[gmx-users] Gromacs 4.6.7 with MPI and OpenMP

Malcolm Tobias mtobias at wustl.edu
Mon May 11 16:24:56 CEST 2015


On Friday 08 May 2015 21:18:12 Szilárd Páll wrote:
> >> What is your goal with using CPUSETs? Node sharing?
> >
> > Correct.  While it might be possible to see the cores that have been assigned to the job and do the correct 'pin setting' it would probably be ugly.
> Not sure what you mean by "see the cores". 

Sorry, I tend to anthropomorphize computers when I try to understand them ;-)

If I request X cores from the queueing system, it will create a CPUSET of X cores.  If I call omp_get_num_procs(), it will report X even if there are more physical cores on the system.  This way OpenMP plays nice with the queuing system.

> Also not sure why is it
> more ugly to construct a CPUSET than a pin offset, but hey, if you
> want both performance and node sharing with automated resource
> allocation, the solution won't be simple, I think.

The queuing system does the work of creating the CPUSET for me.  One thing I was worried about is that I'm not guaranteed a contiguous set of processors in the CPUSET.  If I ask for 4 cores, I may be assigned 1, 3, 5 and 6 for example.  In the end, I think I can live without the performance increase of pin'ing the threads.  Since the threads will be confined to the CPUSET, I'm guessing the threads are less likely to migrate.


Malcolm Tobias

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