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

Alex alexanderwien2k at gmail.com
Tue Apr 3 23:02:42 CEST 2018 

Hi Marc,


On Tue, Apr 3, 2018 at 4:35 PM, Marc Hoemberger <hoemberg at brandeis.edu>
wrote:

> 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.
>

Yes, it think that is the reason. How did you solve it?

>
> Did you try running the command line invocation on the same node you are
> submitting the script to?
>
Actually, I can not find the list of node, otherwise I could log in inside
one of them (if I was allowed) to invoke gromacs there.

The rest of my run script is juts gmx_mpi grompp and mpirun gmx_mpi mdrun .

Best regards,
Alex

>
> -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
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