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

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

Yes, there should be .so files etc. I think by default all envs are
supposed to see the packages from the base env but I would try to install
hdf5 inside scipion3env and try to recompile xmipp

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...


On Tue, Jul 28, 2020 at 11:28 AM Lugmayr, Wolfgang <w.l...@uk...> wrote:

> hi,
>
> no. my hdf5 is in the global conda environment.
>
> here is a grep in the .scipion3env:
> $ find . | grep -i hdf5
>
> ./lib/python3.8/site-packages/PIL/__pycache__/Hdf5StubImagePlugin.cpython-38.pyc
> ./lib/python3.8/site-packages/PIL/Hdf5StubImagePlugin.py
>
> ./lib/python3.8/site-packages/scipy/io/matlab/tests/data/testhdf5_7.4_GLNX86.mat
>
> it should contain a libhdf5.a or .so if the package would be there, right?
>
> cheers,
> wolfgang
>
>
> ------------------------------
> *From: *"Grigory Sharov" <sha...@gm...>
> *To: *"Mailing list for Scipion users" <
> sci...@li...>
> *Sent: *Tuesday, 28 July, 2020 12:04:08
> *Subject: *Re: [scipion-users] scipion 3.0.0 / xmippSrc-v3.20.07b1 / HDF5
> linking error
>
> 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/
>>
>>
>> _______________________________________________
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