AMBER Archive (2004)

Subject: RE: AMBER: parallel of sander_classic

From: Ross Walker (
Date: Mon Oct 25 2004 - 08:15:58 CDT

Hi Xioling

> I am going to run sander_classsic (a module in AMBER6) with parallel.
> However, I can't perform parallel job, whereas sander works fine. Can
> sander_classic run parallel?

My understanding is that it should do. I haven't tried it myself but there
are plenty of MPI directives in the code. Are you certain you are trying to
use the parallel version (compiled with -DMPI)? Do you get an error message
if you do mpirun -np 4 sander_classic? If you run top what do you see?

Try doing a make clean in the amber src tree, verify you have linked MACHINE
to the parallel machine file and then cd to src/sander_classic and type
make. Copy the executable to $AMBERHOME/exe and then try it again.

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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