[gmx-users] Thread affinity error when Running Gromacs 4.6.3 on Bluegene/P

[Szilárd Páll]

That's a "normal" side-effect of mdrun trying to set thread affinities
[1] on a platform which does not support this. Also, this is not an
error, mdrun should have continued to run.

Note that you would be much better off with upgrading to the latest
version, there have been many improvements, especially on BG you
should observe large performance difference.


[1] http://en.wikipedia.org/wiki/Processor_affinity
--
Szilárd


On Wed, Mar 12, 2014 at 2:10 AM, arrow50311 <linxingcheng50311 at gmail.com> wrote:
> Hi,
>
> When trying to run normal mdrun_mpi with Gromacs 4.6.3 on Bluegene/P, I met
> this error:
>
> Can not set thread affinities on the current platform. On NUMA systems this
> can cause performance degradation. If you think your platform should support
> setting affinities, contact the GROMACS developers.
>
> The running stops immediately.
>
> This is the script for running it:
>
> #@ job_name = simulation
> #@ step_name = step1
> #@ comment = "Hello World Job"
> #@ error = $(job_name).$(jobid).err
> #@ output = $(job_name).$(jobid).out
> #@ environment = COPY_ALL
> #@ wall_clock_limit = 24:00:00
> #@ notification = error
> #@ job_type = bluegene
> #@ class = compute
> #@ bg_size = 128
> #@ queue
> dir=/home/bin/gromacs
> runDir=production
> ddir=/bgpscratch/gromacs/$runDir
> export MDRUN=/opt/apps/gromacs/4.6/bin/mdrun_mpi
> mkdir -p $ddir
> cd $ddir
>
> /bgsys/drivers/ppcfloor/bin/mpirun -cwd $ddir -mode VN -np 512 -exe "$MDRUN"
> -args "-s $dir/run.tpr -cpi $ddir/state.cpt -cpo $ddir/state.cpt -maxh 23.9
> -npme 128 -noappend"
>
> I have no idea what can cause that kind of error, could someone offer a
> help?
>
> Thank you,
>
>
>
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/Thread-affinity-error-when-Running-Gromacs-4-6-3-on-Bluegene-P-tp5015095.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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