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.
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