Dear Leena,
Which command lines (or scripts) are you using? I guess you are running on a cluster, so... is there any chance you have messed up with the queue commands?
In any case... running sander on 54 nodes (>500 processors!!!) may be very bad in terms of performance (it generally won't scale much beyond 32 cores or so), you better read some advises from mailing list... for example follow all threads in these mails:
[
http://archive.ambermd.org/201110/0432.html]
[
http://archive.ambermd.org/201609/0451.html]
Best,
Matias
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/laboratorios-eng/lsbm]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Leena Aggarwal" <leena.hrc.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Sábado, 11 de Agosto 2018 7:01:15
Asunto: [AMBER] sander.MPI running on only one node
Dear Amber Users
I have installed Amber 12 and after installation when I was trying to run
a job in parallel then sander.mpi was running on just one node, although
job should run for 54 nodes.
From
Leena Aggarwal
Department of Chemistry
University of Delhi
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Received on Sat Aug 11 2018 - 08:30:03 PDT
