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

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 18 21:47:34 CET 2009

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?

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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