Hi,
> > Are output files produced? YES
> > Do they contain error messages? NO
So output just stops at some point? or mdout is empty? Is the first energy
summary printed?
> > Did Amber12 pass the parallel test suite? YES
> > Did other parallel TI jobs run ok before? NOT IN AMBER12
Hm, did the Amber test suite TI jobs really pass? There is a set of tests
$AMBERHOME/test/ti* and $AMBERHOME/test/softcore/* that try out the TI-MPI
calcs. Make sure these work ok before checking your own system.
> > Do you use the right MPI version (the one compiled with Amber) or the
> pre-installed one?
> We use Debian 604 with pre-installed open MPI 142
There can be problems when Amber and MPI are compiled with different
compilers, I always suggest making a fresh MPI setup with every recompile
of Amber. But if you say your tests passed, maybe thats not it.
> > Does it run on a single machine (with MPI, but no submission queue
> etc) YES
Hm, so you can run the TI calculation on a single machine with MPI, but
not on your cluster? This sounds like a permission or queueing problem
then.
> > Can you run single CPU calculations (no TI) with both of your
> prmtops? YES
> > Maybe your two endstate systems are not identical in composition?
> the files are identical, only whith different charge
> distribution on one HEM-residue.
ok, if your prmtop files differ only in the list of charges and the restrt
files are identical, then not much can go wrong code-wise, focus on
checking if your Amber installation really is fully functional by looking
at the test results etc.
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Thu Jun 21 2012 - 05:00:03 PDT
