Hello,<div><br></div><div>Today I saw this error on SCEC workflow.</div><div><br></div><div><br></div><div><div>could not find variable: _concurrent/var_str-d9e801ee-8aca-431f-99a0-8286c452c779-13-6 [7]</div><div>Invalid path exception org.griphyn.vdl.mapping.InvalidPathException: Invalid path ([7]) for var_str:string[0] - Closed for path [7]</div>
<div>org.griphyn.vdl.mapping.InvalidPathException: Invalid path ([7]) for var_str:string[0] - Closed</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at org.griphyn.vdl.mapping.AbstractDataNode.getField(AbstractDataNode.java:204)</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>at org.griphyn.vdl.mapping.file.ArrayFileMapper.map(ArrayFileMapper.java:55)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at org.griphyn.vdl.karajan.lib.VDLFunction.leafFileName(VDLFunction.java:281)</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>at org.griphyn.vdl.karajan.lib.VDLFunction.leafFileName(VDLFunction.java:270)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at org.griphyn.vdl.karajan.lib.VDLFunction.filename(VDLFunction.java:187)</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>at org.griphyn.vdl.karajan.lib.VDLFunction.filename(VDLFunction.java:175)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at org.griphyn.vdl.karajan.lib.Stagein.function(Stagein.java:54)</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>at org.griphyn.vdl.karajan.lib.VDLFunction.post(VDLFunction.java:62)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.futureModified(AbstractSequentialWithArguments.java:208)</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>at org.griphyn.vdl.karajan.DSHandleFutureWrapper$1.run(DSHandleFutureWrapper.java:63)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at java.util.concurrent.FutureTask.run(FutureTask.java:138)</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>at java.lang.Thread.run(Thread.java:662)</div><div>Execution failed:</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Progress: time: Mon, 12 Sep 2011 16:50:27 -0500 Submitted:1 Active:17 Finished successfully:10</div>
</div><div><br></div><div><br></div><div>Complete log for this run is: <a href="http://www.ci.uchicago.edu/~ketan/postproc-20110912-1642-epj1ebm1.log">http://www.ci.uchicago.edu/~ketan/postproc-20110912-1642-epj1ebm1.log</a></div>
<div><br></div><div>Swift is r5102.<br><div><br></div><div>Regards,</div><div>Ketan</div><div><br><div class="gmail_quote">On Fri, Sep 9, 2011 at 9:33 AM, Michael Wilde <span dir="ltr"><<a href="mailto:wilde@mcs.anl.gov">wilde@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;">So far Im not able to re-create this problem on the prior revision of 0.93.<br>
<br>
Im currently using this variation of the script Mihael posted below:<br>
<div class="im"><br>
type file;<br>
<br>
type struct {<br>
file b;<br>
file c;<br>
}<br>
<br>
app (struct of) echo() {<br>
</div> sh "-c" "echo bee >fileb ; echo see >filec";<br>
}<br>
<br>
struct s <ext;exec="structbug1.map">;<br>
<br>
s = echo();<br>
<br>
I discovered what I think is a new bug in the process: if the shell command string contains the characters >&1 and >&2, Swift complains that it cant process the intermediate xml. Presumably those shell sequences are getting xml parsing confused and need to be escaped.<br>
<br>
- Mike<br>
<div class="im"><br>
----- Original Message -----<br>
> From: "Mihael Hategan" <<a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov</a>><br>
</div><div><div></div><div class="h5">> To: "David Kelly" <<a href="mailto:davidk@ci.uchicago.edu">davidk@ci.uchicago.edu</a>><br>
> Cc: "Swift Devel" <<a href="mailto:swift-devel@ci.uchicago.edu">swift-devel@ci.uchicago.edu</a>><br>
> Sent: Friday, September 9, 2011 1:31:44 AM<br>
> Subject: Re: [Swift-devel] Path.parse(path.toString())<br>
> On Fri, 2011-09-09 at 01:10 -0500, David Kelly wrote:<br>
> > It looks like there are a few scripts in the test suite which write<br>
> > structs and seem to be passing.<br>
><br>
> I suspect they are not staging structs out (just in).<br>
><br>
> > Do you happen to have an example script I could add to the suite?<br>
><br>
> type file;<br>
><br>
> type struct {<br>
> file b;<br>
> file c;<br>
> }<br>
><br>
> app (struct of) echo() {<br>
> bash "echo bee >1 ; echo see >2" stdout=@filename(of.b)<br>
> stderr=@filename(of.c);<br>
> }<br>
><br>
> struct s <simple_mapper;>;<br>
><br>
> s = echo();<br>
><br>
> (I'm not sure if this actually works if the bug is fixed, but I know<br>
> it<br>
> doesn't if it isn't. Anyway, you get the idea).<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>
</div></div><font color="#888888">--<br>
Michael Wilde<br>
Computation Institute, University of Chicago<br>
Mathematics and Computer Science Division<br>
Argonne National Laboratory<br>
</font><div><div></div><div class="h5"><br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Ketan<br><br><br>
</div></div>