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

Wed Apr 4 14:33:57 CEST 2018

Hi,

As I hinted before, this comes back to reading the docs for your cluster
and talking to its admins.

Mark

On Wed, Apr 4, 2018 at 2:30 PM Marc Hoemberger <hoemberg at brandeis.edu>
wrote:

> Hi Alex,
>
> from the looks of the module name it seems that what you are looking for is
> the intel  Composer XE 2015.1.133. What could have happened is that the
> architecture of your login node is different from some of the compute nodes
> (almost certainly the case), so that when this composer was compiled the
> person in charge of the cluster did not compile it for use on the compute
> nodes.
> That is why I did not have access to some of the compilers I wanted to use.
> To fix this I ended up compiling the necessary software myself but making
> sure that they are compiled with either (a) the target system being the
> architecture of the compute node, (b) directly compiled on the compute
> node, which seems difficult if you cannot access the nodes directly.
>
> If you are using one of the standard scheduler you usually should have an
> option to list all nodes and sometimes might be able to request a node
> specifically (e.g. Grid Scheduler uses "qstat -f" to list all nodes, and
> with qrsh you can ask for access to a compute node). If all else fails you
> could always ask the person in charge for software deployment of your
> cluster, although I would first try to exhaust the other paths.
>
> -Marc
>
>
> On Tue, Apr 3, 2018 at 5:01 PM, Alex <alexanderwien2k at gmail.com> wrote:
>
> > 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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>
>
> --
> 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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