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

[Alex]

Thanks Marc.

I removed the two EXPORT line in the script but still missing the library
(removing only the second line also did not help):

ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for
'intel/composerxe/2015.1.133'
--------------------------------------------------------------------------
mpirun was unable to find the specified executable file, and therefore
did not launch the job.  This error was first reported for process
rank 0; it may have occurred for other processes as well.

And .log file:

gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so: cannot
open shared object file: No such file or directory
--------------------------------------------------------------------------
mpirun was unable to find the specified executable file, and therefore
did not launch the job.  This error was first reported for process
rank 0; it may have occurred for other processes as well.

Regards,
Alex


On Tue, Apr 3, 2018 at 2:47 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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