From: HOUSTON Douglas (DouglasR.Houston_at_ed.ac.uk)
Date: Mon Mar 06 2017 - 08:15:25 CST
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
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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