<div dir="ltr">Hi Mihael,<div><br></div><div>The code in _swiftwrap.staging branches based on if STDIN is present or not. See the snippet below:</div><div><br></div><div><div>if [ "$STDIN" == "" ]; then</div><div> if [ "$SWIFT_GEN_SCRIPTS" != "" ]; then</div><div> echo "#!/bin/bash" > run.sh</div><div> echo "\"$EXEC\" \"${CMDARGS[@]}\" 1>\"$STDOUT\" 2>\"$STDERR\"" >> run.sh</div><div> chmod +x run.sh</div><div> fi</div><div> "$EXEC" "${CMDARGS[@]}" 1>"$STDOUT" 2>"$STDERR"</div><div>else</div><div> if [ "$SWIFT_GEN_SCRIPTS" != "" ]; then</div><div> echo "#!/bin/bash" > run.sh</div><div> echo "\"$EXEC\" \"${CMDARGS[@]}\" 1>\"$STDOUT\" 2>\"$STDERR\" <\"$STDIN\"" >> run.sh</div><div> chmod +x run.sh</div><div> fi</div><div> "$EXEC" "${CMDARGS[@]}" 1>"$STDOUT" 2>"$STDERR" <"$STDIN"</div><div>fi</div></div><div><br></div><div>When "stdin=" is not provided the code takes the first branch and hangs. It works otherwise.</div><div><br></div><div>It is possible that it hangs because if mpich bug Mike mentioned. </div><div><br></div><div>I agree we should stick in a </dev/null in there.</div><div><br></div><div>--Ketan</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Mar 4, 2015 at 3:12 PM, Hategan-Marandiuc, Philip M. <span dir="ltr"><<a href="mailto:hategan@mcs.anl.gov" target="_blank">hategan@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">I'm still confused. I don't see any difference in stdin handling between<br>
_swiftwrap and _swiftwrap.staging (which is used for direct staging).<br>
<br>
Maybe we should always feed the app a /dev/null if there is no stdin=<br>
specified.<br>
<br>
Mihael<br>
<div class="HOEnZb"><div class="h5"><br>
On Wed, 2015-03-04 at 08:50 -0600, Ketan Maheshwari wrote:<br>
> I added stdin="/dev/null" to app invocation line and it has worked now.<br>
> --Ketan<br>
><br>
> On Wed, Mar 4, 2015 at 8:44 AM, Ketan Maheshwari <<a href="mailto:ketan@mcs.anl.gov">ketan@mcs.anl.gov</a>> wrote:<br>
><br>
> > Please find one with 59 minutes attached. --Ketan<br>
> ><br>
> > On Tue, Mar 3, 2015 at 11:17 PM, Mihael Hategan <<a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov</a>><br>
> > wrote:<br>
> ><br>
> >> You are using coasters, so what gets queued is the block, not the job.<br>
> >><br>
> >> You should specify execution.options.maxJobTime = "00:59:00".<br>
> >><br>
> >> Then you can probably do a walltime of about "00:50:00". But 7 minutes<br>
> >> vs. 5 minutes isn't much of a difference.<br>
> >><br>
> >> Mihael<br>
> >><br>
> >> On Tue, 2015-03-03 at 22:28 -0600, Ketan Maheshwari wrote:<br>
> >> > Attached is a log for maxWalltime set to 7 minutes beyond which the job<br>
> >> > does not get submitted because of the 1 hour walltime limit of Cetus.<br>
> >> > --Ketan<br>
> >> ><br>
> >> > On Tue, Mar 3, 2015 at 10:15 PM, Ketan Maheshwari <<a href="mailto:ketan@mcs.anl.gov">ketan@mcs.anl.gov</a>><br>
> >> wrote:<br>
> >> ><br>
> >> > > When I check queue with qstat, I see the job is submitted for 40<br>
> >> minutes.<br>
> >> > > When I try to increase maxWallTime the workflow does not get submitted<br>
> >> > > because on Cetus maximum allowed walltime is 60 minutes. --Ketan<br>
> >> > ><br>
> >> > > On Tue, Mar 3, 2015 at 10:03 PM, Hategan-Marandiuc, Philip M. <<br>
> >> > > <a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov</a>> wrote:<br>
> >> > ><br>
> >> > >> Hi,<br>
> >> > >><br>
> >> > >> Looks like almost exactly 5 minutes to me:<br>
> >> > >><br>
> >> > >> 2015-03-04 01:45:43,943+0000 INFO Execute TASK_STATUS_CHANGE<br>
> >> > >> taskid=urn:R-3-0-2-1425432781969 status=2<br>
> >> > >> workerid=0304-3301040-000000:000000<br>
> >> > >> 2015-03-04 01:50:44,676+0000 INFO Execute TASK_STATUS_CHANGE<br>
> >> > >> taskid=urn:R-3-0-2-1425432781969 status=5 Walltime exceeded<br>
> >> > >><br>
> >> > >> Which is what the config file is asking for:<br>
> >> > >><br>
> >> > >> app.bgsh {<br>
> >> > >> env.SUBBLOCK_SIZE: "16" # [R] line<br>
> >> 27<br>
> >> > >> executable: "/home/ketan/SwiftApps/subjobs/bg.sh" # [R] line<br>
> >> 25<br>
> >> > >> maxWallTime: "00:05:00" # [R] line<br>
> >> 26<br>
> >> > >> }<br>
> >> > >><br>
> >> > >> Again, the wrapper log shows the app as still running. Last line is:<br>
> >> > >> Progress 2015-03-04 01:45:43.971393118+0000 EXECUTE<br>
> >> > >><br>
> >> > >> Please do me a favor and increase the walltime to one hour and let's<br>
> >> see<br>
> >> > >> what happens then.<br>
> >> > >><br>
> >> > >> If it still doesn't finish after one hour, we could try to strace it<br>
> >> and<br>
> >> > >> see what is happening there.<br>
> >> > >><br>
> >> > >> Mihael<br>
> >> > >><br>
> >> > >> On Tue, 2015-03-03 at 19:53 -0600, Ketan Maheshwari wrote:<br>
> >> > >> > Please find the log attached. --Ketan<br>
> >> > >> ><br>
> >> > >> > On Tue, Mar 3, 2015 at 7:03 PM, Hategan-Marandiuc, Philip M. <<br>
> >> > >> > <a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov</a>> wrote:<br>
> >> > >> ><br>
> >> > >> > > On Tue, 2015-03-03 at 15:42 -0600, Ketan Maheshwari wrote:<br>
> >> > >> > > > Slow network looks unlikely to be a cause:<br>
> >> > >> > ><br>
> >> > >> > > It's the only variable obvious, so I wouldn't say that.<br>
> >> > >><br>
> >> > >> I meant "only obvious variable" there.<br>
> >> > >><br>
> >> > >><br>
> >> > >><br>
> >> > ><br>
> >><br>
> >><br>
> >> _______________________________________________<br>
> >> Swift-devel mailing list<br>
> >> <a href="mailto:Swift-devel@ci.uchicago.edu">Swift-devel@ci.uchicago.edu</a><br>
> >> <a href="https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel" target="_blank">https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel</a><br>
> >><br>
> ><br>
> ><br>
<br>
<br>
</div></div></blockquote></div><br></div>