Hi,<br><br>It works fine now (log is attached). I'll try sid program next.<br><br>Many thanks,<br>Jing<br><br>On 9/10/07, Mihael Hategan <<a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov</a>> wrote:<br>> You need to do an SVN update for both CoG and Swift.
<br>> <br>> On Mon, 2007-09-10 at 11:03 -0500, Jing Tie wrote:<br>> > Hi,<br>> ><br>> > It has the same exception. Log is attached.<br>> ><br>> > Thanks,<br>> > Jing<br>> ><br>
> > On 9/10/07, Mihael Hategan <<a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov</a>> wrote:<br>> > > On Sun, 2007-09-09 at 12:29 -0500, Mihael Hategan wrote:<br>> > > > It's definitely a bug in the code I put in a few days ago. But I don't
<br>> > > > quite see how it happens. Such simple code. Yet how complex. I'll have<br>> > > > to get back to you on it.<br>> > ><br>> > > Fixed, I think. Can you try again?<br>
> > ><br>> > > Mihael<br>> > ><br>> > > ><br>> > > > On Sun, 2007-09-09 at 12:09 -0500, Jing Tie wrote:<br>> > > > > Sure.<br>> > > > ><br>> > > > > On 9/9/07, Mihael Hategan <
<a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov</a>> wrote:<br>> > > > > > Please post the whole workflow and the whole log.<br>> > > > > ><br>> > > > > > On Sun, 2007-09-09 at 11:43 -0500, Jing Tie wrote:
<br>> > > > > > > Hi,<br>> > > > > > ><br>> > > > > > > I tried duplicate job again using the latest swift with<br>> > > > > > > "log4j.logger.org.globus.cog.abstraction=DEBUG
".<br>> > > > > > ><br>> > > > > > > It didn't generated duplicate-*** directory under simple-wf-***<br>> > > > > > > directory. Details:<br>> > > > > > > Resource (
org.globus.cog.abstraction.impl.file.gridftp.FileResourceImpl@cbc2d3)<br>> > > > > > > successfully released<br>> > > > > > > Task(type=4, identity=urn:0-0-1189348296362) setting status to Failed
<br>> > > > > > > Could not set current directory to "null"<br>> > > > > > > duplicate failed<br>> > > > > > > The following errors have occurred:<br>
> > > > > > > 1. Could not initialize shared directory on NWICG_NotreDame<br>> > > > > > > Caused by:<br>> > > > > > > Could not set current directory to "null"
<br>> > > > > > > Caused by:<br>> > > > > > > Required argument missing<br>> > > > > > ><br>> > > > > > > in simple-wf-fc06kzz28d880.log
:<br>> > > > > > > 2007-09-09 09:31:39,911 DEBUG FileResourceCache Resource<br>> > > > > > > (org.globus.cog.abstraction.impl.file.gridftp.FileResourceImpl@cbc2d3)<br>> > > > > > > successfully released
<br>> > > > > > > 2007-09-09 09:31:39,911 DEBUG TaskImpl Task(type=4,<br>> > > > > > > identity=urn:0-0-1189348296362) setting status to Failed Could not set<br>> > > > > > > current directory to "null"
<br>> > > > > > > 2007-09-09 09:31:39,938 INFO vdl:mains Errors detected. Cleanup not done.<br>> > > > > > > 2007-09-09 09:31:39,963 DEBUG VDL2ExecutionContext Execution completed
<br>> > > > > > > with errors<br>> > > > > > > Execution completed with errors<br>> > > > > > ><br>> > > > > > > There is nothing under<br>
> > > > > > > <a href="http://osg.hpcc.nd.edu/dscratch/osg/data/osg/jtie/simple-wf-fc06kzz28d880">osg.hpcc.nd.edu/dscratch/osg/data/osg/jtie/simple-wf-fc06kzz28d880</a><br>> > > > > > > except empty shared directory.
<br>> > > > > > ><br>> > > > > > > Thanks,<br>> > > > > > > Jing<br>> > > > > > ><br>> > > > > > > On 9/7/07, Mihael Hategan <
<a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov</a>> wrote:<br>> > > > > > > > Nevermind that. It's eating the empty stdin argument. This doesn't make<br>> > > > > > > > sense. Fork used to behave.
<br>> > > > > > > ><br>> > > > > > > > Can you add this to log4j.properties, run again, and post the log?<br>> > > > > > > ><br>> > > > > > > >
log4j.logger.org.globus.cog.abstraction=DEBUG<br>> > > > > > > ><br>> > > > > > > ><br>> > > > > > > > On Fri, 2007-09-07 at 23:02 -0500, Mihael Hategan wrote:
<br>> > > > > > > > > Can you post the workflow?<br>> > > > > > > > ><br>> > > > > > > > > On Fri, 2007-09-07 at 21:56 -0500, Jing Tie wrote:
<br>> > > > > > > > > > Thanks!<br>> > > > > > > > > ><br>> > > > > > > > > > I checked the procedure, and found that the filenames of the output
<br>> > > > > > > > > > files of "myapp" are the same as "File f". So the first option should<br>> > > > > > > > > > not be the problem.<br>> > > > > > > > > >
<br>> > > > > > > > > > Then I tried a very simple swift script that doesn't need R:<br>> > > > > > > > > > app function: add some lines to the input file to generate the output file
<br>> > > > > > > > > > input file name: simpleFile.txt<br>> > > > > > > > > > output file name: simpleFile.output<br>> > > > > > > > > > application script location: $OSG_APP/osg/jtie/duplicate.sh
<br>> > > > > > > > > > jobmanager: jobmanager-fork<br>> > > > > > > > > ><br>> > > > > > > > > > duplicate failed<br>> > > > > > > > > > The following errors have occurred:
<br>> > > > > > > > > > 1. Application "duplicate" failed (Failed to link input file<br>> > > > > > > > > > /dscratch/osg/app/osg/jtie/duplicate.sh)<br>
> > > > > > > > > > Arguments: "simpleFile.txt"<br>> > > > > > > > > > Host: NWICG_NotreDame<br>> > > > > > > > > > Directory: simple-wf-xgh9e9q1z0af2/duplicate-it7hyvgi
<br>> > > > > > > > > > STDERR:<br>> > > > > > > > > > STDOUT:<br>> > > > > > > > > ><br>> > > > > > > > > > after execution, 3 empty directories (not files, and also weird name)
<br>> > > > > > > > > > were generated:<br>> > > > > > > > > > duplicate-gt7hyvgi-simpleFile.output<br>> > > > > > > > > > duplicate-ht7hyvgi-simpleFile.output
<br>> > > > > > > > > > duplicate-it7hyvgi-simpleFile.output<br>> > > > > > > > > ><br>> > > > > > > > > > wrapper.log:<br>> > > > > > > > > > DIR=duplicate-gt7hyvgi
<br>> > > > > > > > > > STDOUT=simpleFile.output<br>> > > > > > > > > > STDERR=stderr.txt<br>> > > > > > > > > > DIRS=simpleFile.output
<br>> > > > > > > > > > LINKS=/dscratch/osg/app/osg/jtie/duplicate.sh<br>> > > > > > > > > > OUTS=simpleFile.txt<br>> > > > > > > > > > ln: creating symbolic link
<br>> > > > > > > > > > `duplicate-gt7hyvgi//dscratch/osg/app/osg/jtie/duplicate.sh' to<br>> > > > > > > > > > `/dscratch/osg/data/osg/jtie/simple-wf-xgh9e9q1z0af2/shared//dscratch/osg/app/osg/jtie/duplicate.sh':
<br>> > > > > > > > > > No such file or directory<br>> > > > > > > > > ><br>> > > > > > > > > > under dir /dscratch/osg/data/osg/jtie/simple-wf-xgh9e9q1z0af2/shared:
<br>> > > > > > > > > > seq.sh, simpleFile.txt, wrapper.sh<br>> > > > > > > > > > under dir /dscratch/osg/data/osg/jtie/simple-wf-xgh9e9q1z0af2/duplicate-it7hyvgi:
<br>> > > > > > > > > > one directory - simpleFile.output<br>> > > > > > > > > > /dscratch/osg/data/osg/jtie/simple-wf-xgh9e9q1z0af2/duplicate-it7hyvgi/simpleFile.output:
<br>> > > > > > > > > > empty<br>> > > > > > > > > ><br>> > > > > > > > > > I think the swift program is right, since I run it successfully using
<br>> > > > > > > > > > localhost duplicate.sh.<br>> > > > > > > > > ><br>> > > > > > > > > ><br>> > > > > > > > > > Many thanks,
<br>> > > > > > > > > > Jing<br>> > > > > > > > > ><br>> > > > > > > > > ><br>> > > > > > > > > > On 9/7/07, Mihael Hategan <
<a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov</a>> wrote:<br>> > > > > > > > > > > So when the output files are not created, there can be two reasons:<br>> > > > > > > > > > > 1. The specification of what files should be created is broken. This is,
<br>> > > > > > > > > > > at this time, done by looking at the filenames of the return values from<br>> > > > > > > > > > > the atomic procedure. Normally one passes those file names to the
<br>> > > > > > > > > > > application as output file parameters. Example:<br>> > > > > > > > > > ><br>> > > > > > > > > > > (File f) proc(...) {
<br>> > > > > > > > > > > app {<br>> > > > > > > > > > > myapp ... "-o" @filename(f);<br>> > > > > > > > > > > }
<br>> > > > > > > > > > > }<br>> > > > > > > > > > ><br>> > > > > > > > > > > 2. The specification is correct, but the application doesn't behave.
<br>> > > > > > > > > > ><br>> > > > > > > > > > > Mihael<br>> > > > > > > > > > ><br>> > > > > > > > > > > On Fri, 2007-09-07 at 12:35 -0500, Jing Tie wrote:
<br>> > > > > > > > > > > > Hi,<br>> > > > > > > > > > > ><br>> > > > > > > > > > > > I tried jobmanger-fork instead of jobmanager-condor on
<a href="http://osg.hpcc.nd.edu">osg.hpcc.nd.edu</a> site:<br>> > > > > > > > > > > > <recall the site used to have the exception - kickstart executable<br>> > > > > > > > > > > > (101-FBchannel18_cwt-
avgResults.Rdata) not found><br>> > > > > > > > > > > ><br>> > > > > > > > > > > > jobmanager-fork:<br>> > > > > > > > > > > > ------------------------
<br>> > > > > > > > > > > > Application exception: The following output files were not created by<br>> > > > > > > > > > > > the application: /dscratch/osg/app/osg/jtie/SIDGrid/wavelet.sh
<br>> > > > > > > > > > > ><br>> > > > > > > > > > > > globus-job-run <a href="http://osg.hpcc.nd.edu/jobmanager">osg.hpcc.nd.edu/jobmanager</a> /bin/ls -al
<br>> > > > > > > > > > > > /dscratch/osg/data/osg/jtie/sid-wf1-2g48a936yixu1/cwtsmall-0bhnnvgi<br>> > > > > > > > > > > > lrwxrwxrwx 1 osg osgusers 93 Sep 7 12:42
<br>> > > > > > > > > > > > 101-FBchannel10_cwt-avgResults.Rdata -><br>> > > > > > > > > > > > /dscratch/osg/data/osg/jtie/sid-wf1-2g48a936yixu1/shared/101-FBchannel10_cwt-
avgResults.Rdata<br>> > > > > > > > > > > > ... (total 28 links, the same number as the number of the expected output files)<br>> > > > > > > > > > > > drwxr-xr-x 2 osg osgusers 4096 Sep 7 12:42 101_FB-
epochs.Rdata<br>> > > > > > > > > > > > drwxr-xr-x 3 osg osgusers 4096 Sep 7 12:42 scripts<br>> > > > > > > > > > > > -rw-r--r-- 1 osg osgusers 58 Sep 7 12:42
stderr.txt<br>> > > > > > > > > > > ><br>> > > > > > > > > > > > globus-job-run <a href="http://osg.hpcc.nd.edu/jobmanager">osg.hpcc.nd.edu/jobmanager
</a> /bin/ls -al<br>> > > > > > > > > > > > /dscratch/osg/data/osg/jtie/sid-wf1-2g48a936yixu1/shared<br>> > > > > > > > > > > > -rw-r--r-- 1 osg osgusers 4109752 Sep 7 12:41 101_FB-
epochs.Rdata<br>> > > > > > > > > > > > drwxr-xr-x 2 osg osgusers 4096 Sep 7 12:41 scripts<br>> > > > > > > > > > > > -rw-r--r-- 1 osg osgusers 571 Sep 7 12:41
seq.sh<br>> > > > > > > > > > > > -rw-r--r-- 1 osg osgusers 3278 Sep 7 12:41 wrapper.sh<br>> > > > > > > > > > > ><br>> > > > > > > > > > > > empty kickstart directory
<br>> > > > > > > > > > > ><br>> > > > > > > > > > > > globus-job-run <a href="http://osg.hpcc.nd.edu/jobmanager">osg.hpcc.nd.edu/jobmanager</a> /bin/cat
<br>> > > > > > > > > > > > /dscratch/osg/data/osg/jtie/sid-wf1-2g48a936yixu1/status/cwtsmall-0bhnnvgi-error<br>> > > > > > > > > > > > The following output files were not created by the application:
<br>> > > > > > > > > > > > /dscratch/osg/app/osg/jtie/SIDGrid/wavelet.sh<br>> > > > > > > > > > > ><br>> > > > > > > > > > > >
<br>> > > > > > > > > > > > jobmanager-condor:<br>> > > > > > > > > > > > -------------------------------<br>> > > > > > > > > > > > Application exception: The following output files were not created by
<br>> > > > > > > > > > > > the application: 101-FBchannel20_cwt-avgResults.Rdata<br>> > > > > > > > > > > ><br>> > > > > > > > > > > > globus-job-run
<a href="http://osg.hpcc.nd.edu/jobmanager">osg.hpcc.nd.edu/jobmanager</a> /bin/ls -al<br>> > > > > > > > > > > > /dscratch/osg/data/osg/jtie/sid-wf1-3my5pn01t3ov0/cwtsmall-cpteovgi<br>
> > > > > > > > > > > > lrwxrwxrwx 1 osg osgusers 76 Sep 7 13:01 101_FB-epochs.Rdata -><br>> > > > > > > > > > > > /dscratch/osg/data/osg/jtie/sid-wf1-3my5pn01t3ov0/shared/101_FB-
epochs.Rdata<br>> > > > > > > > > > > > drwxr-xr-x 3 osg osgusers 4096 Sep 7 13:01 scripts<br>> > > > > > > > > > > > -rw-r--r-- 1 osg osgusers 70 Sep 7 13:01
stderr.txt<br>> > > > > > > > > > > ><br>> > > > > > > > > > > > globus-job-run <a href="http://osg.hpcc.nd.edu/jobmanager">osg.hpcc.nd.edu/jobmanager
</a> /bin/ls -al<br>> > > > > > > > > > > > /dscratch/osg/data/osg/jtie/sid-wf1-3my5pn01t3ov0/shared<br>> > > > > > > > > > > > -rw-r--r-- 1 osg osgusers 4109752 Sep 7 13:00 101_FB-
epochs.Rdata<br>> > > > > > > > > > > > drwxr-xr-x 2 osg osgusers 4096 Sep 7 13:00 scripts<br>> > > > > > > > > > > > -rw-r--r-- 1 osg osgusers 571 Sep 7 13:00
seq.sh<br>> > > > > > > > > > > > -rw-r--r-- 1 osg osgusers 3278 Sep 7 13:00 wrapper.sh<br>> > > > > > > > > > > ><br>> > > > > > > > > > > > I think the descriptions of exception are all right now. The
<br>> > > > > > > > > > > > difference between fork and condor was that fork created the output<br>> > > > > > > > > > > > links to the shared directory, but condor didn't. But the essential
<br>> > > > > > > > > > > > problem is the output files not being created. I will do more<br>> > > > > > > > > > > > experiments to see whether the problem of file system or application.
<br>> > > > > > > > > > > ><br>> > > > > > > > > > > > Thanks,<br>> > > > > > > > > > > > Jing<br>> > > > > > > > > > > > _______________________________________________
<br>> > > > > > > > > > > > Swift-user mailing list<br>> > > > > > > > > > > > <a href="mailto:Swift-user@ci.uchicago.edu">Swift-user@ci.uchicago.edu
</a><br>> > > > > > > > > > > > <a href="http://mail.ci.uchicago.edu/mailman/listinfo/swift-user">http://mail.ci.uchicago.edu/mailman/listinfo/swift-user</a><br>> > > > > > > > > > > >
<br>> > > > > > > > > > ><br>> > > > > > > > > > ><br>> > > > > > > > > ><br>> > > > > > > > ><br>
> > > > > > > > > _______________________________________________<br>> > > > > > > > > Swift-user mailing list<br>> > > > > > > > > <a href="mailto:Swift-user@ci.uchicago.edu">
Swift-user@ci.uchicago.edu</a><br>> > > > > > > > > <a href="http://mail.ci.uchicago.edu/mailman/listinfo/swift-user">http://mail.ci.uchicago.edu/mailman/listinfo/swift-user</a><br>> > > > > > > > >
<br>> > > > > > > ><br>> > > > > > > ><br>> > > > > > ><br>> > > > > ><br>> > > > > ><br>> > > ><br>> > > > _______________________________________________
<br>> > > > Swift-user mailing list<br>> > > > <a href="mailto:Swift-user@ci.uchicago.edu">Swift-user@ci.uchicago.edu</a><br>> > > > <a href="http://mail.ci.uchicago.edu/mailman/listinfo/swift-user">
http://mail.ci.uchicago.edu/mailman/listinfo/swift-user</a><br>> > > ><br>> > ><br>> > ><br>> <br>> <br>