From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Dec 03 2013 - 06:12:08 CST
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 don't 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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