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

[Mark Abraham]

On Wed, Mar 12, 2014 at 9:56 AM, Szilárd Páll <pall.szilard at gmail.com>wrote:

> 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.
>

Indeed. To find the function in which the actual problem oocurs you will
need to run a version configured with -DCMAKE_BUILD_TYPE=Debug and inspect
the backtrace. You can see what I think the problem is likely to be at
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083507.htmlbut
unfortunately nobody then supplied the information needed for a proper
resolution.

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.
>

No, BG/P has no support in 4.6.

Mark


>
>
> [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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