 'int __gambit_plugin_polychord__t__scanner__v__1_16___namespace__::PLUGIN_MAIN()':
/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:124:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (fast_params.size() != 0 and fast_params.size() != settings.nDims)
                                       ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp: In member function 'void Gambit::PolyChord::LogLikeWrapper::dumper(int, int, int, double*, double*, double*, double, double)':
/home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:351:46: error: call of overloaded 'exp(double&)' is ambiguous
              txt_stream->print( std::exp(logw), "Posterior", myrank, pointID);
                                              ^
In file included from /home/fabiobz/Desktop/Masterthesis/misc/gambit_np/ScannerBit/src/scanners/polychord/polychord.cpp:23:0:
/home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:222:3: note: candidate: constexpr float std::exp(float)
   exp(float __x)
   ^~~
/home/fabiobz/miniconda3/envs/myenv/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:226:3: note: candidate: constexpr long double std::exp(long double)
   exp(long double __x)
   ^~~
fzeiser commented 4 years ago

Yep, the problem was something about the virtual environment. I'll have to fix it myself I guess :ghost:

anderkve commented 4 years ago

There is no immediate hurry, I still need to finish working on the OMpy article and I have some other stuff. But thank you so much for helping me here!

Yeah, I know -- I just wanted to get our basic setup up and running, so that when you have time to work on this you don't have to wait for me to set up the basic GAMBIT system :)

Yep, the problem was something about the virtual environment. I'll have to fix it myself I guess

Hehe, OK, let me know if I can help.

fzeiser commented 4 years ago

installed boost and glib via conda now, too; This will be a very nice and irreproducible environment :upside_down_face:

export PYTHON_EXECUTABLE=/home/fabiobz/miniconda3/envs/myenv/bin/python3.7
export PYTHON_INCLUDE_DIR=/home/fabiobz/miniconda3/envs/myenv/include/python3.7m
export PYTHON_LIBRARY=/home/fabiobz/miniconda3/envs/myenv/lib/libpython3.7m.so

cmake -D PYTHON_EXECUTABLE=$PYTHON_EXECUTABLE -D PYTHON_INCLUDE_DIR=$PYTHON_INCLUDE_DIR -D PYTHON_LIBRARY=$PYTHON_LIBRARY -D BOOST_ROOT:PATHNAME=~/miniconda3/envs/myenv/ ..

but still results in an error [I just log my progress here, don't expect that you have to answer, Anders]

[...]
[100%] Building CXX object Printers/CMakeFiles/Printers.dir/src/printers/coutprinter/coutprinter.cpp.o
[100%] Built target Printers
Scanning dependencies of target gambit
[100%] Building CXX object CMakeFiles/gambit.dir/Core/src/gambit.cpp.o
[100%] Linking CXX executable ../gambit
/home/fabiobz/miniconda3/envs/myenv/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/librt.so: undefined reference to `__pthread_barrier_init@GLIBC_PRIVATE'
/home/fabiobz/miniconda3/envs/myenv/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libsqlite3.so: undefined reference to `memcpy@GLIBC_2.14'
/home/fabiobz/miniconda3/envs/myenv/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/librt.so: undefined reference to `__clock_nanosleep@GLIBC_PRIVATE'
/home/fabiobz/miniconda3/envs/myenv/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/librt.so: undefined reference to `__clock_gettime@GLIBC_PRIVATE'
/home/fabiobz/miniconda3/envs/myenv/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/librt.so: undefined reference to `__clock_getres@GLIBC_PRIVATE'
/home/fabiobz/miniconda3/envs/myenv/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/librt.so: undefined reference to `__socket@GLIBC_PRIVATE'
/home/fabiobz/miniconda3/envs/myenv/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/librt.so: undefined reference to `__clock_getcpuclockid@GLIBC_PRIVATE'
/home/fabiobz/miniconda3/envs/myenv/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/librt.so: undefined reference to `__shm_directory@GLIBC_PRIVATE'
/home/fabiobz/miniconda3/envs/myenv/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/librt.so: undefined reference to `__libc_pread@GLIBC_PRIVATE'
/home/fabiobz/miniconda3/envs/myenv/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/librt.so: undefined reference to `__pthread_barrier_wait@GLIBC_PRIVATE'
/home/fabiobz/miniconda3/envs/myenv/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/librt.so: undefined reference to `__clock_settime@GLIBC_PRIVATE'
/home/fabiobz/miniconda3/envs/myenv/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/librt.so: undefined reference to `__recv@GLIBC_PRIVATE'
/home/fabiobz/miniconda3/envs/myenv/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/librt.so: undefined reference to `__pthread_get_minstack@GLIBC_PRIVATE'
collect2: error: ld returned 1 exit status
CMakeFiles/gambit.dir/build.make:342: recipe for target '../gambit' failed
make[2]: *** [../gambit] Error 1
CMakeFiles/Makefile2:287: recipe for target 'CMakeFiles/gambit.dir/all' failed
make[1]: *** [CMakeFiles/gambit.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2
fzeiser commented 4 years ago

even after some more trial and error I didn't manage it with the conda environment, so I'm falling back to deactivating it. Then the installation works :smile:.

So I use

export PYTHON_EXECUTABLE=/home/fabiobz/miniconda3/envs/myenv/bin/python3.7
export PYTHON_INCLUDE_DIR=/home/fabiobz/miniconda3/envs/myenv/include/python3.7m
export PYTHON_LIBRARY=/home/fabiobz/miniconda3/envs/myenv/lib/libpython3.7m.so

cmake -D PYTHON_EXECUTABLE=$PYTHON_EXECUTABLE -D PYTHON_INCLUDE_DIR=$PYTHON_INCLUDE_DIR -D PYTHON_LIBRARY=$PYTHON_LIBRARY ..