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

[Mark Abraham]

Hi,

On Tue, Apr 3, 2018 at 8:56 PM Alex <alexanderwien2k at gmail.com> wrote:

> 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'
>

Why isn't this module being found?


> --------------------------------------------------------------------------
> 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.
>

If this was the error message, then you won't get a log file from the
executable that wasn't found, so I presume that below you are looking at an
old log file...


> And .log file:
>
> gmx_mpi: error while loading shared libraries: libmkl_intel_lp64.so: cannot
> open shared object file: No such file or directory
>

That's a library that has to come from the module that didn't load, so look
there.

Mark


> --------------------------------------------------------------------------
> 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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