Re: [scipion-users] Scipion + Centos 8

[Marc H. L. <mh...@ib...>]

Hi Alberto!

Sorry to answer late, I have tried the instructions and in the end I was
also missing a repository:

   - libsqlite3x.x86_64  libsqlite3x-devel.x86_64

Thank you very much for the help. Now it was installed fine!
Best regards,

El mar, 30 nov 2021 a las 14:25, Alberto Garcia Mena (<
alb...@cn...>) escribió:

> Hello Marc Hsiao Le,
>
> There is an installation 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
> --
>
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>
> Marcos H.Lee
>
> IBMB-CSIC
>
> E-mail: mh...@ib...
>
>
>
>
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>
> --
> - Alberto GM -
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[image: IBMB - Institut de Biología Molecular de Barcelona]
<https://www.ibmb.csic.es/en/>

Marcos H.Lee

IBMB-CSIC

E-mail: mh...@ib...