Hi Mark, Sorry for the confusion, what I meant to say was that each node on the cluster has 8 GPUs and 16 CPUs.
When I attempt to specify the GPU IDs for running 8 simulations on a node using the "-multi" and "-gpu_id", each .log file has the following: "8 GPUs user-selected for this run. Mapping of GPUs to the 8 PP ranks in this node: #0, #1, #2, #3, #4, #5, #6, #7" This makes me think that each simulation is competing for each of the GPUs, explaining my performance loss per simulation compared to running 1 simulation on 1 GPU and 2 CPUs. If this interpretation is correct, is there a better way to pin each simulation to a single GPU and 2 CPUs? If my interpretation is incorrect, is there a more efficient way to use the "-multi" option to match the performance I see of running a single simulation * 8? Regards, -Maxwell ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abra...@gmail.com> Sent: Wednesday, September 16, 2015 3:52 AM To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Efficiently running multiple simulations Hi, I'm confused by your description of the cluster as having 8 GPUs and 16 CPUs. The relevant parameters are the number of GPUs and CPU cores per node. See the examples at http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-features.html#running-multi-simulations Mark On Tue, Sep 15, 2015 at 11:38 PM Zimmerman, Maxwell <mizim...@wustl.edu> wrote: > Hello, > > > I am having some troubles efficiently running simulations in parallel on a > gpu-cluster. The cluster has 8 GPUs and 16 CPUs. Currently, the command > that I am using is: > > > mpirun -np 8 mdrun_mpi -multi 8 -nice 4 -s md -o md -c after_md -v -x > frame -pin on > > > Per-simulation, the performance I am getting with this command is > significantly lower than running 1 simulation that uses 1 GPU and 2 CPUs > alone. This command seems to use all 8 GPUs and 16 CPUs on the 8 parallel > simulations, although I think this would be faster if I could pin each > simulation to a specific GPU and pair of CPUs. The -gpu_id option does not > seem to change anything when I am using the mpirun. Is there a way that I > can efficiently run the 8 simulations on the cluster by specifying the GPU > and CPUs to run with each simulation? > > > Thank you in advance! > > > Regards, > > -Maxwell > -- > 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.
