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Perhaps try redirecting stdin on the $turbine call with "<
/dev/null"<br>
<br>
Some older versions of mpiexec had a bug when stdin was not a tty or
ptty.<br>
<br>
Not sure if thats the case here, but easy to try.<br>
<br>
- Mike<br>
<br>
<div class="moz-cite-prefix">On 5/8/14, 5:10 PM, Ketan Maheshwari
wrote:<br>
</div>
<blockquote
cite="mid:CAMUuviq7W-e3=Hn+4kw2sKmwmGKFdGB4CkTc5qmwyJ_Hj_gHOQ@mail.gmail.com"
type="cite">
<pre wrap="">Hi,
Trying invoke turbine from Galaxy as follows:
$turbine -V -n $n $wdir/script.tcl "${swiftargs}"
Each of the variables being set in previous lines.
The process tree shows mpiexec as defunct processes:
PID TTY TIME CMD
389 ? 00:00:00 sshd
390 pts/39 00:00:00 bash
804 pts/39 00:00:00 sh
990 pts/39 00:00:38 python
1189 pts/39 00:00:00 sh
1190 pts/39 00:00:00 bash
1330 pts/39 00:00:00 turbine
1332 pts/39 00:00:00 mpiexec <defunct>
1547 pts/39 00:00:00 sh
1548 pts/39 00:00:00 bash
1683 pts/39 00:00:00 turbine
1686 pts/39 00:00:00 mpiexec <defunct>
2046 pts/39 00:00:00 sh
2047 pts/39 00:00:00 bash
2299 pts/39 00:00:00 turbine
2302 pts/39 00:00:00 mpiexec <defunct>
Not sure how to debug this. The same call works outside of Galaxy.
Any suggestions?
Thanks,
Ketan
</pre>
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Michael Wilde
Mathematics and Computer Science Computation Institute
Argonne National Laboratory The University of Chicago
</pre>
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