[gmx-users] Efficiently running multiple simulations

[Mark Abraham]

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 <mizimmer at 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
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