Hi Ray:
You might want to post on the grid engine list. If you are using
the mpich compiled into ROCKS, it uses ssh, and doesn't preserve
environment variables in remote children, unless you explicitly ask for it.
Did you modify rsh-wrapper as indicated as well?
Joe
Raymond Chan wrote:
Hi all,
Sorry as this is not totally a MPIBLAST question, but I hope someone can
point me in the right direction. I’m running MPIBLAST-1.4.0 on AMD
Opteron systems using ROCKS 4.0.0 cluster. I recently noticed that
while running MPIBLAST w/ Sun Grid Engine, when I delete the job in SGE,
my MPIBLAST processes stay on the compute nodes. I followed the tight
integration instructions here:
http://gridengine.sunsource.net/howto/mpich-integration.html (by
choosing to set the environment variable *MPICH_PROCESS_GROUP=no)*
* *
Upon closer inspection of the stopmpi.sh script that SGE uses for its
parallel jobs, all the script does is delete the machine file SGE
creates for MPI. It does not even mention anything about killing
processes created (i.e MPIBLAST in this case). If anyone has gotten
tight integration working with MPIBLAST, can you point me in the right
direction of how/if I have to edit that stopmpi.sh script, or do
something different?
Thank you in advance,
Ray
Univ of CA Davis
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