[gmx-users] multiple GPU on multiple nodes

Szilárd Páll pall.szilard at gmail.com
Tue Feb 4 16:33:48 CET 2014


I strongly suggest that you consult the Blue Waters or other XK7
manual or talk to the support team. Understanding this hardware in
crucial in getting any reasonable performance.

As I said before, the inconsistency in your commands is that you
request nnodes x nppn = 2 x 16 MPI ranks which does match with the
"aprun -n 32" launch requirements, i.e 2x16=32. However, requesting
2x16 ranks and than running "aprun -n 2" is simply incorrect. Instead
you can do e.g.
qsub  -l nodes=2:ppn=4
aprun -n 8 mdrun_mpi -gpu_id 0000


On Tue, Feb 4, 2014 at 4:09 PM, cyberjhon <cyberjhon at hotmail.com> wrote:
> On Tue, Feb 4, 2014 at 1:51 AM, cyberjhon <cyberjhon@> wrote:
>> 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
>>Those qsub and aprun commands are not in like with each other. Your
>>submission requests 2 nodes and 16 ranks/processes per node, that this
>>32 ranks in total. However, your aprun lauch requests only a single
>>rank (and only two below). Please consult the machine's documentation
>>on how to launch jobs correctly.
> I now what you are saying, an I am agree with you. When I run gromacs using
> only CPUs I do
>  aprun -n 32 mdrun_mpi -deffnm protein
> And this works perfectly !!!
> But when I am trying to use the GPUs in those two nodes, if I run this
> command, I get the error that I told you 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 32 PP MPI processes per node, but only 1 GPU
>> were
>> detected.
>> For more information and tips for troubleshooting, please check the
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
> So according to this the problem is not in the aprun command, it looks like
> the problem is in gromacs.
> In your presentation
> http://www.gromacs.org/@api/deki/files/213/=gromacs_parallelization_acceleration.pdf
> Page 49 you show that  you run gromacs in Blue waters in multiple nodes, and
> base on the date you used 4.6.2, how you did that?
> Thanks
> John Michael
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