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

[Grigory S. <sha...@gm...>]

Hi Wolfgang,

Do you have hdf5 inside .scipion3env?

On Tue, Jul 28, 2020, 10:46 Lugmayr, Wolfgang <w.l...@uk...> wrote:

> 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)
> Notkestrasse 85 Gebäude 15
> 22607 Hamburg, Germany
> Tel.: +49 40 8998-87652
> Email: wol...@cs...
> http://www.cssb-hamburg.de/
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>