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

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

hi, 

i made a complete first time install of scipion 3.0.0 

thanks the fix worked now the following way: 

deleted the target install dir but not the .scipion3env 
conda activate .scipion3env 
conda install hdf5 -c defaults 
python -m scipioninstaller /beegfs/cssb/software/em/scipion/3.0.0 -j 20 
then the main project selection gui comes up with scipion3 

i don't know if its related but maybe it helps to find the problem: 
my ~/.condarc had conda-forge before defaults in the channels list. 

and the hdf5 from conda-forge reports: 

The following NEW packages will be INSTALLED: 
hdf5 conda-forge/linux-64::hdf5-1.10.6-nompi_h3c11f04_100 
libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.5.0-hdf63c60_10 
CondaVerificationError: The package for hdf5 located at /beegfs/cssb/software/anaconda3/pkgs/hdf5-1.10.6-nompi_h3c11f04_100 
appears to be corrupted. The path 'bin/h5perf_serial' specified in the package manifest cannot be found. 

but it workd with the default channel and the following packages: 
hdf5 pkgs/main/linux-64::hdf5-1.10.6-hb1b8bf9_0 
libgfortran-ng pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0 

cheers, 
wolfgang 


From: "Pablo Conesa" <pc...@cn...> 
To: "Mailing list for Scipion users" <sci...@li...> 
Sent: Tuesday, 28 July, 2020 13:58:41 
Subject: Re: [scipion-users] scipion 3.0.0 / xmippSrc-v3.20.07b1 / HDF5 linking error 



Hi wolfgang, 


it seems the installer went for a conda installation ("/beegfs/cssb/software/anaconda3/envs/.scipion3env/lib") 

xmipp installation, at the beginning should detect the the conda environment and trigger the installation of the hdf5 lib and others. 

I'm right now realizing the output log of the installation is not kept..probably something to do. 

Do you, by any change kept the output log of the installation. Or maybe triggering the installation again will work to check if xmipp was detecting the "conda mode" and trigger 




One thing you can do is: 

1.- conda activate .scipion3env 

2.- conda install hdf5 

3.- scipion3 installb xmippSrc 




If other libraries are missing repeat adapting step 2. 

It would be great to learn why is not doing this xmipp itself. 



On 28/7/20 11:21, Lugmayr, Wolfgang 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 -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 



-- 
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team 


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