[Swift-user] follow up of kickstart executable not found problem

[Mihael Hategan]

Can you post the workflow?

On Fri, 2007-09-07 at 21:56 -0500, Jing Tie wrote:
> Thanks!
> 
> I checked the procedure, and found that the filenames of the output
> files of "myapp" are the same as "File f". So the first option should
> not be the problem.
> 
> Then I tried a very simple swift script that doesn't need R:
> app function: add some lines to the input file to generate the output file
> input file name: simpleFile.txt
> output file name: simpleFile.output
> application script location: $OSG_APP/osg/jtie/duplicate.sh
> jobmanager: jobmanager-fork
> 
> duplicate failed
> The following errors have occurred:
> 1. Application "duplicate" failed (Failed to link input file
> /dscratch/osg/app/osg/jtie/duplicate.sh)
>         Arguments: "simpleFile.txt"
>         Host: NWICG_NotreDame
>         Directory: simple-wf-xgh9e9q1z0af2/duplicate-it7hyvgi
>         STDERR:
>         STDOUT:
> 
> after execution, 3 empty directories (not files, and also weird name)
> were generated:
> duplicate-gt7hyvgi-simpleFile.output
> duplicate-ht7hyvgi-simpleFile.output
> duplicate-it7hyvgi-simpleFile.output
> 
> wrapper.log:
> DIR=duplicate-gt7hyvgi
> STDOUT=simpleFile.output
> STDERR=stderr.txt
> DIRS=simpleFile.output
> LINKS=/dscratch/osg/app/osg/jtie/duplicate.sh
> OUTS=simpleFile.txt
> ln: creating symbolic link
> `duplicate-gt7hyvgi//dscratch/osg/app/osg/jtie/duplicate.sh' to
> `/dscratch/osg/data/osg/jtie/simple-wf-xgh9e9q1z0af2/shared//dscratch/osg/app/osg/jtie/duplicate.sh':
> No such file or directory
> 
> under dir /dscratch/osg/data/osg/jtie/simple-wf-xgh9e9q1z0af2/shared:
> seq.sh, simpleFile.txt, wrapper.sh
> under dir /dscratch/osg/data/osg/jtie/simple-wf-xgh9e9q1z0af2/duplicate-it7hyvgi:
> one directory - simpleFile.output
> /dscratch/osg/data/osg/jtie/simple-wf-xgh9e9q1z0af2/duplicate-it7hyvgi/simpleFile.output:
> empty
> 
> I think the swift program is right, since I run it successfully using
> localhost duplicate.sh.
> 
> 
> Many thanks,
> Jing
> 
> 
> On 9/7/07, Mihael Hategan <hategan at mcs.anl.gov> wrote:
> > So when the output files are not created, there can be two reasons:
> > 1. The specification of what files should be created is broken. This is,
> > at this time, done by looking at the filenames of the return values from
> > the atomic procedure. Normally one passes those file names to the
> > application as output file parameters. Example:
> >
> > (File f) proc(...) {
> >   app {
> >     myapp ... "-o" @filename(f);
> >   }
> > }
> >
> > 2. The specification is correct, but the application doesn't behave.
> >
> > Mihael
> >
> > On Fri, 2007-09-07 at 12:35 -0500, Jing Tie wrote:
> > > Hi,
> > >
> > > I tried jobmanger-fork instead of jobmanager-condor on osg.hpcc.nd.edu site:
> > > <recall the site used to have the exception - kickstart executable
> > > (101-FBchannel18_cwt-avgResults.Rdata) not found>
> > >
> > > jobmanager-fork:
> > > ------------------------
> > > Application exception: The following output files were not created by
> > > the application: /dscratch/osg/app/osg/jtie/SIDGrid/wavelet.sh
> > >
> > > globus-job-run osg.hpcc.nd.edu/jobmanager /bin/ls -al
> > > /dscratch/osg/data/osg/jtie/sid-wf1-2g48a936yixu1/cwtsmall-0bhnnvgi
> > > lrwxrwxrwx  1 osg osgusers   93 Sep  7 12:42
> > > 101-FBchannel10_cwt-avgResults.Rdata ->
> > > /dscratch/osg/data/osg/jtie/sid-wf1-2g48a936yixu1/shared/101-FBchannel10_cwt-avgResults.Rdata
> > > ... (total 28 links, the same number as the number of the expected output files)
> > > drwxr-xr-x  2 osg osgusers 4096 Sep  7 12:42 101_FB-epochs.Rdata
> > > drwxr-xr-x  3 osg osgusers 4096 Sep  7 12:42 scripts
> > > -rw-r--r--  1 osg osgusers   58 Sep  7 12:42 stderr.txt
> > >
> > > globus-job-run osg.hpcc.nd.edu/jobmanager /bin/ls -al
> > > /dscratch/osg/data/osg/jtie/sid-wf1-2g48a936yixu1/shared
> > > -rw-r--r--  1 osg osgusers 4109752 Sep  7 12:41 101_FB-epochs.Rdata
> > > drwxr-xr-x  2 osg osgusers    4096 Sep  7 12:41 scripts
> > > -rw-r--r--  1 osg osgusers     571 Sep  7 12:41 seq.sh
> > > -rw-r--r--  1 osg osgusers    3278 Sep  7 12:41 wrapper.sh
> > >
> > > empty kickstart directory
> > >
> > > globus-job-run osg.hpcc.nd.edu/jobmanager /bin/cat
> > > /dscratch/osg/data/osg/jtie/sid-wf1-2g48a936yixu1/status/cwtsmall-0bhnnvgi-error
> > > The following output files were not created by the application:
> > > /dscratch/osg/app/osg/jtie/SIDGrid/wavelet.sh
> > >
> > >
> > > jobmanager-condor:
> > > -------------------------------
> > > Application exception: The following output files were not created by
> > > the application: 101-FBchannel20_cwt-avgResults.Rdata
> > >
> > > globus-job-run osg.hpcc.nd.edu/jobmanager /bin/ls -al
> > > /dscratch/osg/data/osg/jtie/sid-wf1-3my5pn01t3ov0/cwtsmall-cpteovgi
> > > lrwxrwxrwx  1 osg osgusers   76 Sep  7 13:01 101_FB-epochs.Rdata ->
> > > /dscratch/osg/data/osg/jtie/sid-wf1-3my5pn01t3ov0/shared/101_FB-epochs.Rdata
> > > drwxr-xr-x  3 osg osgusers 4096 Sep  7 13:01 scripts
> > > -rw-r--r--  1 osg osgusers   70 Sep  7 13:01 stderr.txt
> > >
> > > globus-job-run osg.hpcc.nd.edu/jobmanager /bin/ls -al
> > > /dscratch/osg/data/osg/jtie/sid-wf1-3my5pn01t3ov0/shared
> > > -rw-r--r--  1 osg osgusers 4109752 Sep  7 13:00 101_FB-epochs.Rdata
> > > drwxr-xr-x  2 osg osgusers    4096 Sep  7 13:00 scripts
> > > -rw-r--r--  1 osg osgusers     571 Sep  7 13:00 seq.sh
> > > -rw-r--r--  1 osg osgusers    3278 Sep  7 13:00 wrapper.sh
> > >
> > > I think the descriptions of exception are all right now. The
> > > difference between fork and condor was that fork created the output
> > > links to the shared directory, but condor didn't. But the essential
> > > problem is the output files not being created. I will do more
> > > experiments to see whether the problem of file system or application.
> > >
> > > Thanks,
> > > Jing
> > > _______________________________________________
> > > Swift-user mailing list
> > > Swift-user at ci.uchicago.edu
> > > http://mail.ci.uchicago.edu/mailman/listinfo/swift-user
> > >
> >
> >
>