<div dir="ltr">Dear Prof. Marks,<div><br></div><div> Could you, please, send me a template for the parallel_options file where this implementation was done ?</div><div> I am sorry for that, but I am really far from being an expert.</div>
<div> All the best,</div><div> Luis</div><div class="gmail_extra"><br><br><div class="gmail_quote">2013/7/22 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">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 $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>
<div class="HOEnZb"><div class="h5"><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 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 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>
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</div></div></blockquote></div><br></div></div>