[scipion-users] scipion 3.0.0 / xmippSrc-v3.20.07b1 / HDF5 linking error

[Lugmayr, W. <w.l...@uk...>]

hi,

i tried to install the (unreleased) scipion3 and came to a hdf5 linking error (full log at end of mail):

/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
Some error occurred during the compilation of 'xmipp' ('bin/xmipp_mpi_reconstruct_fourier_accel').

my conda environment contains hdf5 
$ conda list | grep hdf5
hdf5                      1.10.4               hb1b8bf9_0  
but the hidden .scipion3env does not contain one.

do i need the latest hdf5 1.12.0 or is this a buildscript problem?

cheers,
wolfgang




mpicxx -o lib/libXmippParallelCuda.so -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -shared libraries/parallel_adapt_cuda/mpi_reconstruct_fourier_gpu.os -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp -lXmippInterfaceCuda -lXmippCuda -lcudart -lcufft -lnvidia-ml -lcuFFTAdvisor
mpicxx -o lib/libXmippParallel.so -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/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/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -lXmipp -lpython3.8
mpicxx -o bin/xmipp_mpi_reconstruct_fourier_accel applications/programs/mpi_reconstruct_fourier_accel/mpi_reconstruct_fourier_accel_main.o -L/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib -Llib -Llib -L/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib -L/beegfs/cssb/software/devel/gcc/8.4.0/lib64 -L/beegfs/cssb/software/devel/mpc/1.0.3/lib -L/beegfs/cssb/software/devel/mpfr/3.1.4/lib -L/beegfs/cssb/software/devel/hwloc/2.1.0/lib -L/beegfs/cssb/software/devel/ucx/1.8.0/lib -L/beegfs/cssb/software/devel/openmpi/4.0.3/lib -L/usr/local/cuda-10.1/lib64 -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore -lXmippParallel
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 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'
/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmippSrc-v3.20.07b1/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName[abi:cxx11]() const'
collect2: error: ld returned 1 exit status
scons: *** [bin/xmipp_mpi_reconstruct_fourier_accel] Error 1
scons: building terminated because of errors.
 
Some error occurred during the compilation of 'xmipp' ('bin/xmipp_mpi_reconstruct_fourier_accel').

Traceback (most recent call last):
  File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 443, in <module>
    main()
  File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 287, in main
    installPluginMethods()
  File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods
    plugin.installBin({'args': ['-j', numberProcessor]})
  File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
    environment.execute()
  File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
    self._executeTargets(targetList)
  File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
    tgt.execute()
  File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 220, in execute
    command.execute()
  File "/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 160, in execute
    assert glob(t), ("target '%s' not built (after "
AssertionError: target '/beegfs/cssb/software/em/scipion/3.0.0/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmip

-- 
Universitätsklinikum Hamburg-Eppendorf (UKE)
@ Centre for Structral Systems Biology (CSSB)
@ Deutsches Elektronen-Synchrotron (DESY)
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