[gmx-users] problems with intel I7 (2.67 GHz)
alexxyum at gmail.com
Fri Dec 18 22:40:01 CET 2009
On Пятница 18 декабря 2009 23:47:34 David van der Spoel wrote:
> Alexey Shvetsov wrote:
> > On Пятница 18 декабря 2009 19:29:15 XAvier Periole wrote:
> >> Dears,
> >> we have been trying to run gmx-4.0.X on new machines with the
> >> Intel I7 CPUs. It is a quad core intel on which multi-threading is
> >> a "default" feature. This makes the system to behave as a 8 cores
> >> machine.
> >> We observed some strange behavior of gromacs. Note that is
> >> certainly not due to gromacs itself.
> >> Running jobs using 4 cores we have observed the following behavior:
> >> - the info on the output files (log, xtc, edr ...) is not always printed
> >> - gromacs switches cores, eg: cores 1,2,4,5, and then 2,3,5,6 ... and
> >> this
> >> with no apparent logic.
> >> Jobs using 8 cores become extremely slow, more than expected,
> >> and if running at all.
> >> Running 2 jobs with 4 cores each, one was running with 4 cores, the
> >> second was using only 2 cores although mpirun was asked to use 4.
> >> This is more disturbing since it was also possible to run two jobs
> >> using 4 cores each successfully and have effectively increased
> >> efficiency: each job running at 5/6 of the speed of one run on 4 cores
> >> and running alone.
> >> This was observed with:
> >> - Ubuntu-9.10 (karmic) / kernel linux 2.6.31-14-generic (GNOME 2.28.1)
> >> - openmpi-1.3.2/1.4.X
> >> - gromacs 4.0.5/4.0.7
> >> Anyone has any idea what could be going on on those I7?
> >> Thanks,
> >> We: Djurre (& XAvier)
> > Well its usual behavior of systems with HT (Hyper threading) enabled. so
> > its better to disable HT on such cpus so any cpu eating application like
> > gromacs will run faster on it.
> No, this is not what I have heard from Berk Hess, he said that running 8
> processes on 4 cores gives a speed up of 6-7 times a single core.
> It sounds more like you need to tune the kernel such that jobs stay on
> the core they are on. As far as I know Ubuntu is a Desktop OS, maybe you
> want a Server OS?
In this case seems cpuaffinity was turned off for mpi apps. check that kernel has
alexxy at xeon /misc/_Work/RecA/pca $ zgrep CPUSET /proc/config.gz
And check that your openmpi compiled with support of cpusets
Alexey 'Alexxy' Shvetsov
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru
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