[gmx-users] Gromacs 5.0.2 no parallei run

Szilárd Páll pall.szilard at gmail.com
Fri Oct 3 14:52:18 CEST 2014


As the note suggests, mdrun noticed that the process affinity mask is
non-default and to not interfere it did not set thread affinities.
This typically happens when the affinity of your job is set at
startup, typically done by the job scheduler, but in some cases the
MPI runtimes can mess with the thread affinities too. In your case the
thread affinity is most likely not set correctly and two or more of
mdrun's threads get pinned to the same core.

The best solution to this problem is to identify what sets the
incorrect affinity and disable or try passing "-pin on" to mdrun which
should override the externally set affinity.


On Fri, Oct 3, 2014 at 2:05 PM, Jernej Zidar <jernej.zidar at gmail.com> wrote:
> Hi all,
>   Lately I noticed I have a rather weird problem with Gromacs on my
> workstation and I'm unable to pinpoint whether it's a hardware or a
> software problem.
>   The problem is that none of the jobs are using all the CPUs or
> threads. I compiled Gromacs with support for OpenMP and without
> support for MPI and GPU as instructed on the documentation page. FFTW
> was pulled of the internet during the make stage.
>   After building Gromacs I load up the environment and start a job:
> mdrun -v -deffnm system1-npt-prod -maxh 0.1 -nsteps -1
> Until recently, the job would start with 1 MPI thread and 12 OpenMP
> threads and use all the available CPUs (the machine is a dual Xeon
> X5650 machine with hyperthreading disabled) as evidenced by the usage
> in utilities like 'top'/'htop'. The end result is relatively decent
> performance of ~20 ns/day for the system1.
> What happens now is that I get this message from Gromacs:
> Non-default thread affinity set, disabling internal thread affinity
> Using 1 MPI thread
> Using 12 OpenMP threads
> On another machine that is similar in terms of hardware, the job
> starts without any complaints:
> Overriding nsteps with value passed on the command line: -1 steps, -0.002 ps
> Using 1 MPI thread
> Using 12 OpenMP threads
> I can't find any error in the log file. It appears the CPUs are
> somewhat off-limits for me. Running the job as root or rebooting
> doesn't help.
> I'm running Debian stable (Wheezy) with nothing much installed.
> Any advice will be appreciated!
> Thanks in advance,
> Jernej Zidar
> --
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list