[Wien] A trick for mpi debugging

[Luis Ogando]

Dear Prof. Marks,

   Just a quick question : in case that the openmpi launcher replaces ssh,
should I change USE_REMOTE to 0 in a cluster ?
   Thank you one more time,
                Luis



2013/7/27 Laurence Marks <L-marks at northwestern.edu>

> 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 $WIENROOT/hopen -n _NP_
> -machinefile _HOSTS_ _EXEC_ "
>
> set sleepy = 0.2
> set delay = 0.1
> unset DAPL_DBG
> #Turn on Hydra debug on Quest
> #setenv I_MPI_HYDRA_DEBUG 1
> #Turn on MPI DEBUG
> #setenv I_MPI_DEBUG 1
> #setenv I_MPI_DEBUG_OUTPUT mpi_debug%h_%r
> setenv I_MPI_FABRICS_LIST dapl,tcp
> setenv I_MPI_FALLBACK enable
>
>
>
>
> On Sat, Jul 27, 2013 at 2:53 PM, Luis Ogando <lcodacal at gmail.com> wrote:
> > Dear Prof. Marks,
> >
> >    Could you, please, send me a template for the parallel_options file
> where
> > this implementation was done ?
> >    I am sorry for that, but I am really far from being an expert.
> >    All the best,
> >                     Luis
> >
> >
> > 2013/7/22 Laurence Marks <L-marks at northwestern.edu>
> >>
> >> A brief followup which may be useful (or not) for others in the future
> >> with mpi problems. I have been able to work around a mysterious
> >> impi/ssh bug on NU's supercomputer by replacing ssh by the
> >> openmpi/mpirun launcher. The hack is gross, but very stable.
> >>
> >> Step 1:
> >> 1) Add "--bootstrap-exec=$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
> >> <L-marks at northwestern.edu> 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
> >> Wien at zeus.theochem.tuwien.ac.at
> >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> >> SEARCH the MAILING-LIST at:
> >> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/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
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at:
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