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

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Fri Feb 4 16:41:52 CET 2005


> 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
> and I can read the number of steps, the expectation time, etc ...
> I have tried some tips I have found in the mailing list about this
> problem, but no one was successful (at / nohup / ...): I think that I
> should be able to run BOTH in the background mpirun and mdrun, by how ?

Open a second ssh connection, if you do not want this you can also start this 
in a screen ( type screen than ran mpirun with mdrun  in this, and you can 
switch out with strg a d and into it with screen -r ).

Think you should install a batch system like openpbs ( www.openpbs.org)
for further job submit.



 Florian Haberl                            Universitaet Erlangen/
 Computer-Chemie-Centrum    Nuernberg
                                                      Naegelsbachstr. 25
                                                      D-91052 Erlangen
  Mailto: florian.haberl AT chemie.uni-erlangen.de

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