Re: [scipion-users] Scipion + Centos 8

[Alberto G. M. <alb...@cn...>]

Hello Marc Hsiao Le,

There is aninstallation guide for Centos7 
<https://github.com/I2PC/xmipp/wiki/Installing-Xmipp-on-CentOS-7-9.2009>, 
please follow those steps in that order; first install openmpi-devel, 
then the compilers (gcc g++).

On 30/11/21 11:24, Marc Hsiao Lee wrote:
> Hi guys!
>
> I hope someone can help me, I have the Centos8 version, and I'm 
> standing at this point with conda:
>
>   * python -m scipion installp -p scipion-em-xmipp -j 12
>
> and the error output is:
>
>     ...
>     * mpirun or mpiexec have failed.*
>     * Cannot compile with MPI or use it*
>     * rm xmipp_mpi_test_main**
>     *rm: cannot remove 'xmipp_mpi_test_main*': No such file or directory*
>     /*Check failed! Something wrong with the configuration.*/
>
> /
> /
>
>     /Traceback (most recent call last):/
>     /  File
>     "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py",
>     line 470, in <module>/
>     /    main()/
>     /  File
>     "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py",
>     line 293, in main/
>     /    installPluginMethods()/
>     /  File
>     "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py",
>     line 232, in installPluginMethods/
>     /    plugin.installBin({'args': ['-j', numberProcessor]})/
>     /  File
>     "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py",
>     line 166, in installBin/
>     /    environment.execute()/
>     /  File
>     "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
>     line 748, in execute/
>     /    self._executeTargets(targetList)/
>     /  File
>     "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
>     line 690, in _executeTargets/
>     /    tgt.execute()/
>     /  File
>     "/cryoem-apps/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
>     line 221, in execute/
>     /    command.execute()/
>     /  File
>     "/cryoem-apps/miniconda/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
>     '/cryoem-apps/scipion/scipion3.0/software/em/xmipp/bin/xmipp_reconstruct_significant'
>     not built (after running 'cd . && ./xmipp config noAsk && ./xmipp
>     check_config && ./xmipp compileAndInstall N=12 && ln -srfn build
>     /cryoem-apps/scipion/scipion3.0/software/em/xmipp && cd - && touch
>     installation_finished && rm bindings_linked 2> /dev/null')/
>     /Error at main: target
>     '/cryoem-apps/scipion/scipion3.0/software/em/xmipp/bin/xmipp_reconstruct_significant'
>     not built (after running 'cd . && ./xmipp config noAsk && ./xmipp
>     check_config && ./xmipp compileAndInstall N=12 && ln -srfn build
>     /cryoem-apps/scipion/scipion3.0/software/em/xmipp && cd - && touch
>     installation_finished && rm bindings_linked 2> /dev/null')/
>
> /
> /
> Thanks and regards
> -- 
>
> IBMB - Institut de Biología Molecular de Barcelona
>
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>
> 	
>
> Marcos H.Lee
>
> IBMB-CSIC
>
> E-mail: mh...@ib... <mailto:mh...@ib...>
>
>
>
>
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- Alberto GM -