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 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.