[Swift-user] swift on midway: apps and modules

[David Kelly]

Hi Neil,

It could possibly be something environmental. Are the modules loaded automatically when you log in through your .bashrc? If they are not already, could you give that a try?

If that doesn't work, try editing sites.xml and try changing

<workdirectory>/scratch/local/swift</workdirectory>
to
<workdirectory>/project/joshuaelliott/narr</workdirectory>

Then try the run again and let me know when it's finished. That will just make some extra debugging information available that might better explain why it's failing.

Thanks,
David

----- Original Message -----
> From: "Neil Best" <nbest at ci.uchicago.edu>
> To: swift-user at ci.uchicago.edu
> Sent: Thursday, November 29, 2012 4:29:05 PM
> Subject: [Swift-user] swift on midway: apps and modules
> Running on Midway, it looks like there is a problem with defining apps
> that come from software modules.
> 
> [nbest at midway-login1 narr]$ pwd
> /project/joshuaelliott/narr
> [nbest at midway-login1 narr]$ runswift narr.swift
> ++ swift -config config -tc.file applist -sites.file sites.xml
> narr.swift
> Warning: Parameter grb, on line 12, shadows variable of same name on
> line 5
> Swift trunk swift-r6083 cog-r3522
> 
> RunID: 20121129-2115-mos5x5ad
> Progress: time: Thu, 29 Nov 2012 21:15:40 +0000
> Progress: time: Thu, 29 Nov 2012 21:15:57 +0000 Initializing:6
> Progress: time: Thu, 29 Nov 2012 21:15:58 +0000 Selecting site:1022
> Initializing site shared directory:1 Stage in:1
> Progress: time: Thu, 29 Nov 2012 21:15:59 +0000 Selecting site:623
> Stage in:399 Submitting:2
> Progress: time: Thu, 29 Nov 2012 21:16:00 +0000 Selecting site:623
> Stage in:388 Submitted:13
> Progress: time: Thu, 29 Nov 2012 21:16:01 +0000 Selecting site:623
> Stage in:371 Submitting:1 Submitted:29
> Progress: time: Thu, 29 Nov 2012 21:16:02 +0000 Selecting site:623
> Stage in:359 Submitting:1 Failed but can retry:41
> Progress: time: Thu, 29 Nov 2012 21:16:03 +0000 Selecting site:623
> Stage in:341 Active:1 Failed but can retry:59
> Progress: time: Thu, 29 Nov 2012 21:16:04 +0000 Selecting site:623
> Stage in:322 Submitting:1 Failed but can retry:78
> Progress: time: Thu, 29 Nov 2012 21:16:05 +0000 Selecting site:623
> Stage in:302 Active:1 Failed but can retry:98
> . . .
> Progress: time: Thu, 29 Nov 2012 21:18:16 +0000 Selecting site:623
> Stage in:14 Submitting:1 Failed but can retry:386
> Progress: time: Thu, 29 Nov 2012 21:18:17 +0000 Selecting site:623
> Stage in:10 Submitting:1 Failed but can retry:390
> Progress: time: Thu, 29 Nov 2012 21:18:19 +0000 Selecting site:623
> Stage in:5 Submitting:1 Failed but can retry:395
> Progress: time: Thu, 29 Nov 2012 21:18:20 +0000 Selecting site:622
> Stage in:2 Failed:3 Failed but can retry:397
> Execution failed:
> Exception in cnvgrib:
> Arguments: [-g12, -nv,
> data/grb/197901/narr-a_221_19790116_0600_000.grb,
> data/grb2/197901/narr-a_221_19790116_0600_000.grb2]
> Host: cluster
> Directory: narr-20121129-2115-mos5x5ad/jobs/r/cnvgrib-ricszn1l
> Caused by:
> Job failed with and exit code of 127
> org.globus.cog.abstraction.impl.common.execution.JobException: Job
> failed with and exit code of 127 (exit code: 127)
> at
> org.globus.cog.abstraction.coaster.service.local.JobStatusHandler.requestComplete(JobStatusHandler.java:38)
> at
> org.globus.cog.karajan.workflow.service.handlers.RequestHandler.receiveCompleted(RequestHandler.java:90)
> at
> org.globus.cog.karajan.workflow.service.channels.AbstractKarajanChannel.handleRequest(AbstractKarajanChannel.java:502)
> at
> org.globus.cog.karajan.workflow.service.channels.AbstractStreamKarajanChannel.stepNIO(AbstractStreamKarajanChannel.java:238)
> at
> org.globus.cog.karajan.workflow.service.channels.NIOMultiplexer.loop(NIOMultiplexer.java:97)
> at
> org.globus.cog.karajan.workflow.service.channels.NIOMultiplexer.run(NIOMultiplexer.java:56)
> (exit code: 127)
> cnvgrib, narr.swift, line 17
> [nbest at midway-login1 narr]$ cat applist
> cluster cnvgrib /software/cnvgrib-1.4-el6-x86_64/bin/cnvgrib null null
> null
> cluster wgrib2 /software/wgrib2-0.1-el6-x86_64/bin/wgrib2 null null
> null
> 
> My app definition looks like this:
> 
> app (file grb2) cnvgrib (file grb) {
> cnvgrib "-g12" "-nv" @grb @grb2;
> }
> 
> I don't see the directory referenced in the "Exception" stanza. Where
> should that be?
> 
> Does this have anything to do with the fact that I am calling an
> executable from Modules, and therefore the Swift workers have bad
> environments?
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