On 4/18/14, 6:53 PM, maggin wrote:
Hi,
I use
grompp -f nvt.mdp -c em.gro -p box.6.top -o nvt.tpr
mpirun -np 8 mdrun_mpi -deffnm nvt
and get
NOTE: The number of threads is not equal to the number of (logical) cores
and the -pin option is set to auto: will not pin thread to cores.
This can lead to significant performance degradation.
Consider using -pin on (and -pinoffset in case you run multiple jobs).
So, I fix it as mpirun -np 8 mdrun_mpi -deffnm nvt -pinoffset
is it right?
No. The -pinoffset option takes an integer argument to define the first logical
core to be used. It is only relevant in the case that multiple jobs are using
the same set of nodes.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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