<div dir="ltr">Dear Prof. Marks,<div><br></div><div style> Thank you again !</div><div style> I will do the tests and tell you what happen.</div><div style> All the best,</div><div style> Luis</div><div style>
<br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2013/8/3 Laurence Marks <span dir="ltr"><<a href="mailto:L-marks@northwestern.edu" target="_blank">L-marks@northwestern.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I am not sure if I can give you the right answer; My guess is to have<br>
it as 1, but I do not know all the details of your system and if I<br>
remember right you have an sgi system. Try both, then let us/me know<br>
what works (or does not).<br>
<br>
For reference, I have it working fine with USE_REMOTE 1, and I don't<br>
currently want to change to test (particularly as I am on travel).<br>
<div class="im HOEnZb"><br>
On Fri, Aug 2, 2013 at 8:36 AM, Luis Ogando <<a href="mailto:lcodacal@gmail.com">lcodacal@gmail.com</a>> wrote:<br>
> Dear Prof. Marks,<br>
><br>
</div><div class="im HOEnZb">> Just a quick question : in case that the openmpi launcher replaces ssh,<br>
> should I change USE_REMOTE to 0 in a cluster ?<br>
> Thank you one more time,<br>
> Luis<br>
><br>
><br>
><br>
> 2013/7/27 Laurence Marks <<a href="mailto:L-marks@northwestern.edu">L-marks@northwestern.edu</a>><br>
>><br>
</div><div class="HOEnZb"><div class="h5">>> WARNING 1: To be used with care, and customized as needed<br>
>> WARNING 2: Valid for impi and perhaps other, but not all variants<br>
>> WARNING 3: Please look at what these options mean...<br>
>><br>
>> My parallel_options file with NU's supercomputer, which contains<br>
>> various debug and other options (some recommended by Intel, some by<br>
>> the local sys_admin):<br>
>><br>
>> setenv USE_REMOTE 1<br>
>> setenv MPI_REMOTE 0<br>
>> setenv WIEN_GRANULARITY 1<br>
>> setenv DAPL_DBG_TYPE 0<br>
>> # Normal<br>
>> #setenv WIEN_MPIRUN "mpirun -n _NP_ -machinefile _HOSTS_ _EXEC_ "<br>
>><br>
>> # To turn on verbose<br>
>> #setenv WIEN_MPIRUN "mpirun -bootstrap-exec ~/bin/hssh -n _NP_<br>
>> -machinefile _HOSTS_ _EXEC_ "<br>
>><br>
>> # To use more recent, privately compiled ssh<br>
>> #setenv WIEN_MPIRUN "mpirun -bootstrap-exec $HOME/local/bin/ssh -n<br>
>> _NP_ -machinefile _HOSTS_ _EXEC_ "<br>
>><br>
>> # To use openmpi to launch<br>
>> setenv WIEN_MPIRUN "mpirun -bootstrap-exec $WIENROOT/hopen -n _NP_<br>
>> -machinefile _HOSTS_ _EXEC_ "<br>
>><br>
>> set sleepy = 0.2<br>
>> set delay = 0.1<br>
>> unset DAPL_DBG<br>
>> #Turn on Hydra debug on Quest<br>
>> #setenv I_MPI_HYDRA_DEBUG 1<br>
>> #Turn on MPI DEBUG<br>
>> #setenv I_MPI_DEBUG 1<br>
>> #setenv I_MPI_DEBUG_OUTPUT mpi_debug%h_%r<br>
>> setenv I_MPI_FABRICS_LIST dapl,tcp<br>
>> setenv I_MPI_FALLBACK enable<br>
>><br>
>><br>
>><br>
>><br>
>> On Sat, Jul 27, 2013 at 2:53 PM, Luis Ogando <<a href="mailto:lcodacal@gmail.com">lcodacal@gmail.com</a>> wrote:<br>
>> > Dear Prof. Marks,<br>
>> ><br>
>> > Could you, please, send me a template for the parallel_options file<br>
>> > where<br>
>> > this implementation was done ?<br>
>> > I am sorry for that, but I am really far from being an expert.<br>
>> > All the best,<br>
>> > Luis<br>
>> ><br>
>> ><br>
>> > 2013/7/22 Laurence Marks <<a href="mailto:L-marks@northwestern.edu">L-marks@northwestern.edu</a>><br>
>> >><br>
>> >> A brief followup which may be useful (or not) for others in the future<br>
>> >> with mpi problems. I have been able to work around a mysterious<br>
>> >> impi/ssh bug on NU's supercomputer by replacing ssh by the<br>
>> >> openmpi/mpirun launcher. The hack is gross, but very stable.<br>
>> >><br>
>> >> Step 1:<br>
>> >> 1) Add "--bootstrap-exec=$WIENROOT/hopen" to<br>
>> >> $WIENROOT/parallel_options.<br>
>> >> 2) Create the executable file $WIENROOT/hopen containing<br>
>> >> #!/bin/bash<br>
>> >> a=`echo $@ | sed -e 's/-x -q//'`<br>
>> >> $OPENMPI/bin/mpirun -np 1 --host $a<br>
>> >><br>
>> >> (change $OPENMPI to where it has been compiled).<br>
>> >><br>
>> >> On Thu, Jul 18, 2013 at 10:38 AM, Laurence Marks<br>
>> >> <<a href="mailto:L-marks@northwestern.edu">L-marks@northwestern.edu</a>> wrote:<br>
>> >> > On a cluster I am using I am having a problem with ssh connections as<br>
>> >> > part of impi/mpirun about 0.1-0.2% of the time; what happens is that<br>
>> >> > they fail to launch and become zombie's (ps shows "[ssh] <defunct>").<br>
>> >> > Since fiddling through all the options within mpirun can be hard<br>
>> >> > (particularly for impi which is rather fast), I found (after a<br>
>> >> > comment<br>
>> >> > from someone on the openssh list) a useful hack. I am providing it<br>
>> >> > here as it is a nice way around things, and might be useful to others<br>
>> >> > in the future.<br>
>> >> ><br>
>> >> > The "trick" is to add --bootstrap-exec ~/bin/hssh or similar to the<br>
>> >> > mpirun line in $WIENROOT/parallel_options, then create the executable<br>
>> >> > ~/bin/hssh with something similar to:<br>
>> >> ><br>
>> >> > #!/bin/bash<br>
>> >> > a=`echo $@ | sed -e 's/-q/-v/'`<br>
>> >> > ssh $a<br>
>> >> ><br>
>> >> ><br>
>> >> > The above allows me to turn verbose output on in the ssh command<br>
>> >> > since<br>
>> >> > impi insists on setting -q (quiet). For other cases something similar<br>
>> >> > can be done.<br>
>> >> ><br>
>> >> > --<br>
>> >> > Professor Laurence Marks<br>
>> >> > Department of Materials Science and Engineering<br>
>> >> > Northwestern University<br>
>> >> > <a href="http://www.numis.northwestern.edu" target="_blank">www.numis.northwestern.edu</a> <a href="tel:1-847-491-3996" value="+18474913996">1-847-491-3996</a><br>
>> >> > "Research is to see what everybody else has seen, and to think what<br>
>> >> > nobody else has thought"<br>
>> >> > Albert Szent-Gyorgi<br>
>> >><br>
>> >><br>
>> >><br>
>> >> --<br>
>> >> Professor Laurence Marks<br>
>> >> Department of Materials Science and Engineering<br>
>> >> Northwestern University<br>
>> >> <a href="http://www.numis.northwestern.edu" target="_blank">www.numis.northwestern.edu</a> <a href="tel:1-847-491-3996" value="+18474913996">1-847-491-3996</a><br>
>> >> "Research is to see what everybody else has seen, and to think what<br>
>> >> nobody else has thought"<br>
>> >> Albert Szent-Gyorgi<br>
>> >> _______________________________________________<br>
>> >> Wien mailing list<br>
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>> >> <a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien" target="_blank">http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a><br>
>> >> SEARCH the MAILING-LIST at:<br>
>> >> <a href="http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html" target="_blank">http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html</a><br>
>> ><br>
>> ><br>
>><br>
>><br>
>><br>
>> --<br>
>> Professor Laurence Marks<br>
>> Department of Materials Science and Engineering<br>
>> Northwestern University<br>
>> <a href="http://www.numis.northwestern.edu" target="_blank">www.numis.northwestern.edu</a> <a href="tel:1-847-491-3996" value="+18474913996">1-847-491-3996</a><br>
>> "Research is to see what everybody else has seen, and to think what<br>
>> nobody else has thought"<br>
>> Albert Szent-Gyorgi<br>
>> _______________________________________________<br>
>> Wien mailing list<br>
>> <a href="mailto:Wien@zeus.theochem.tuwien.ac.at">Wien@zeus.theochem.tuwien.ac.at</a><br>
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>> SEARCH the MAILING-LIST at:<br>
>> <a href="http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html" target="_blank">http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html</a><br>
><br>
><br>
<br>
<br>
<br>
--<br>
Professor Laurence Marks<br>
Department of Materials Science and Engineering<br>
Northwestern University<br>
<a href="http://www.numis.northwestern.edu" target="_blank">www.numis.northwestern.edu</a> <a href="tel:1-847-491-3996" value="+18474913996">1-847-491-3996</a><br>
"Research is to see what everybody else has seen, and to think what<br>
nobody else has thought"<br>
Albert Szent-Gyorgi<br>
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</div></div></blockquote></div><br></div>