[gmx-users] how to order gpus on different nodes

[Mark Abraham]

Hi,

On Thu, May 12, 2016 at 8:28 AM Ming Tang <m21.tang at qut.edu.au> wrote:

> Dear experts,
>
> I can order 2 gpus on one node from HPC using the following script:
>
> #PBS -l select=1:ncpus=2:ngpus=2:mpiprocs=2:mem=2gb
>
> mpiexec_mpt -n 2 gmx_mpi mdrun -v -deffnm npt -nb gpu -gpu_id 01 -ntomp 2
>
> however when I used the following script to order 4 gpus on 2 nodes, it
> gave me an error saying gpu cannot be detected.
>

Please copy and paste the actual error message. Details are important for
computer-related problems.

#PBS -l select=2:ncpus=2:ngpus=2:mpiprocs=2:mem=4gb
>
>
> mpiexec_mpt -n 4 gmx_mpi mdrun -cpi -cpo -c relax.pdb -nb gpu -gpu_id 0011
> -ntomp4
>
> Does anybody know how to order gpus on different nodes?
>

See
http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html#examples-for-mdrun-on-more-than-one-node,
and note that -gpu_id indexes GPUs on each node, so probably you want
-gpu_id 01 for the mapping from the two ranks on each node to the two GPUs
on each node.

Mark


> Thank you.
>
>
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