RE: AMBER: how to include mpirun in this script

From: Ross Walker <>
Date: Tue, 21 Aug 2007 11:45:23 -0700

Hi Syed,

> I am attaching you a script that i download but i want
> to run it on cluster to run simulation. Should i
> include " mpirun -np no.of processors " before the
> command line in this script, if you suggest "yes" then
> plz suggest me where should i add or kindly assist me
> to use this script on cluster system.

This is really a question you need to pose to the administrator of your
cluster since the answer is extremely dependent on how your system is setup,
how the queuing system works, which mpi implementation is used, what is the
processor count, what is the interconnect etc etc... One example would be to
put the mpirun command in front of the sander command, and use the
sander.MPI executable. E.g.

mpirun -np x -machinefile foo $AMBERHOME/exe/sander.MPI -O -i \

Where x is the cpu count and foo is the machine file provided by your queing
system. However, there are an extremely large number of variations on this
for the reasons I gave above so please ask your cluster admin for some
example job submission scripts.

Note for production calculations in parallel you probably want to use the
pmemd executable in place of sander.MPI. See the amber manual for more
details on this. It is NOT built by default.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Wed Aug 22 2007 - 06:07:46 PDT
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