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Re: [scipion-users] error occurred during the compilation of 'xmipp'
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From: Carlos O. S. <co...@cn...> - 2021-02-11 07:29:07
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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')
>
> _______________________________________________________________________________________
>
> | |
>
> | Installation failed |
>
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