[scipion-users] error occurred during the compilation of 'xmipp'

[Xiaochu L. <Xia...@UT...>]

Dear The Scipion Team,

I am trying to install Scipion V3.0 with Miniconda (python 3.8), and I can install successfully on my Centos7 virtual machine following the official instruction of "CentOS with conda". However, I met some errors when I try to install it on a RHEL server (without admin permit). On the RHEL server, instead of "sudo yum -y install libzstd-devel hdf5-devel gcc gcc-c++ openmpi-devel", I load the modules such as " hdf5/gcc/1.12.0, cuda80/toolkit/8.0.61, java/oracle/jdk1.8.0_231, openmpi/gcc/64/4.0.3, gcc/5.4.0"  and export their /bin path to The $PATH. I tried different cuda version and/or gcc version (eg: cuda10.1 and gcc/8.3). Could you please have a look at the error message below and let me know what package and/or lib I missed? Or if there any config I can modify? Please let me know if you need more information about my installation process. Thank you ahead for your help!

Best,

Xiaochu
============================================


lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const'
lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const'
/home2/s******/installs/scipion/software/em/xmippSrc-v3.20.07/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const'
collect2: error: ld returned 1 exit status
g++ -o bin/xmipp_angular_commonline applications/programs/angular_commonline/angular_commonline_main.o -L/home2/s******/installs/scipion/software/em/xmippSrc-v3.20.07/src/xmippCore/lib -Llib -Llib -L/home2/s******/miniconda3/envs/scipion3/lib -L/cm/shared/apps/gcc/5.4.0/lib -L/cm/shared/apps/gcc/5.4.0/lib64 -L/cm/shared/apps/cuda80/toolkit/8.0.61/extras/CUPTI/lib64 -L/cm/local/apps/cuda/libs/current/lib64 -L/cm/shared/apps/cuda80/toolkit/8.0.61/lib64 -L/cm/shared/apps/openmpi/gcc/64/4.0.3/lib -L/cm/shared/apps/hdf5/gcc/1.12.0/lib -L/cm/shared/apps/java/oracle/jdk1.8.0_231/lib -L/cm/shared/apps/slurm/16.05.8/lib64/slurm -L/cm/shared/apps/slurm/16.05.8/lib64 -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore
scons: *** [bin/xmipp_angular_break_symmetry] Error 1
lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const'
lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const'
/home2/s******/installs/scipion/software/em/xmippSrc-v3.20.07/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const'
collect2: error: ld returned 1 exit status
scons: *** [bin/xmipp_angular_commonline] Error 1
scons: building terminated because of errors.

Some error occurred during the compilation of 'xmipp' ('bin/xmipp_angular_commonline').

Traceback (most recent call last):
  File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module>
    main()
  File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main
    installPluginMethods()
  File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods
    plugin.installBin({'args': ['-j', numberProcessor]})
  File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
    environment.execute()
  File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
    self._executeTargets(targetList)
  File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
    tgt.execute()
  File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute
    command.execute()
  File "/home2/s******/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute
    assert glob(t), ("target '%s' not built (after "
AssertionError: target '/home2/s******/installs/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home2/s******/installs/scipion/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')
Error at main: target '/home2/s******/installs/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln -srfn build /home2/s******/installs/scipion/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')


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| Installation failed                                                                   |
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