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clithero
Junior Member
37 Posts |
 Posted - Nov 15 2007 : 10:29:11 AM
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Some of my scripts are not working and the bugs are eluding me. Is there some reason not all of my scripts are outputting log files?
Thanks,
John |
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deshmukh
BIAC Alum
40 Posts |
Posted - Nov 15 2007 : 10:49:45 AM
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Are you having problems with multiple jobs using the same script i.e. some of the jobs using the script run ok but others fail or are these different scripts ?
You might want to do a basic syntax check on scripts by running
sh -n script
If the script passes that test without errors, then check to see if all the data is in the expected location. This tends to be the most common issue.
The job level log files are generated on job completion. If the job dies due to command errors (usually generated by incorrect paths) then these files are never generated. You can however debug scripts by adding your own debug messages in the "USER SCRIPT" section to a specific file in your Experiment folder. For eg. here is the most common debug message,
echo "GOT HERE" >> $EXPERIMENT/Analysis/Logs/debug.txt
You can always add your own tags to messages so you can identify which job generated a particular message eg:
echo " $EXAM_NUMBER : Running feat" >> $EXPERIMENT/Analysis/Logs/debug.txt
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clithero
Junior Member
37 Posts |
Posted - Nov 15 2007 : 11:37:00 AM
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Thanks, I will use that check.
However, it appears that the cluster may not be accepting new jobs. Multiple people have tried running scipts that worked fine before, but now are not running. Node 7 in particular. The jobs seem to run for about 5 minutes and then quit without error. The scripts themselves are (as far as I can tell) bug free. |
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deshmukh
BIAC Alum
40 Posts |
Posted - Nov 15 2007 : 11:55:58 AM
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| I was able to submit a job to the cluster without problems so the cluster is accepting jobs. The node7 problem was related to experiment access and is fixed now. |
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wang
BIAC Alum
USA
57 Posts |
Posted - Nov 28 2007 : 5:38:41 PM
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Does anyone have problem with running scripts in the Cluster now? A script that worked previously does not work now. Here is the error message for the Log file:
Tcl_InitNotifier: unable to start notifier thread
Have we already upgraged fsl to 4.0.2? Thanks. |
lihong |
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Carpenter
New Member
16 Posts |
Posted - Nov 28 2007 : 5:49:31 PM
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| I just got the same error... |
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josh.bizzell
BIAC Staff
USA
118 Posts |
Posted - Nov 29 2007 : 09:55:28 AM
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We did not update FSL to 4.0.2 on the cluster just yet; we're waiting to make sure it is completely bug-free before doing that.
This error seems to have been caused by a change in the configuration we made to the grid engine late yesterday. We've reverted back to the original setting and now it seems to work.
-Josh |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Jan 04 2008 : 3:50:18 PM
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I am trying to get my first cluster script running. I have run sh -n script.sh on it and do not get any error messages.
I've also inserted the echo "GOT HERE" command as the first line in USER SCRIPT, but the job never gets to this portion of the script.
Also, the job keeps exiting with exit code "1", which means(?) that I'm misusing a built-in shell command.
Any help appreciated.
Thanks,
Dharol |
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dvsmith
Advanced Member
USA
218 Posts |
Posted - Jan 04 2008 : 4:38:03 PM
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I was having exit code "1" pop up when node6 wasn't working earlier today, but I thought that was fixed. If your jobs are going to node6 (should be able tell from the email) and you're not getting a log file, try a different node.
qsub -l hostname=node7 -v EXPERIMENT=whateverexp whateverscript.sh |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Jan 07 2008 : 12:29:55 PM
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FYI, the problem appears to have been that the flag -v is required to run any script.
dharol |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jan 07 2008 : 12:44:09 PM
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Just to clarify Dharol's observation. It's not only that -v is necessary for scripts that access data on BIAC file servers -- it's that if you are specifying a variable to qsub (like EXPERIMENT=Dummy.01), you do that on the command line by using -v, so
in:
qsub -v EXPERIMENT=Dummy.01 ...
-v must be right before EXPERIMENT=Dummy.01 |
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cluster logs?
