Try: mpirun -npernode 2 -Trayder
On Wed, Oct 15, 2014 at 8:42 AM, Siva Dasetty <sdas...@g.clemson.edu> wrote: > Thank you Mark for the reply, > > We use pbs for submitting jobs on our cluster and this is how I request the > nodes and processors > > #PBS -l > select=2:ncpus=8:mem=8gb:mpiprocs=8:ngpus=2:gpu_model=k20:interconnect=fdr > > > Do you think the problem could be with the way I installed mdrun using Open > MPI? > > > Can you please suggest the missing environmental settings that I may need > to include in the job script in order for the MPI to consider 2 ranks on > one node? > > > Thank you for your time. > > > > On Tue, Oct 14, 2014 at 5:20 PM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > On Tue, Oct 14, 2014 at 10:51 PM, Siva Dasetty <sdas...@g.clemson.edu> > > wrote: > > > > > Dear All, > > > > > > I am currently able to run simulation on a single node containing 2 > gpus, > > > but I get the following fatal error when I try to run the simulation > > using > > > multiple gpus (2 on each node) on multiple nodes (2 for example) using > > OPEN > > > MPI. > > > > > > > Here you say you want 2 ranks on each of two nodes... > > > > > > > Fatal error: > > > > > > Incorrect launch configuration: mismatching number of PP MPI processes > > and > > > GPUs > > > > > > per node. > > > > > > mdrun was started with 4 PP MPI processes per node, > > > > > > ... but here mdrun means what it says... > > > > > > > but you provided only 2 > > > GPUs. > > > > > > The command I used to run the simulation is > > > > > > mpirun -np 4 mdrun -s <tpr file> -deffnm <...> -gpu_id 01 > > > > > > > ... which means your MPI environment (hostfile, job script settings, > > whatever) doesn't have the settings you think it does, since it's putting > > all 4 ranks on one node. > > > > Mark > > > > > > > > > > > > > However It at least runs if I use the following command, > > > > > > > > > mpirun -np 4 mdrun -s <tpr file> -deffnm <...> -gpu_id 0011 > > > > > > > > > But after referring to the following thread, I highly doubt if I am > using > > > all the 4 gpus available in the 2 nodes combined. > > > > > > > > > > > > > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2014-May/007682.html > > > > > > > > > > > > Thank you for your help in advance, > > > > > > -- > > > Siva > > > -- > > > 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. > > > > > > -- > Siva > -- > 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.