I have a script teste.sh which contains: #!/bin/bash #$ -S /bin/bash
#PBS -l nodes=8:ppn=6 source /home/dadalt/gmx-5.0.4/bin/ grompp -f md.mdp -c 1UBQ_400_npt.gro -t 1UBQ_400_npt.cpt -p topol.top -o product.tpr /usr/lib64/openmpi/bin/mpirun -np 8 mdrun_mpi -v -deffnm product I use the command qsub to run teste.sh : qsub -cwd -pe mpi 4 teste.sh Through this steps the simulation is perfomed using just ONE node, but I want to use 8 nodes. What I am doing wrong? What I need to change? I am using Rock Cluster distribution. Thanks in advance Lucas > Date: Tue, 14 Apr 2015 16:14:18 +0200 > From: pall.szil...@gmail.com > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Clusters > > 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. -- 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.