[gmx-users] Using -multidir option on Cray (aprun)

[Mark Abraham]

Hi,

Putting the mdrun_mpi command into a variable makes sense, but the rest of
the command line makes sense directly, so you get the shell expansions you
might intend.

Mark

On Wed, 11 Sep 2019 at 08:53, Suman Chakrabarty <chakrabarty.suman at gmail.com>
wrote:

> Dear all,
>
> I have managed to resolve this issue, which was a shell scripting mistake.
> My mistake was to keep "-multidir remd_{1..2}" inside quotes, hence the
> Bash expansion of remd_{1..2} did not work as intended. Instead, "-multidir
> $(echo remd_{1..2})" works. But if anybody has any better suggestion,
> please let me know. Thanks.
>
> Regards,
> Suman.
>
> On Wed, Sep 11, 2019 at 12:04 PM Suman Chakrabarty <
> chakrabarty.suman at gmail.com> wrote:
>
> > Hello!
> >
> > I am trying to use the -multidir feature of mdrun for setting up a REMD
> > simulation on a Cray XT system. It requires the "aprun" launcher to spawn
> > the parallel processes rather than the usual mpirun (which I have
> > successfully used with -multidir before).
> >
> > I am using the 2019.3 version of Gromacs and I can successfully run
> normal
> > parallel Gromacs jobs (without -multidir) in this system.
> >
> > I have the following setup in my submission script:
> >
> > exec1="/home/chs1/soft/GMX2019.3/bin/mdrun_mpi -ntomp 1 -deffnm nvt
> > -multidir remd_{1..2}"
> >
> > aprun -n 64 -N32 -d1 ${exec1}
> >
> >
> > I get the following error message from all 64 MPI processes:
> >
> > MPI rank:    8 (out of 64)
> >
> > Source file: src/gromacs/mdrun/multisim.cpp (line 77)
> >
> > To run mdrun in multiple simulation mode, more then one actual simulation
> > is required. The single simulation case is not supported.
> >
> > I don't understand why Gromacs is treating this as "single simulation
> > case"! Can anybody with more experience in using the -multidir option in
> a
> > Cray system suggest any solution to this problem? Thanks.
> >
> >
> > Regards,
> >
> > Suman.
> >
> >
> >
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