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Re: [scipion-users] scipion 3.0.0 / xmippSrc-v3.20.07b1 / HDF5 linking error
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From: Pablo C. <pc...@cn...> - 2020-07-28 14:21:36
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You mean passing "-c defaults" ?
On 28/7/20 15:57, Grigory Sharov wrote:
> Great!
>
> @Pablo Conesa <mailto:pc...@cn...> I guess we should specify
> to use the defaults channel for installing xmipp libs (fftw hdf5
> libtiff openjdk) inside conda env.
>
> 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 <tel:+44%201223%20267228>
> e-mail: gs...@mr... <mailto:gs...@mr...>
>
>
> On Tue, Jul 28, 2020 at 2:30 PM Lugmayr, Wolfgang <w.l...@uk...
> <mailto:w.l...@uk...>> wrote:
>
> 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...
> <mailto:pc...@cn...>>
> *To: *"Mailing list for Scipion users"
> <sci...@li...
> <mailto: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 Scipion <http://scipion.i2pc.es> team*
>
>
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--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
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