Re: Running NAMD on SGE cluster - multiple modes and cores

From: Anna Gorska (gvalchca.agr_at_gmail.com)
Date: Tue Dec 03 2013 - 09:23:30 CST

Hello,
thank you for the quick response although it still doesnt work. Without MPI it does not even produce error message, but you were right,
I set the MPI environment variable to give the file with hosts to the mpi.

But still it runs only on the one node.
My new command looks like this:
charmrun ++mpiexec ++remote-shell mpirun +p124 namd2 conf > out

Regards,
Anna Gorska

> Of course, if you use mpiexec, it is expected that the queuing system provides the list of machines to the mpirun directly, so the nodelist is not used. Try
>
> charmrun ++nodelist namd-machines +p104 namd2 in > out
>
> And read the instructions for using mpiexec again, as I dont know it by heart now.
>
> Norman Geist.
>
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Anna Gorska
> Gesendet: Dienstag, 3. Dezember 2013 12:26
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: Running NAMD on SGE cluster - multiple modes and cores
>
> Hello,
>
> I try to run a NAMD (using NAMD_2.9_Linux-x86_64 version) on multiple nodes on SGE cluster.
>
> I am able to generate adequate file with list of nodes subscribed to me by the queuing system,
> but the NAMD runs always only on one node taking the specified number of cores -
> it behaves as if the ++nodelist was not there at all.
>
> This is the command I use:
>
> charmrun ++mpiexec ++remote-shell mpirun ++nodelist namd-machines +p104 namd2 in > out
>
>
> and the namd-machines file looks as follows:
>
> group main ++pathfix /step2_2_tmp
> host node508
> host node508
> host node508
> host node508
> host node508
> host node508
> host node508
> host node508
> host node508
> host node508
> host node508
> host node503
> host node503
> host node503
> host node503
> host node503
> host node503
>
>
> Sincerely,
> Anna Gorska
> ____________
>
> PHD student
> Algorithms in Bioinformatics
> University of Tuebingen
> Germany
>
>
>
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>

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