<div dir="ltr">Can you attach to the mpiexec processes with gdb and get a stack trace? This seems like an MPI-level problem since there's only the mpi launcher process running.<br></div><div class="gmail_extra"><br><br>
<div class="gmail_quote">On Thu, May 8, 2014 at 5:10 PM, Ketan Maheshwari <span dir="ltr"><<a href="mailto:ketan@mcs.anl.gov" target="_blank">ketan@mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi,<div><br></div><div>Trying invoke turbine from Galaxy as follows:</div><div><br></div><div>$turbine -V -n $n $wdir/script.tcl "${swiftargs}" </div><div><br></div><div>Each of the variables being set in previous lines.</div>
<div><br></div><div>The process tree shows mpiexec as defunct processes:</div><div><div> PID TTY TIME CMD</div><div> 389 ? 00:00:00 sshd</div><div> 390 pts/39 00:00:00 bash</div><div> 804 pts/39 00:00:00 sh</div>
<div> 990 pts/39 00:00:38 python</div><div> 1189 pts/39 00:00:00 sh</div><div> 1190 pts/39 00:00:00 bash</div><div> 1330 pts/39 00:00:00 turbine</div><div> 1332 pts/39 00:00:00 mpiexec <defunct></div>
<div> 1547 pts/39 00:00:00 sh</div><div> 1548 pts/39 00:00:00 bash</div><div> 1683 pts/39 00:00:00 turbine</div><div> 1686 pts/39 00:00:00 mpiexec <defunct></div>
<div>
2046 pts/39 00:00:00 sh</div><div> 2047 pts/39 00:00:00 bash</div><div> 2299 pts/39 00:00:00 turbine</div><div> 2302 pts/39 00:00:00 mpiexec <defunct></div></div>
<div><br></div><div><br></div><div>Not sure how to debug this. The same call works outside of Galaxy.</div><div><br></div><div>Any suggestions?</div><div><br></div><div>Thanks,</div><div>Ketan</div></div>
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<br></blockquote></div><br></div>