You can always try mdrun -dlb yes whch will turn on dynamic load balancing from the beginning.. ________________________________________ From: [email protected] [[email protected]] On Behalf Of delara aghaie [[email protected]] Sent: Wednesday, April 13, 2011 4:41 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] 2nd question related to load imbalance
Dear Dr. van der Spoel many thanks for your explanations. I want to know how I can overcome the performance loss due to load imbalance? Thanks regards Delara --- On Wed, 4/13/11, David van der Spoel <[email protected]> wrote: From: David van der Spoel <[email protected]> Subject: Re: [gmx-users] 2nd question related to load imbalance To: "Discussion list for GROMACS users" <[email protected]> Date: Wednesday, April 13, 2011, 2:01 PM On 2011-04-13 11.26, delara aghaie wrote: > Hello > Previously I used gromacs/3.3 for my simulations of DPPc > monolayer+Tip4P2005. I saw that it uses particle decomposition > Now I want to use versin 4.0.7 because I need tcoupl=v-rescale > This version does the domain decomposition which causes load imbalance. > with this version because of load imbalance and loss of performance the > simulation needs longer time to run. > so the question: > what is the benefit of this domain decomposition. I think it causes the > runs to be done slower !!!. > thanks > D.aghaie > 4.0.7 is a lot better than 3.3 for scaling, but the latest version 4.5.4 is even better. In addition it contains new features and bugfixes. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. [email protected]<http://us.mc1301.mail.yahoo.com/mc/[email protected]> http://folding.bmc.uu.se<http://folding.bmc.uu.se/> -- gmx-users mailing list [email protected]<http://us.mc1301.mail.yahoo.com/mc/[email protected]> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]<http://us.mc1301.mail.yahoo.com/mc/[email protected]>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
