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

Tue Apr 3 22:36:04 CEST 2018

Hi Alex,

I have had a similar issue on our cluster (different module files etc.) for
me it turned out that on the actual compute nodes this module was not
available. Thus if you run it from the command line on e.g. your login node
you might have access to this compiler / modulefile, but when moving to a
compute node it might not be there.

Did you try running the command line invocation on the same node you are
submitting the script to?

-Marc

On Tue, Apr 3, 2018 at 4:13 PM, Alex <alexanderwien2k at gmail.com> wrote:

> On Tue, Apr 3, 2018 at 3:46 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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?
> >
> I do not know. The funny point is that, the intel/composerxe/2015.1.133 is
> needed when I invoke gmx_mpi in command line, and after loading it, the
> gmx_works fine. But I do not know why it can not be found inside script.
>
> >
> >
> > > ------------------------------------------------------------
> > --------------
> > > 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...
> >
> > No, it can generate .log file, I ran it again and a new log file was
> generated.
>
> >
> > > 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.
> >
> >
> Best regards,
> Alex
>
>
> > 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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-- 
Marc Hoemberger
Ph.D. Candidate, Biochemistry and Biophysics,
Laboratory of Dorothee Kern
MS-009, 415 South St.
Brandeis University
Waltham, MA, 02453