[gmx-users] gmx_mpi works in command line but not in script

[Mark Abraham]

Hi,

It looks like you are choosing to mismanage LD_LIBRARY_PATH. Try letting
the modules do it, since it is their job.

Mark

On Tue, Apr 3, 2018, 20:29 Alex <alexanderwien2k at gmail.com> wrote:

> Dear all,
>
> I have installed the gromacs2018.1 parallel in a cluster, it works
> perfectly in the command line, of course after loading some module.
> But when I put the commands along with loading module commands in a bash
> script to be submitted in the cluster, it crashes with the below massage:
>
> ++++++++++++++++++
> ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for
> 'intel/composerxe/2015.1.133'
> gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.20' not found (required by
> /home/alex23/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
>
> And part of the log file:
>
> gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.20' not found (required by
> /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.20' not found (required by
> /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> gmx_mpi: /cm/shared/apps/gcc/4.8.1/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.20' not found (required by
> /home/alex44/.local/gromacs-2018.1/bin/../lib64/libgromacs_mpi.so.3)
> gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so: cannot
> open shared object file: No such file or directory
> ++++++++++++++++++
>
> Here is part of my script.sh file
> ++++++++++++++++++
> . /etc/profile.d/modules.sh
> module load intel/composerxe/2015.1.133
> module load shared
> module load clusterA
> module load gcc/4.8.1
> module load sge/univa
> module load clusterA-openmpi/intel/2015/1.8.1-mlnx-ofed
> export PATH=$HOME/.local/gromacs-2018.1/bin:$PATH
> export
>
> LD_LIBRARY_PATH=$HOME/.local/gromacs-2018.1/lib64${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}
> ++++++++++++++++
>
> Do you know what I am missing?
> Thanks
> Alex
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