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

XAvier Periole x.periole at rug.nl
Fri Dec 18 17:29:15 CET 2009


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

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  
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?

We: Djurre (& XAvier)

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