On Wed, 9 May 2012, Jiri Polach wrote:
You might want to use a smaller number of processors than those made
available by SGE.
Thanks for replying. I can imagine that in some special cases it might be
useful to request N processors from SGE and than use M<N; in such cases I
would specify "-np M" for mpirun, of course.
But this does not answer the question - if I just want to use as many
processors as I request from SGE - do I need to specify "-np N" for mpirun or
not?
Openmpi can be compiled with SGE integration. If present, you don't need
to use the -np argument (I'm checking one of my submit scripts).
Otherwise I use
-np $NSLOTS
$NSLOTS is given transparently by SGE with the total number of slots
If sge integration is not available (check through ompi_info) you also
might have to build the hostfile.
(which could be achieved, for instance, with
HOSTFILE=hostfile
awk '{print $1" cpu="$2}' ${PE_HOSTFILE} > ${HOSTFILE}
mpirun -machinefile ${HOSTFILE} -np ${NSLOTS} ${EXEC}
)
best (sorry if I extended the answer)
Ricardo Reis
'Non Serviam'
PhD/MSc Mechanical Engineering | Lic. Aerospace Engineering
Computational Fluid Dynamics, High Performance Computing, Turbulence
http://www.lasef.ist.utl.pt
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Ricardo J.N. dos Reis
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