A brief followup which may be useful (or not) for others in the future with mpi problems. I have been able to work around a mysterious impi/ssh bug on NU's supercomputer by replacing ssh by the openmpi/mpirun launcher. The hack is gross, but very stable.
Step 1: 1) Add "--bootstrap-exec=$WIENROOT/hopen" to $WIENROOT/parallel_options. 2) Create the executable file $WIENROOT/hopen containing #!/bin/bash a=`echo $@ | sed -e 's/-x -q//'` $OPENMPI/bin/mpirun -np 1 --host $a (change $OPENMPI to where it has been compiled). On Thu, Jul 18, 2013 at 10:38 AM, Laurence Marks <[email protected]> wrote: > On a cluster I am using I am having a problem with ssh connections as > part of impi/mpirun about 0.1-0.2% of the time; what happens is that > they fail to launch and become zombie's (ps shows "[ssh] <defunct>"). > Since fiddling through all the options within mpirun can be hard > (particularly for impi which is rather fast), I found (after a comment > from someone on the openssh list) a useful hack. I am providing it > here as it is a nice way around things, and might be useful to others > in the future. > > The "trick" is to add --bootstrap-exec ~/bin/hssh or similar to the > mpirun line in $WIENROOT/parallel_options, then create the executable > ~/bin/hssh with something similar to: > > #!/bin/bash > a=`echo $@ | sed -e 's/-q/-v/'` > ssh $a > > > The above allows me to turn verbose output on in the ssh command since > impi insists on setting -q (quiet). For other cases something similar > can be done. > > -- > Professor Laurence Marks > Department of Materials Science and Engineering > Northwestern University > www.numis.northwestern.edu 1-847-491-3996 > "Research is to see what everybody else has seen, and to think what > nobody else has thought" > Albert Szent-Gyorgi -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 "Research is to see what everybody else has seen, and to think what nobody else has thought" Albert Szent-Gyorgi _______________________________________________ Wien mailing list [email protected] http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/[email protected]/index.html
