Hi, On Mon, May 25, 2015 at 4:08 PM Zhang, Cheng <c.zhang...@ucl.ac.uk> wrote:
> Dear GROMACS, > > I am now using openmpi nodes to run GROMACS (e.g. mdrun_mpi) on our > cluster. When the nodes required are too many (e.g. more than 8), jobs > always take a long time to wait in the queue. So I wonder if there is a > possibility that we can > > > 1) convert the job into many serial jobs? > Only if you are prepared to run a separate simulation in every concurrent single-node job, or you can get better throughput by chaining single-node jobs than you can get by running in parallel. If you have measured this, you should complain bitterly - people probably paid good money for the network, and you would have evidence that it got bought for the pre-production benchmarks, and is now being wasted in practice. If they wanted to build a single-node throughput cluster, then they should do that and e.g. not bother to install MPI on it. ;-) 2) convert the job into several openmpi jobs but with only 1 node in each > job? > No. All the cores synchronize every few milliseconds. Nothing can start until all the nodes are ready. > When serial jobs are submitted, hundreds of jobs can be run within just a > few minutes. > Sounds like you will be able to generate a good complaint :-) Mark > Thank you very much. > > > Yours sincerely > > Cheng > -- > 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.