[gmx-users] Efficiently running multiple simulations
mizimmer at wustl.edu
Wed Sep 16 16:41:09 CEST 2015
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?
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abraham at gmail.com>
Sent: Wednesday, September 16, 2015 3:52 AM
To: gmx-users at gromacs.org; gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Efficiently running multiple simulations
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
On Tue, Sep 15, 2015 at 11:38 PM Zimmerman, Maxwell <mizimmer at wustl.edu>
> 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!
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