AMBER Archive (2006)

Subject: RE: AMBER: paralelization and sander problems

From: Ross Walker (
Date: Tue Feb 14 2006 - 11:48:06 CST

Dear Cristian,

> We have running a cluster of 12 processors in linux Debian
> platform (mpich
> 1.2.6. and fortran intel_fc_80 compiler), and our results in
> sander8 outputs
> are different depending the queue (4 or 8) that we are using,
> around 0.0001 %
> in the final energy in the third step.

Could you possibly post your output files, then it would be easier to see if
the problem is benign or not. When you say third step do you mean NSTEP=3 or
the third time information is written to the output file? This could be
after 300 steps if ntpr=100. If the difference you are seeing is in the last
decimal place after 300 steps then the problems are largely benign and due
to different orders of execution and hence rounding on different numbers of
cpus. If however the two trajectories start to diverge after just 3 steps
(assuming that you have a stable system) then the problem 'could' be an
issue. Either way if you can post your output files it would be easier to
diagnose things.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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