[gmx-users] Using several cores for MD production
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. Thank you. *"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.
Re: [gmx-users] Using several cores for MD production
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.
Re: [gmx-users] Using several cores for MD production
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 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.
Re: [gmx-users] Using several cores for MD production
On 12/3/13 10:58 AM, MUSYOKA THOMMAS 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. It still depends entirely on the architecture and how mdrun was compiled (which can be checked with ldd), but if it's standard MPI: mpirun -np 64 mdrun_mpi -whatever_else -Justin Thank you On Tue, Dec 3, 2013 at 5:37 PM, Justin Lemkul 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. -- == 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.
Re: [gmx-users] Using several cores for MD production
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 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 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.
