WARNING 1: To be used with care, and customized as needed WARNING 2: Valid for impi and perhaps other, but not all variants WARNING 3: Please look at what these options mean...
My parallel_options file with NU's supercomputer, which contains various debug and other options (some recommended by Intel, some by the local sys_admin): setenv USE_REMOTE 1 setenv MPI_REMOTE 0 setenv WIEN_GRANULARITY 1 setenv DAPL_DBG_TYPE 0 # Normal #setenv WIEN_MPIRUN "mpirun -n _NP_ -machinefile _HOSTS_ _EXEC_ " # To turn on verbose #setenv WIEN_MPIRUN "mpirun -bootstrap-exec ~/bin/hssh -n _NP_ -machinefile _HOSTS_ _EXEC_ " # To use more recent, privately compiled ssh #setenv WIEN_MPIRUN "mpirun -bootstrap-exec $HOME/local/bin/ssh -n _NP_ -machinefile _HOSTS_ _EXEC_ " # To use openmpi to launch setenv WIEN_MPIRUN "mpirun -bootstrap-exec $WIENROOT/hopen -n _NP_ -machinefile _HOSTS_ _EXEC_ " set sleepy = 0.2 set delay = 0.1 unset DAPL_DBG #Turn on Hydra debug on Quest #setenv I_MPI_HYDRA_DEBUG 1 #Turn on MPI DEBUG #setenv I_MPI_DEBUG 1 #setenv I_MPI_DEBUG_OUTPUT mpi_debug%h_%r setenv I_MPI_FABRICS_LIST dapl,tcp setenv I_MPI_FALLBACK enable On Sat, Jul 27, 2013 at 2:53 PM, Luis Ogando <[email protected]> wrote: > Dear Prof. Marks, > > Could you, please, send me a template for the parallel_options file where > this implementation was done ? > I am sorry for that, but I am really far from being an expert. > All the best, > Luis > > > 2013/7/22 Laurence Marks <[email protected]> >> >> A brief followup which may be useful (or not) for others in the future >> with mpi problems. I have been able to work around a mysterious >> impi/ssh bug on NU's supercomputer by replacing ssh by the >> openmpi/mpirun launcher. The hack is gross, but very stable. >> >> Step 1: >> 1) Add "--bootstrap-exec=$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 > > -- 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
