The invocation line depends on the MPI tool installed on the cluster. E.g. in case of openmpi, you write openmpi -np 64 mdrun -dd 4 4 4
Dr. Vitaly V. Chaban On Tue, Dec 3, 2013 at 4:58 PM, MUSYOKA THOMMAS <mutemibiochemis...@gmail.com> wrote: > Dear Justin, > Well it seems i am the first one to do MD simulations in my lab and i am > using a chemistry department cluster and nobody has prior knowledge on > GROMACS. I can use all the cores in the cluster but need to know if there > is a specific mdrun command that can allow me specify the number of cores > to be used for the MD run. > > Thank you > > > On Tue, Dec 3, 2013 at 5:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 12/3/13 10:23 AM, MUSYOKA THOMMAS wrote: >> >>> Dear Users, >>> >>> I am using a cluster of 64 cores to perform my MD simulations using >>> GROMACS >>> version 4.5.5. >>> >>> I would be glad to know the exact mdrun command that will allow me use the >>> available resources. >>> >>> >> The answer depends entirely on the architecture of the cluster. Your sys >> admin should know. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> 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 >> >> ================================================== >> -- >> 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. >> > > > > -- > > *MUSYOKA THOMMAS MUTEMIMob nos **+27844846540* > *B.Sc Biochemistry (Kenyatta University), MSc Pharmaceutical Science > (Nagasaki University)* > > *PhD Student - Research Unit in Bioinformatics (RUBi - Rhodes > University)*Skype > ID- MUSYOKA THOMMAS MUTEMI > Alternative email - thom...@sia.co.ke > > > > > > > > > *"Do all the good you can, By all the means you can, In all the ways you > can, In all the places you can,At all the times you can,To all the people > you can,As long as ever you can." - John Wesley. * > -- > 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. -- 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.