Running NAMD on SGE cluster - multiple modes and cores

From: Anna Gorska (gvalchca.agr_at_gmail.com)
Date: Tue Dec 03 2013 - 05:25:37 CST

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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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