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Re: [scipion-users] scipion 3.0.0 / xmippSrc-v3.20.07b1 / HDF5 linking error
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From: Lugmayr, W. <w.l...@uk...> - 2020-07-28 10:28:05
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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 < [ mailto:w.l...@uk... | 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: [ mailto:wol...@cs... | wol...@cs... ]
[ http://www.cssb-hamburg.de/ | http://www.cssb-hamburg.de/ ]
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