Fwd: [gmx-users] Re: Running Gromacs in Clusters

Dr. Vitaly Chaban vvchaban at gmail.com
Wed Nov 7 23:48:27 CET 2012

On Wed, Nov 7, 2012 at 11:24 PM, Marcelo Depolo <marcelodepolo at gmail.com> wrote:
> I thought that at first, but other softwares run in parallel. If there's a
> problem, it' s somehow in the PBS.
> My guess is that my PBS don't allow the LAM library "see" others nodes. But
> I have no clue where the problem could be.

I would be very surprised if this is true. The "nornal" sequences of
events during submission process is the following:

1) The system looks into your submission script and finds out the
resource requirements.

2) If the requirements are met, the job gets "R" status and the
remaining commands (which do not start with #PBS) are executed.

3) If there is a problem with the message parallel interface or the
[scientific] code, the job dies with some MPI-specific error message,
or with code-specific message, or usually both of them.

What I see in your report, your "error" message comes from PBS, i.e.
neither MPI nor gromacs are launched.

Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark

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