My guess is that the two jobs are using the same cores -- either all cores/threads or only half of them, but the same set.
You should use -pinoffset; see: - Docs and example: http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html - More explanation on the thread pinning behavior on the old website: http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Pinning_threads_to_physical_cores Cheers, -- Szilárd On Wed, Sep 13, 2017 at 6:35 PM, gromacs query <gromacsqu...@gmail.com> wrote: > Sorry forgot to add; we thought the two jobs are using same GPU ids but > cuda visible devices show both jobs are using different ids (0,1 and 2,3) > > - > J > > On Wed, Sep 13, 2017 at 5:33 PM, gromacs query <gromacsqu...@gmail.com> > wrote: > >> Hi All, >> >> I have some issues with gromacs performance. There are many nodes and each >> node has number of gpus and the batch process is controlled by slurm. >> Although I get good performance with some settings of number of gpus and >> nprocs but when I submit same job twice on the same node then the >> performance is reduced drastically. e.g >> >> For 2 GPUs I get 300 ns per day when there is no other job running on the >> node. When I submit same job twice on the same node & at the same time, I >> get only 17 ns/day for both the jobs. I am using this: >> >> mpirun -np 4 gmx_mpi mdrun -deffnm test -ntomp 2 -maxh 0.12 >> >> Any suggestions highly appreciated. >> >> Thanks >> >> Jiom >> > -- > 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.