[Swift-user] Montage+Swift+Coasters
Emalayan Vairavanathan
svemalayan at yahoo.com
Mon Jan 23 13:25:56 CST 2012
Jon,
Please find the detail below and let me know if you have any questions about my setup.
Thank you
Emalayan
==========================================================
site.xml
<config>
<pool handle="localhost">
<execution provider="coaster-persistent" url="http://localhost:1984" jobmanager="local:local"/>
<profile namespace="globus" key="workerManager">passive</profile>
<profile namespace="globus" key="workersPerNode">4</profile>
<profile namespace="globus" key="maxTime">100000</profile>
<profile namespace="globus" key="lowOverAllocation">100</profile>
<profile namespace="globus" key="highOverAllocation">100</profile>
<profile namespace="globus" key="slots">100</profile>
<profile namespace="globus" key="nodeGranularity">1</profile>
<profile namespace="globus" key="maxNodes">10</profile>
<profile namespace="karajan" key="jobThrottle">25.00</profile>
<profile namespace="karajan" key="initialScore">10000</profile>
<profile namespace="swift" key="stagingMethod">proxy</profile>
<filesystem provider="local"/>
<workdirectory>/tmp/swift.workdir</workdirectory>
</pool>
</config>
=======================================================
tc
localhost sh /bin/sh null null null
localhost cat /bin/cat null null null
localhost echo /bin/echo null null null
localhost do_merge /home/emalayan/App/forEmalayan/app/modmerge null null null
localhost mProjExec /home/emalayan/App/Montage_v3.3/bin/mProjExec null null null
localhost mImgtbl /home/emalayan/App/Montage_v3.3/bin/mImgtbl null null null
localhost mAdd /home/emalayan/App/Montage_v3.3/bin/mAdd null null null
localhost mOverlaps /home/emalayan/App/Montage_v3.3/bin/mOverlaps null null null
localhost mJPEG /home/emalayan/App/Montage_v3.3/bin/mJPEG null null null
localhost mDiffExec_wrap /home/emalayan/App/Montage_v3.3/bin/mDiffExec null null null
localhost mFitExec /home/emalayan/App/Montage_v3.3/bin/mFitExec null null null
localhost mBgModel /home/emalayan/App/Montage_v3.3/bin/mBgModel null null null
localhost mBgExec /home/emalayan/App/Montage_v3.3/bin/mBgExec null null null
localhost mConcatFit /home/emalayan/App/Montage_v3.3/bin/mConcatFit null null nul
localhost Background_list /home/emalayan/App/montage-swift/SwiftMontage/apps/Background_list.py null null null
localhost create_status_table /home/emalayan/App/montage-swift/SwiftMontage/apps/create_status_table.py null null null
localhost mProjectPP_wrap /home/emalayan/App/montage-swift/SwiftMontage/apps/mProjectPP_wrap.py null null null
localhost mProject_wrap /home/emalayan/App/montage-swift/SwiftMontage/apps/mProject_wrap.py null null null
localhost mBackground_wrap /home/emalayan/App/montage-swift/SwiftMontage/apps/mBackground_wrap.py null null null
localhost mDiffFit_wrap /home/emalayan/App/montage-swift/SwiftMontage/apps/mDiffFit_wrap.py null null null
=================================================================
cf
wrapperlog.always.transfer=true
sitedir.keep=true
execution.retries=1
lazy.errors=true
status.mode=provider
use.provider.staging=true
provider.staging.pin.swiftfiles=false
foreach.max.threads=100
provenance.log=false
===================================================================
________________________________
From: Jonathan Monette <jonmon at mcs.anl.gov>
To: Ketan Maheshwari <ketancmaheshwari at gmail.com>
Cc: Emalayan Vairavanathan <svemalayan at yahoo.com>; swift user <swift-user at ci.uchicago.edu>
Sent: Monday, 23 January 2012 11:08 AM
Subject: Re: [Swift-user] Montage+Swift+Coasters
Emalayan,
So I have ran the scripts with some of my own test cases and do not see it failing. Could you provide your config files? Please provide the tc, sites, and config file(if you use a config file).
On Jan 20, 2012, at 9:39 AM, Ketan Maheshwari wrote:
Emalayan,
>
>
>I would check all the mappers and the resulting paths in the Swift source.
>
>
>Also try running the failed job something like this:
>
>
>cd <swift.workdir>/SwiftMontage-20120119-1749-rjshh1r9/jobs/b/mConcatFit-b1sa4vlk
>
>
>mConcatFit _concurrent/status_tbl-7a8340c2-045d-4039-a77c-00429b78d9c9-5 fits.tbl stat_dir
>
>
>error 520 indicates workers are not able to reach the data.
>
>
>Also check if swift.workdir is writable on the site by the worker nodes.
>
>
>On Thu, Jan 19, 2012 at 7:55 PM, Emalayan Vairavanathan <svemalayan at yahoo.com> wrote:
>
>Hi Ketan,
>>
>>
>>This was with swift-0.92.1.Now I have downloaded the latest swift 0.93 and getting totally different error messages with swift 0.93. I can ask Jon about these messages. (These scripts was working well with only Swift)
>>
>>
>>
>>Please let me know if you have any idea.
>>
>>
>>
>>Regards
>>Emalayan
>>
>>
>>
>>===============================================================================================
>>
>>Swift 0.93 swift-r5501 cog-r3350
>>
>>RunID: 20120119-1749-rjshh1r9
>> (input): found 10 files
>>Progress: time: Thu, 19 Jan 2012 17:49:20 -0800
>>Find: http://localhost:1984
>>Find: keepalive(120), reconnect - http://localhost:1984
>>Progress: time: Thu, 19 Jan 2012 17:49:22 -0800 Stage in:1 Submitted:9
>>Progress: time: Thu, 19 Jan 2012 17:49:25 -0800 Active:9 Stage out:1
>>Progress: time: Thu, 19 Jan 2012 17:49:26 -0800 Stage out:3 Finished successfully:7
>>Progress: time: Thu, 19 Jan 2012 17:49:28 -0800 Active:1 Finished successfully:10
>>Progress: time: Thu, 19 Jan 2012 17:49:29 -0800 Stage in:1 Submitting:11 Submitted:6 Finished successfully:12
>>Progress: time: Thu, 19 Jan 2012 17:49:30 -0800 Stage in:4 Submitted:1 Active:6 Stage out:2 Finished successfully:17
>>Progress: time: Thu, 19 Jan 2012 17:49:31 -0800 Active:1 Finished successfully:30
>>Exception in mConcatFit:
>>Arguments: [_concurrent/status_tbl-7a8340c2-045d-4039-a77c-00429b78d9c9-5, fits.tbl, stat_dir]
>>Host: localhost
>>Directory: SwiftMontage-20120119-1749-rjshh1r9/jobs/b/mConcatFit-b1sa4vlk
>>- - -
>>
>>Caused by: null
>>Caused by: org.globus.cog.abstraction.impl.common.execution.JobException: Job failed with an exit code of 520
>>Execution failed:
>> back_list:Table = org.griphyn.vdl.mapping.DataDependentException - Closed not derived due to errors in data dependencies
>>
>>
>>
>>
>>________________________________
>> From: Ketan Maheshwari <ketancmaheshwari at gmail.com>
>>To: Emalayan Vairavanathan <svemalayan at yahoo.com>
>>Cc: swift user <swift-user at ci.uchicago.edu>
>>Sent: Thursday, 19 January 2012 4:49 PM
>>Subject: Re: [Swift-user] Montage+Swift+Coasters
>>
>>
>>
>>Emalayan,
>>
>>
>>From your symptoms, it seems you are facing the same issue as I've been. Could you tell more about the amount of data that needs to be staged to run the Montage stages during which these warnings turn up? How much time elapses since the start of your workflow after which you see these messages?
>>
>>Also, what version of Swift is this?
>>
>>
>>Regards,
>>Ketan
>>
>>
>>On Thu, Jan 19, 2012 at 5:51 PM, Emalayan Vairavanathan <svemalayan at yahoo.com> wrote:
>>
>>Dear All,
>>>
>>>
>>>I have a problem in running Montage with Coasters (in our local cluster - no batch schedulers). After few stages the swift run-time continuously prints the warnings below. Any ideas ? Should I increase the heartbeat count ?
>>>
>>>
>>>
>>>Everything works fine when I try to run the same montage-scripts with swift on a single machine.
>>>
>>>
>>>
>>>Thank you
>>>Emalayan
>>>
>>>
>>>
>>>
>>>
>>>2012-01-19 15:38:09,207-0800 WARN Command Command(119, HEARTBEAT): handling reply timeout; sendReqTime=120119-153609.206, sendTime=120119-153609.206,
now=120119-153809.207
>>>2012-01-19 15:38:09,207-0800 INFO Command Command(119, HEARTBEAT): re-sending
>>>2012-01-19 15:38:09,209-0800 WARN Command Command(119, HEARTBEAT)fault was: Reply timeout
>>>org.globus.cog.karajan.workflow.service.ReplyTimeoutException
>>> at org.globus.cog.karajan.workflow.service.commands.Command.handleReplyTimeout(Command.java:288)
>>> at org.globus.cog.karajan.workflow.service.commands.Command$Timeout.run(Command.java:293)
>>> at java.util.TimerThread.mainLoop(Timer.java:534)
>>> at java.util.TimerThread.run(Timer.java:484)
>>>_______________________________________________
>>>Swift-user mailing list
>>>Swift-user at ci.uchicago.edu
>>>https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>>>
>>
>>
>>
>>--
>>Ketan
>>
>>
>>
>>
>>
>
>
>
>--
>Ketan
>
>
>
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