Re: [gmx-users] Performance drops when simulating protein with small ligands
On 3/20/15 1:13 PM, Yunlong Liu wrote: Hi, I am running my protein with two ligands. Both ligands are small molecules like ATP. However, my simulation performance drops a lot by adding this two ligands with the same set of other parameters. Previously with ligands, I have 30 ns/day with 64-cpus and 4gpus. But now I can only gain 17 ns/day with the same setting. I want to know whether this is a common phenomenon or I do something stupid. Probably some other process is using resources and degrading your performance, or you're using different run settings (the .log file is definitive here). The mere addition of ligands does not degrade performance. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
[gmx-users] Performance drops when simulating protein with small ligands
Hi, I am running my protein with two ligands. Both ligands are small molecules like ATP. However, my simulation performance drops a lot by adding this two ligands with the same set of other parameters. Previously with ligands, I have 30 ns/day with 64-cpus and 4gpus. But now I can only gain 17 ns/day with the same setting. I want to know whether this is a common phenomenon or I do something stupid. Yunlong -- 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] Performance drops when simulating protein with small ligands
Hi Justin, I am running this simulation on Stampede/TACC. I don't think there are other processes running on the nodes assigned to me. This is a little weird. Yunlong On Mar 20, 2015, at 2:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/20/15 1:13 PM, Yunlong Liu wrote: Hi, I am running my protein with two ligands. Both ligands are small molecules like ATP. However, my simulation performance drops a lot by adding this two ligands with the same set of other parameters. Previously with ligands, I have 30 ns/day with 64-cpus and 4gpus. But now I can only gain 17 ns/day with the same setting. I want to know whether this is a common phenomenon or I do something stupid. Probably some other process is using resources and degrading your performance, or you're using different run settings (the .log file is definitive here). The mere addition of ligands does not degrade performance. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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. -- 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] Performance drops when simulating protein with small ligands
On 3/20/15 2:32 PM, Yunlong Liu wrote: Hi Justin, I am running this simulation on Stampede/TACC. I don't think there are other processes running on the nodes assigned to me. This is a little weird. Well, as I said, the .log files will be the definitive source of run settings and configuration. Look for differences. If there are none, take it up with the cluster admins. If predictable behavior is not being observed, it's worth looking into. Maybe a node is simply having issues. -Justin Yunlong On Mar 20, 2015, at 2:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/20/15 1:13 PM, Yunlong Liu wrote: Hi, I am running my protein with two ligands. Both ligands are small molecules like ATP. However, my simulation performance drops a lot by adding this two ligands with the same set of other parameters. Previously with ligands, I have 30 ns/day with 64-cpus and 4gpus. But now I can only gain 17 ns/day with the same setting. I want to know whether this is a common phenomenon or I do something stupid. Probably some other process is using resources and degrading your performance, or you're using different run settings (the .log file is definitive here). The mere addition of ligands does not degrade performance. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
