On Tue, Apr 14, 2015 at 2:45 AM, Lucas Dadalt Morero <ld...@hotmail.com> wrote: > Sorry, it's 8 cores. Network is good.
Good for what? I was hoping to hear that it's e.g IB QDR. Otherwise it's unlikely that you'll scale to all nodes. > The hardware setup is ok, I just want to know how to perform a gromacs > simulation using all the nodes.. Compile with MPI and run just like you'd run any MPI application. See if it scales at all on your network, if it does you can try tweaking the performance (e.g. PP-PME ratio, mutiple OpenMP threads per rank, nstlist, etc.) I suggest you check out that following page: http://www.gromacs.org/Documentation/Acceleration_and_parallelization -- Szilárd > > > Lucas > >> Date: Tue, 14 Apr 2015 02:06:49 +0200 >> From: pall.szil...@gmail.com >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Clusters >> >> What network do you have? Unless it's fast (that is low latency) you >> won't be able to run across nodes. Are you sure about 9 cores, that >> number seems strange? >> -- >> Szilárd >> >> >> On Mon, Apr 13, 2015 at 11:52 PM, Lucas Dadalt Morero <ld...@hotmail.com> >> wrote: >> > Are there any tutorial or tips to use cluster in Gromacs? >> > I have 5 nodes with 9 cores each node and want use all them in one >> > simulation, is that possible? >> > I've read something about gromacs MPI but I don't know how to use. >> > Can someone suggest some text or some tutorial for me? >> > >> > Thanks in advance, >> > Lucas >> > >> > -- >> > 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. > > -- > 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.
