[Wien] A trick for mpi debugging

[Laurence Marks]

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
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>
>



-- 
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