<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix"><br>
Can you tell us which MPI you are using? We will have to address
this...<br>
<br>
On 05/09/2014 10:08 AM, Tim Armstrong wrote:<br>
</div>
<blockquote
cite="mid:CAC0jiV7_V8U4Nkqz6NmUP=ep-mCzkd8toJVEoHtSgED0h=+iag@mail.gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<div dir="ltr">Nice!<br>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Fri, May 9, 2014 at 9:30 AM, Ketan
Maheshwari <span dir="ltr"><<a moz-do-not-send="true"
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 Mike,
<div><br>
</div>
<div>Thanks! Redirecting stdin from /dev/null with turbine
call worked right away!</div>
<div><br>
</div>
<div>So, now we have a first working version of
Swift/T-foreach-Galaxy. </div>
<div>
<br>
</div>
<div>Thanks,</div>
<div>Ketan</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">
<div class="">On Thu, May 8, 2014 at 8:33 PM, Wilde,
Michael J. <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:wilde@mcs.anl.gov" target="_blank">wilde@mcs.anl.gov</a>></span>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div class="">
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
<div>
<div><br>
<br>
<div>On 5/8/14, 5:10 PM, Ketan Maheshwari
wrote:<br>
</div>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="h5">
<div>
<div>
<pre>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>
<br>
<fieldset></fieldset>
<br>
</div>
</div>
</div>
</div>
<div class="">
<div>
<pre>_______________________________________________
ExM-user mailing list
<a moz-do-not-send="true" href="mailto:ExM-user@lists.mcs.anl.gov" target="_blank">ExM-user@lists.mcs.anl.gov</a>
<a moz-do-not-send="true" href="https://lists.mcs.anl.gov/mailman/listinfo/exm-user" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/exm-user</a>
</pre>
</div>
</div>
</blockquote>
<div class=""><span><font color="#888888">
<br>
<pre cols="72">--
Michael Wilde
Mathematics and Computer Science Computation Institute
Argonne National Laboratory The University of Chicago
</pre>
</font></span></div>
</div>
</blockquote>
</div>
<br>
</div>
<br>
_______________________________________________<br>
ExM-user mailing list<br>
<a moz-do-not-send="true"
href="mailto:ExM-user@lists.mcs.anl.gov">ExM-user@lists.mcs.anl.gov</a><br>
<a moz-do-not-send="true"
href="https://lists.mcs.anl.gov/mailman/listinfo/exm-user"
target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/exm-user</a><br>
<br>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
ExM-user mailing list
<a class="moz-txt-link-abbreviated" href="mailto:ExM-user@lists.mcs.anl.gov">ExM-user@lists.mcs.anl.gov</a>
<a class="moz-txt-link-freetext" href="https://lists.mcs.anl.gov/mailman/listinfo/exm-user">https://lists.mcs.anl.gov/mailman/listinfo/exm-user</a>
</pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Justin M Wozniak</pre>
</body>
</html>