Hi,

Our cluster has identical nodes with two 64 bit Xeon CPUs in each machine.
One CPU has 4 cores, so we have 8 cores per node. We have SGE and OpenMPI
(version 1.3.) on the machines. I installed R, Rmpi and snow and it seemed
to work but then I realized by measuring the running time of a test script
that only 4 cores per computer is used. Running the program parallel up to 4
cores works fine but above 4 cores the running time doesn't decrease. If I
start the program setting the number of processes to 8 I got 8 processes all
using 100% of the CPU (e. g, a full core) but I read on the home page of
Rmpi that under OpenMPI slaves are using 100% of the CPU even if they are
only waiting for commands. I got the same when I tried to use more than one
nodes: when I set the number of processes to 16 I got two nodes working but
both with only half capacity.

It seems that somehow only one processor is used in each nodes. Do you have
any idea?

Thank you in advance!

Balázs

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Balazs Szappanos

Evolutionary Systems Biology Group
Biological Research Center
Szeged, Hungary

tel:  +36 62 599659
email: szbalazs@brc.hu
web: http://www.brc.hu/sysbiol/
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