[gmx-users] problems with intel I7 (2.67 GHz)

Alexey Shvetsov alexxyum at gmail.com
Fri Dec 18 21:32:39 CET 2009

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.
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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