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

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

Hi Carlos,

Thanks a lot for your help.

I have been able to compile xmipp now, seems by installing hdf5 in the scipion conda env.

Best,

Xiaochu

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From: Carlos Oscar Sorzano<mailto:co...@cn...>
Sent: Thursday, February 11, 2021 1:29 AM
To: Mailing list for Scipion users<mailto:sci...@li...>; Xiaochu Lou<mailto:Xia...@UT...>
Subject: Re: [scipion-users] error occurred during the compilation of 'xmipp'

EXTERNAL MAIL

Dear Xiaochu,

it seems as if the headers of the hdf5 library are visible, but the binary lib file is not. Can that be?

Kind regards, Carlos Oscar
El 11/02/2021 a las 1:07, Xiaochu Lou escribió:
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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