[gmx-users] lAM/MPI

delara aghaie d_aghaie at yahoo.com
Sun May 23 10:13:38 CEST 2010

Dear gromacs users,
Our university network is LAM/MPI.
I connect to the network from my office computer to submit simulation job in gromacs.
In order to boot the MPI invironment I use lamboot command. 
$ lamboot -v lamhosts
the lamhosts is a text file where I should introduce the processeros which I want to boot them and here I should include the (lnx-server) which is where I connect to, from my office computer and run the lamboot order there.
Now when I want to submit simulation job I use (grompp) order which is in the path
/usr/local/gromacs/bin/grompp (with the necessary options) including -np (to introduce the number of processors).
Here again it seems that I should add the server to the number of processors and also it is the same for the order mpiexec .
I think in this way the server will become one of the processors that my job starts to run on it and because always the server is very busy with other jobs, the speed that I get is very very low !!!
please let me know if it is a way that can tell the system not to run job on the server.
I think this can solve the speed problem.
your answer would be greatly appreciated
This oprder makes the topol.tpr file 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100523/8b1b0780/attachment.html>

More information about the gromacs.org_gmx-users mailing list