From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Mar 06 2017 - 09:26:00 CST
Charmrun and NAMD will distribute the cores and nodes across the replica
which must be evenly possible. You assumptions look correct, so I think it
should work.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von HOUSTON Douglas
Gesendet: Montag, 6. März 2017 15:15
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: REMD on HPC
Hi all,
I am trying to get REMD working on our local HPC machine. The setup consists
of 16-core nodes connected via gigabit ethernet. I'd like to run the example
REMD that comes with NAMD such that each replica is running on a single
node, and is utilising all 16 cores. This is the example I mean:
NAMD_2.12_Linux-x86_64-netlrts/lib/replica/example/
However, I am having trouble working out what the command should look like.
So far I have:
charmrun ++verbose +p16 ++nodelist nodelist.txt ++mpiexec mpirun -np 8 namd2
+replicas 8 job0.conf +stdout output/%d/job0.%d.log
but I don't really know if this will achieve what I want. Do I need to use
charmrun at all? Will this result in all 16 cores in all 8 nodes being
utilised, with one replica on each node? Unfortunately testing via trial and
error is tricky due to the length of the job queue.
I have managed to get standard MD running across multiple nodes, so
passwordless ssh etc. is not a problem.
Regards,
_________________________________________________________________
Dr. Douglas R. Houston
Senior Lecturer in Computational Biochemistry
Institute of Quantitative Biology, Biochemistry and Biotechnology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
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