[gmx-users] problem with -multi

[Anton Feenstra]

Nguyen Hoang Phuong wrote:

> Dear All,
> 
> we have tried to get mdrun run with the option -multi
> 
> mpirun -np 2 mdrun_d -np 2 -multi -s x.tpr

On some systems (with some mpi versions), for some reason, mpirun
will run your process in the directory where your *binary* (in this
case mdrun_d) is. That would explain your problems.

A solution is to make a soft link for mdrun to your working directory,
like
# ln -s /usr/local/gmx3.2.1/bin/mdrun_d .
# mpirun -np 2 ./mdrun_d -np 2 -multi -s x.tpr

P.S., the -multi option is only useful on (large) supercomputing
facilities where jobs *must* be multi-processor, but you want to run
several separate runs on a single CPU each anyway. You should *NOT*
use it if you want to run a normal run in parallel.

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
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