[gmx-users] ssh on parallel machine for mdrun: any way for background execution of the command?

[Anton Feenstra]

Tivadar Orban wrote:

> On 2/4/05 9:22 AM, "Luca Mollica" <mollica.luca at hsr.it> wrote:
> 
> 
>>Dear all,
>>
>>I am trying to test GROMACS 3.X performance on an IBM PPC64 we have
>>recently got in our institute: we have successfully installed GROMACS
>>parallel version (we use MYRINET) and I'm trying to monitor the
>>performance and start the first simulations. Evereything seems to be
>>fine, but I don't understand how to run the simulation using SSH being
>>also able, at the same time, to log out from the system after I have
>>lauched the calculation without stopping it.
>>
>>I start the simulation with the following command (8 CPU):
>>
>>mpirun -np 8 -nolocal -nopoll mdrun -s MD_prova -np 8 -v
> 
> 
> mpirun -np 8 -nolocal -nopoll mdrun -s MD_prova -np 8 -v &

That will often fail (for rather obscure reasons). WHat *does* work is 
to mak a simple script, like:

#!/bin/sh

mpirun -np 8 -nolocal -nopoll mdrun -s MD_prova -np 8 -v 2&>1 > md.job

#last line

(I'm not completely sure about the redirection (2&>1 >) syntax in sh...)

Unfortunately, you may have to find/set the path to your mpirun as well 
as mdrun because the environment in your script may be different from 
the commandline. Easiest way is to type:
# which mpirun
and
# which mdrun
and include the full paths in the script (although, mpirun may yet 
depend on some environment variables).
Finally, you should be able to run this script in the background using 
(assuming the script is named 'script' and is executable):
# script &

-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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