[Swift-devel] RE: [Swift-user] Execution error
Glen Hocky
hockyg at uchicago.edu
Thu Apr 30 16:13:34 CDT 2009
I have the identical response on ranger. It started yesterday evening.
Possibly a problem that the TACC folks need to fix?
Glen
Yue, Chen - BMD wrote:
> Hi Michael,
>
> Thank you for the advices. I tested ranger with 1 job and new
> specifications of maxwalltime. It shows the following error message. I
> don't know if there is other problem with my setup. Thank you!
>
> /////////////////////////////////////////////////
> [yuechen at communicado PTMap2]$ swift PTMap2-unmod.swift -sites.file
> sites.xml -tc.file tc.data
> Swift 0.9rc2 swift-r2860 cog-r2388
> RunID: 20090430-1559-2vi6x811
> Progress:
> Progress: Stage in:1
> Progress: Submitting:1
> Progress: Submitting:1
> Progress: Submitted:1
> Progress: Active:1
> Failed to transfer wrapper log from
> PTMap2-unmod-20090430-1559-2vi6x811/info/i on ranger
> Progress: Active:1
> Failed to transfer wrapper log from
> PTMap2-unmod-20090430-1559-2vi6x811/info/k on ranger
> Progress: Stage in:1
> Progress: Active:1
> Failed to transfer wrapper log from
> PTMap2-unmod-20090430-1559-2vi6x811/info/m on ranger
> Progress: Failed:1
> Execution failed:
> Exception in PTMap2:
> Arguments: [e04.mzXML, ./seqs-ecolik12/fasta01, inputs-unmod.txt,
> parameters.txt]
> Host: ranger
> Directory: PTMap2-unmod-20090430-1559-2vi6x811/jobs/m/PTMap2-mbe6m5aj
> stderr.txt:
> stdout.txt:
> ----
> Caused by:
> Failed to start worker:
> null
> null
> org.globus.gram.GramException: The job manager detected an invalid
> script response
> at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.statusChanged(JobSubmissionTaskHandler.java:530)
> at org.globus.gram.GramJob.setStatus(GramJob.java:184)
> at
> org.globus.gram.GramCallbackHandler.run(CallbackHandler.java:176)
> at java.lang.Thread.run(Thread.java:619)
> Cleaning up...
> Shutting down service at https://129.114.50.163:45562
> <https://129.114.50.163:45562>
> Got channel MetaChannel: 20903429 -> GSSSChannel-null(1)
> - Done
> [yuechen at communicado PTMap2]$
> ///////////////////////////////////////////////////////////
>
> Chen, Yue
>
>
> *From:* Michael Wilde [mailto:wilde at mcs.anl.gov]
> *Sent:* Thu 4/30/2009 3:02 PM
> *To:* Yue, Chen - BMD; swift-devel
> *Subject:* Re: [Swift-user] Execution error
>
> Back on list here (I only went off-list to discuss accounts, etc)
>
> The problem in the run below is this:
>
> 2009-04-30 14:29:41,265-0500 DEBUG vdl:execute2 APPLICATION_EXCEPTION
> jobid=PTMap2-abeii5aj - Application exception: Job cannot be run with
> the given max walltime worker constraint (task: 3000, \
> maxwalltime: 2400s)
>
> You have this on the ptmap app in your tc.data:
>
> globus::maxwalltime=50
>
> But you only gave coasters 40 mins per coaster worker. So its
> complaining that it cant run a 50 minute job in a 40 minute (max)
> coaster worker. ;)
>
> I mentioned in a prior mail that you need to set the two time vals in
> your sites.xml entry; thats what you need to do next, now.
>
> change the coaster time in your sites.xml to:
> key="coasterWorkerMaxwalltime">00:51:00</profile>
>
> If you have more info on the variability of your ptmap run times, send
> that to the list, and we can discuss how to handle.
>
>
> (NOTE: doing grp -i of the log for "except" or scanning for "except"
> with an editor will often locate the first "exception" that your job
> encountered. Thats how I found the error above).
>
> Also, Yue, for testing new sites, or for validating that old sites still
> work, you should create the smallest possible ptmap workflow - 1 job if
> that is possible - and verify that this works. Then say 10 jobs to make
> sure scheduling etc is sane. Then, send in your huge jobs.
>
> With only 1 job, its easier to spot the errors in the log file.
>
> - Mike
>
>
> On 4/30/09 2:34 PM, Yue, Chen - BMD wrote:
> > Hi Michael,
> >
> > I run into the same messages again when I use Ranger:
> >
> > Progress: Selecting site:146 Stage in:25 Submitting:15 Submitted:821
> > Failed but can retry:16
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/q on ranger
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/l on ranger
> > Progress: Selecting site:146 Stage in:3 Submitting:1 Submitted:857
> > Failed but can retry:16
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/v on ranger
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/b on ranger
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/0 on ranger
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/a on ranger
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/8 on ranger
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/7 on ranger
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/4 on ranger
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/a on ranger
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/4 on ranger
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/8 on ranger
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/7 on ranger
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/x on ranger
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/3 on ranger
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1428-v0c5di5c/info/q on ranger
> > The log for the search is at :
> > /home/yuechen/PTMap2/PTMap2-unmod-20090430-1428-v0c5di5c.log
> >
> > The sites.xml I have is:
> >
> > <pool handle="ranger">
> > <execution provider="coaster"
> > url="gatekeeper.ranger.tacc.teragrid.org"
> > jobManager="gt2:gt2:SGE"/>
> > <gridftp url="gsiftp://gridftp.ranger.tacc.teragrid.org:2811/" />
> > <profile namespace="env"
> > key="SWIFT_JOBDIR_PATH">/tmp/yuechen/jobdir</profile>
> > <profile namespace="globus" key="project">TG-CCR080022N</profile>
> > <profile namespace="globus" key="coastersPerNode">16</profile>
> > <profile namespace="globus" key="queue">development</profile>
> > <profile namespace="globus"
> > key="coasterWorkerMaxwalltime">00:40:00</profile>
> > <profile namespace="globus" key="maxwalltime">31</profile>
> > <profile namespace="karajan" key="initialScore">50</profile>
> > <profile namespace="karajan" key="jobThrottle">10</profile>
> > <workdirectory>/work/01164/yuechen/swiftwork</workdirectory>
> > </pool>
> > The tc.data I have is:
> >
> > ranger PTMap2
> > /share/home/01164/yuechen/PTMap2/PTMap2 INSTALLED
> > INTEL32::LINUX globus::maxwalltime=50
> >
> > I'm using swift 0.9 rc2
> >
> > Thank you very much for help!
> >
> > Chen, Yue
> >
> >
> >
> > ------------------------------------------------------------------------
> > *From:* Michael Wilde [mailto:wilde at mcs.anl.gov]
> > *Sent:* Thu 4/30/2009 2:05 PM
> > *To:* Yue, Chen - BMD
> > *Subject:* Re: [Swift-user] Execution error
> >
> >
> >
> > On 4/30/09 1:51 PM, Yue, Chen - BMD wrote:
> > > Hi Michael,
> > >
> > > When I tried to activate my account, I encountered the following
> error:
> > >
> > > "Sorry, this account is in an invalid state. You may not activate
> your
> > > at this time."
> > >
> > > I used the username and password from TG-CDA070002T. Should I use a
> > > different password?
> >
> > If you can already login to Ranger, then you are all set - you must have
> > done this previously.
> >
> > I thought you had *not*, because when I looked up your login on ranger
> > ("finger yuechen") it said "never logged in". But seems like that info
> > is incorrect.
> >
> > If you have ptmap compiled, seems like you are almost all set.
> >
> > Let me know if it works.
> >
> > - Mike
> >
> > > Thanks!
> > >
> > > Chen, Yue
> > >
> > >
> > >
> ------------------------------------------------------------------------
> > > *From:* Michael Wilde [mailto:wilde at mcs.anl.gov]
> > > *Sent:* Thu 4/30/2009 1:07 PM
> > > *To:* Yue, Chen - BMD
> > > *Cc:* swift user
> > > *Subject:* Re: [Swift-user] Execution error
> > >
> > > Yue, use this XML pool element to access ranger:
> > >
> > > <pool handle="ranger">
> > > <execution provider="coaster"
> > > url="gatekeeper.ranger.tacc.teragrid.org"
> > > jobManager="gt2:gt2:SGE"/>
> > > <gridftp
> url="gsiftp://gridftp.ranger.tacc.teragrid.org:2811/" />
> > > <profile namespace="env"
> > > key="SWIFT_JOBDIR_PATH">/tmp/yuechen/jobdir</profile>
> > > <profile namespace="globus"
> key="project">TG-CCR080022N</profile>
> > > <profile namespace="globus" key="coastersPerNode">16</profile>
> > > <profile namespace="globus" key="queue">development</profile>
> > > <profile namespace="globus"
> > > key="coasterWorkerMaxwalltime">00:40:00</profile>
> > > <profile namespace="globus" key="maxwalltime">31</profile>
> > > <profile namespace="karajan" key="initialScore">50</profile>
> > > <profile namespace="karajan" key="jobThrottle">10</profile>
> > > <workdirectory>/work/00306/tg455797/swiftwork</workdirectory>
> > > </pool>
> > >
> > >
> > > You will need to also do these steps:
> > >
> > > Go to this web page to enable your Ranger account:
> > >
> > > https://tas.tacc.utexas.edu/TASMigration/AccountActivation.aspx
> > >
> > > Then login to Ranger via the TeraGrid portal and put your ssh keys in
> > > place (assuming you use ssh keys, which you should)
> > >
> > > While on Ranger, do this:
> > >
> > > echo $WORK
> > > mkdir $work/swiftwork
> > >
> > > and put the full path of your $WORK/swiftwork directory in the
> > > <workdirectory> element above. (My login is tg455etc, yours is
> yuechen)
> > >
> > > Then scp your code to Ranger and compile it.
> > >
> > > Then create a tc.data entry for your ptmap app
> > >
> > > Next, set your time values in the sites.xml entry above to suitable
> > > values for Ranger. You'll need to measure times, but I think you will
> > > find Ranger about twice as fast as Mercury for CPU-bound jobs.
> > >
> > > The values above were set for one app job per coaster. I think
> you can
> > > probably do more.
> > >
> > > If you estimate a run time of 5 minutes, use:
> > >
> > > <profile namespace="globus"
> > > key="coasterWorkerMaxwalltime">00:30:00</profile>
> > > <profile namespace="globus" key="maxwalltime">5</profile>
> > >
> > > Other people on the list - please sanity check what I suggest here.
> > >
> > > - Mike
> > >
> > >
> > > On 4/30/09 12:40 PM, Michael Wilde wrote:
> > > > I just checked - TG-CDA070002T has indeed expired.
> > > >
> > > > The best for now is to move to use (only) Ranger, under this
> account:
> > > > TG-CCR080022N
> > > >
> > > > I will locate and send you a sites.xml entry in a moment.
> > > >
> > > > You need to go to a web page to activate your Ranger login.
> > > >
> > > > Best to contact me in IM and we can work this out.
> > > >
> > > > - Mike
> > > >
> > > >
> > > >
> > > > On 4/30/09 12:23 PM, Michael Wilde wrote:
> > > >> Also, what account are you running under? We may need to change
> > you to
> > > >> a new account - as the OSG Training account expires today.
> > > >> If that happend at Noon, it *might* be the problem.
> > > >>
> > > >> - Mike
> > > >>
> > > >>
> > > >> On 4/30/09 12:08 PM, Yue, Chen - BMD wrote:
> > > >>> Hi,
> > > >>>
> > > >>> I came back to re-run my application on NCSA Mercury which was
> > tested
> > > >>> successfully last week after I just set up coasters with
> swift 0.9,
> > > >>> but I got many messages like the following:
> > > >>>
> > > >>> Progress: Stage in:219 Submitting:803 Submitted:1
> > > >>> Progress: Stage in:129 Submitting:703 Submitted:190 Failed
> > but can
> > > >>> retry:1
> > > >>> Progress: Stage in:38 Submitting:425 Submitted:556 Failed
> but can
> > > >>> retry:4
> > > >>> Failed to transfer wrapper log from
> > > >>> PTMap2-unmod-20090430-1203-r19dxq10/info/h on NCSA_MERCURY
> > > >>> Failed to transfer wrapper log from
> > > >>> PTMap2-unmod-20090430-1203-r19dxq10/info/j on NCSA_MERCURY
> > > >>> Failed to transfer wrapper log from
> > > >>> PTMap2-unmod-20090430-1203-r19dxq10/info/p on NCSA_MERCURY
> > > >>> Failed to transfer wrapper log from
> > > >>> PTMap2-unmod-20090430-1203-r19dxq10/info/1 on NCSA_MERCURY
> > > >>> Failed to transfer wrapper log from
> > > >>> PTMap2-unmod-20090430-1203-r19dxq10/info/b on NCSA_MERCURY
> > > >>> Failed to transfer wrapper log from
> > > >>> PTMap2-unmod-20090430-1203-r19dxq10/info/c on NCSA_MERCURY
> > > >>> Progress: Stage in:1 Submitted:1013 Active:1 Failed but can
> > retry:8
> > > >>> Progress: Submitted:1011 Active:1 Failed but can retry:11
> > > >>> The log file for the successful run last week is ;
> > > >>> /home/yuechen/PTMap2/PTMap2-unmod-20090422-1216-4s3037gf.log
> > > >>>
> > > >>> The log file for the failed run is :
> > > >>> /home/yuechen/PTMap2/PTMap2-unmod-20090430-1151-rf2uuhb7.log
> > > >>>
> > > >>> I don't think I did anything different, so I don't know why this
> > time
> > > >>> they failed. The sites.xml for Mercury is:
> > > >>>
> > > >>> <pool handle="NCSA_MERCURY">
> > > >>> <gridftp url="gsiftp://gridftp-hg.ncsa.teragrid.org"/>
> > > >>> <execution provider="coaster"
> url="grid-hg.ncsa.teragrid.org"
> > > >>> jobManager="gt2:PBS"/>
> > > >>>
> <workdirectory>/gpfs_scratch1/yuechen/swiftwork</workdirectory>
> > > >>> <profile namespace="globus" key="queue">debug</profile>
> > > >>> </pool>
> > > >>>
> > > >>> Thank you for help!
> > > >>>
> > > >>> Chen, Yue
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
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> > > >>>
> > > >>>
> > > >>>
> > >
> ------------------------------------------------------------------------
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