AMBER Archive (2008)

Subject: RE: AMBER: sander.MPI setup with SGE

From: Ross Walker (
Date: Sat Apr 05 2008 - 11:18:45 CDT

Hi Sasha,

It's good to hear from you.

It's a little hard to help out much with the problems you are seeing since
there isn't really enough information. A couple of points though. Firstly
with sander.MPI always try to use a power of 2 cpus, so in this case 16
rather than 20. This will make a big difference on performance. With PMEMD
it is not as critical.

My second guess to the problem would be one of the environment not being
identical on the compute nodes to the compilation node such that there are
missing dynamic libraries needed by sander.MPI. You could try compiling
things statically and see if this helps - not always possible due to
restrictions on mpi libraries etc but worth a try. Add

./configure -static ....

Then recompile.

I'd also try something simple as well to make sure it is sander causing the
problem. I.e. try just running 'ls' instead of sander and see if you get
output from twenty copies of ls.

As for error messages there should be a job submission output file somewhere
that any error message will likely have gone into. With pbs this starts in a
directory called ~/.pbs_spool and then ultimately gets copied into the
directory from which the job submission was done. I'm not sure where sun
grid engine puts things but I would search around for that.

I'm sorry I can't help much more than that but if you can track down where
the error message went it will be much easier to help.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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