[gmx-users] multiple GPU on multiple nodes

[cyberjhon]

Dear Szilárd 

Thanks for your answer.

To submit the job I do;

qsub -l nodes=2:ppn=16,walltime=12:00:00 

Then, to run gromacs I can do:
aprun -n 1 mdrun_mpi -deffnm protein

And, I get the message that you mention, which is good
"1 GPU detected on host nid00900:" does not mean that only one GPU was
detected."

But If I do:
aprun -n 2 mdrun_mpi -deffnm protein

I get the error mentioned before
-------------------------------------------------------
Program mdrun_mpi, VERSION 4.6.2
Source code file:
/N/soft/cle4/gromacs/gromacs-4.6.2/src/gmxlib/gmx_detect_hardware.c, line:
356

Fatal error:
Incorrect launch configuration: mismatching number of PP MPI processes and
GPUs per node.
mdrun_mpi was started with 2 PP MPI processes per node, but only 1 GPU were
detected.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Even if I use -gpu_id 0 or -gpu_id 00, they do not work

I also tried what you told me before about CRAY_CUDA_MPS  and
CRAY_CUDA_PROXY
export CRAY_CUDA_MPS= 1 
export CRAY_CUDA_PROXY=1   

I executed these commands before the aprun, and they did not work

So, can you tell me what is the command that you use on BW to use the GPU
located in each node?

Thanks

John Michael







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