[Swift-devel] ssh:pbs to beagle

Mihael Hategan hategan at mcs.anl.gov
Thu Apr 28 14:26:34 CDT 2011 

That EOFException doesn't make much sense.

On beagle you should have something called coaster.log in
~/.globus/coasters.

Can post a link to that?

Mihael

On Thu, 2011-04-28 at 14:21 -0500, Ketan Maheshwari wrote:
> On Apr 28, 2011, at 2:17 PM, Mihael Hategan wrote:
> 
> > What does your sites file look like?
> 
> ** For beagle **
> 
> <config>
>     <!--<pool handle="pbs">-->
>   <pool handle="beagle-remote-pbs-coasters-ssh">
>     <execution provider="coaster" url="login1.beagle.ci.uchicago.edu" jobmanager="ssh:pbs"/>
>     <profile namespace="globus" key="project">CI-CCR000013</profile>
> 
>     <profile namespace="globus" key="ppn">24:cray:pack</profile>
> 
>     <profile namespace="globus" key="workersPerNode">24</profile>
>     <profile namespace="globus" key="maxTime">1000</profile>
>     <profile namespace="globus" key="slots">1</profile>
>     <profile namespace="globus" key="nodeGranularity">1</profile>
>     <profile namespace="globus" key="maxNodes">1</profile>
> 
>     <profile namespace="karajan" key="jobThrottle">.63</profile>
>     <profile namespace="karajan" key="initialScore">10000</profile>
> 
>     <filesystem provider="ssh" url="login1.beagle.ci.uchicago.edu" />
>     <workdirectory>$HOME/swift.workdir</workdirectory>
>   </pool>
> </config>
> 
> 
> 
> ** for communicado **
> 
> <config>
>     <!--<pool handle="pbs">-->
>   <pool handle="communicado-ssh">
>     <execution provider="coaster" url="communicado.ci.uchicago.edu" jobmanager="ssh:ssh"/>
>    
>     <profile namespace="karajan" key="jobThrottle">.63</profile>
>     <profile namespace="karajan" key="initialScore">10000</profile>
> 
>     <filesystem provider="ssh" url="communicado.ci.uchicago.edu" />
>     <workdirectory>$HOME/swift.workdir</workdirectory>
>   </pool>
> </config>
> 
> 
> 
> > 
> > On Thu, 2011-04-28 at 13:36 -0500, Ketan Maheshwari wrote:
> >> Ok, I got past CredentialException with grid-proxy-init, now I am facing this (note: I have turned on provider staging)  :
> >> 
> >> ========
> >> [ketan at bridled catsn.works]$ swift -config cf -tc.file tc -sites.file beagle-coaster-ssh-pbs.xml catsn.swift -n=1
> >> Swift svn swift-r4252 (swift modified locally) cog-r3088 (cog modified locally)
> >> 
> >> RunID: 20110428-1332-llaa031f
> >> Progress:
> >> Could not start connection handler
> >> java.io.EOFException
> >> 	at org.globus.gsi.gssapi.net.impl.GSIGssInputStream.readHandshakeToken(GSIGssInputStream.java:61)
> >> 	at org.globus.gsi.gssapi.net.impl.GSIGssSocket.readToken(GSIGssSocket.java:65)
> >> 	at org.globus.gsi.gssapi.net.GssSocket.authenticateServer(GssSocket.java:127)
> >> 	at org.globus.gsi.gssapi.net.GssSocket.startHandshake(GssSocket.java:147)
> >> 	at org.globus.gsi.gssapi.net.GssSocket.getInputStream(GssSocket.java:177)
> >> 	at org.globus.cog.karajan.workflow.service.channels.AbstractTCPChannel.setSocket(AbstractTCPChannel.java:30)
> >> 	at org.globus.cog.karajan.workflow.service.channels.GSSChannel.<init>(GSSChannel.java:47)
> >> 	at org.globus.cog.karajan.workflow.service.ConnectionHandler.<init>(ConnectionHandler.java:41)
> >> 	at org.globus.cog.abstraction.coaster.service.local.LocalService.handleConnection(LocalService.java:63)
> >> 	at org.globus.net.BaseServer.run(BaseServer.java:247)
> >> 	at java.lang.Thread.run(Thread.java:662)
> >> Progress:  Submitted:1
> >> Could not start connection handler
> >> java.io.EOFException
> >> 	at org.globus.gsi.gssapi.net.impl.GSIGssInputStream.readHandshakeToken(GSIGssInputStream.java:61)
> >> 	at org.globus.gsi.gssapi.net.impl.GSIGssSocket.readToken(GSIGssSocket.java:65)
> >> 	at org.globus.gsi.gssapi.net.GssSocket.authenticateServer(GssSocket.java:127)
> >> 	at org.globus.gsi.gssapi.net.GssSocket.startHandshake(GssSocket.java:147)
> >> 	at org.globus.gsi.gssapi.net.GssSocket.getInputStream(GssSocket.java:177)
> >> 	at org.globus.cog.karajan.workflow.service.channels.AbstractTCPChannel.setSocket(AbstractTCPChannel.java:30)
> >> 	at org.globus.cog.karajan.workflow.service.channels.GSSChannel.<init>(GSSChannel.java:47)
> >> 	at org.globus.cog.karajan.workflow.service.ConnectionHandler.<init>(ConnectionHandler.java:41)
> >> 	at org.globus.cog.abstraction.coaster.service.local.LocalService.handleConnection(LocalService.java:63)
> >> 	at org.globus.net.BaseServer.run(BaseServer.java:247)
> >> 	at java.lang.Thread.run(Thread.java:662)
> >> Progress:  Submitted:1
> >> Exception in cat:
> >> Arguments: [data.txt]
> >> Host: beagle-remote-pbs-coasters-ssh
> >> Directory: catsn-20110428-1332-llaa031f/jobs/b/cat-bxal1d9kTODO: outs
> >> ----
> >> 
> >> Caused by: Could not submit job
> >> Caused by: org.globus.cog.abstraction.impl.common.task.TaskSubmissionException: Could not submit job
> >> Caused by: org.globus.cog.abstraction.impl.common.task.TaskSubmissionException: Could not start coaster service
> >> Caused by: org.globus.cog.abstraction.impl.common.task.TaskSubmissionException: Task ended before registration was received. 
> >> STDOUT: 
> >> STDERR: 
> >> Caused by: org.globus.cog.abstraction.impl.common.execution.JobException: Job failed with an exit code of 1
> >> Final status:  Failed:1
> >> The following errors have occurred:
> >> 1. Job failed with an exit code of 1
> >> 
> >> ========
> >> 
> >> 
> >> From bridled to communicado, I see the following error:
> >> 
> >> **************
> >> [ketan at bridled catsn.works]$ swift -config cf -tc.file tc -sites.file coaster-local-ssh-communicado.xml catsn.swift -n=1
> >> Swift svn swift-r4252 (swift modified locally) cog-r3088 (cog modified locally)
> >> 
> >> RunID: 20110428-1335-k685b2ye
> >> Progress:
> >> Progress:  Submitted:1
> >> Progress:  Active:1
> >> Exception in cat:
> >> Arguments: [data.txt]
> >> Host: communicado-ssh
> >> Directory: catsn-20110428-1335-k685b2ye/jobs/c/cat-coip1d9kTODO: outs
> >> ----
> >> 
> >> Caused by: Job failed with an exit code of 524
> >> Caused by: org.globus.cog.abstraction.impl.common.execution.JobException: Job failed with an exit code of 524
> >> Final status:  Failed:1
> >> The following errors have occurred:
> >> 1. Job failed with an exit code of 524
> >> 
> >> ************
> >> 
> >> 
> >> --
> >> Ketan
> >> 
> >> 
> >> 
> >> 
> >> On Apr 28, 2011, at 1:03 PM, Michael Wilde wrote:
> >> 
> >>> For now - create a proxy using grid-proxy-init on the swift execution machine.
> >>> I think there is an option to set "no security" for this config but I cant recall where that is specified.  Maybe swift.properties, I cant recall.
> >>> 
> >>> - Mike
> >>> 
> >>> ----- Original Message -----
> >>>> Hi,
> >>>> 
> >>>> It looks better now. However, I am getting the following:
> >>>> 
> >>>> =====
> >>>> 
> >>>> [ketan at bridled catsn.works]$ swift -config cf -tc.file tc -sites.file
> >>>> beagle-coaster-ssh-pbs.xml catsn.swift -n=1
> >>>> Swift svn swift-r4252 (swift modified locally) cog-r3088 (cog modified
> >>>> locally)
> >>>> 
> >>>> RunID: 20110428-1251-oi9theh8
> >>>> Progress:
> >>>> Progress: Stage in:1
> >>>> Could not submit job
> >>>> Caused by:
> >>>> org.globus.cog.abstraction.impl.common.task.TaskSubmissionException:
> >>>> Could not submit job
> >>>> Caused by:
> >>>> org.globus.cog.abstraction.impl.common.task.TaskSubmissionException:
> >>>> Could not start coaster service
> >>>> Caused by:
> >>>> org.globus.cog.abstraction.impl.common.task.InvalidSecurityContextException:
> >>>> org.globus.gsi.GlobusCredentialException: [JGLOBUS-5] Proxy file
> >>>> (/tmp/x509up_u2006) not found.
> >>>> Caused by: org.globus.gsi.GlobusCredentialException: [JGLOBUS-5] Proxy
> >>>> file (/tmp/x509up_u2006) not found.
> >>>> Failed to transfer wrapper log from
> >>>> catsn-20110428-1251-oi9theh8/info/e on beagle-remote-pbs-coasters-ssh
> >>>> 
> >>>> =====
> >>>> 
> >>>> How do I specify "-nosec" on automatic coasters?
> >>>> 
> >>>> Ketan
> >>>> 
> >>>> On Apr 28, 2011, at 12:00 PM, Michael Wilde wrote:
> >>>> 
> >>>>> OK. Was there a cookbook on the ssh settings? Did you set up a
> >>>>> $HOME/.ssh/auth.defaults per the user guide?
> >>>>> 
> >>>>> Here is an auth.defaults example. Im not sure its 100% correct, but
> >>>>> could serve as a base for you:
> >>>>> 
> >>>>> xlogin1.pads.ci.uchicago.edu.type=password
> >>>>> xlogin1.pads.ci.uchicago.edu.username=wilde
> >>>>> 
> >>>>> login.pads.ci.uchicago.edu.type=key
> >>>>> login.pads.ci.uchicago.edu.username=wilde
> >>>>> login.pads.ci.uchicago.edu.key=/home/wilde/.ssh/swift_rsa
> >>>>> login.pads.ci.uchicago.edu.passphrase=yourpassphrasehere # MAKE SURE
> >>>>> mode=600!!!
> >>>>> 
> >>>>> login1.pads.ci.uchicago.edu.type=key
> >>>>> login1.pads.ci.uchicago.edu.username=wilde
> >>>>> login1.pads.ci.uchicago.edu.key=/home/wilde/.ssh/swift_rsa
> >>>>> login1.pads.ci.uchicago.edu.passphrase=yourpassphrasehere # MAKE
> >>>>> SURE mode=600!!!
> >>>>> 
> >>>>> login.mcs.anl.gov.type=key
> >>>>> login.mcs.anl.gov.username=wilde
> >>>>> login.mcs.anl.gov.key=/home/wilde/.ssh/swift_rsa
> >>>>> login.mcs.anl.gov.passphrase=yourpassphrasehere # MAKE SURE
> >>>>> mode=600!!!
> >>>>> 
> >>>>> - Mike
> >>>>> 
> >>>>> ----- Original Message -----
> >>>>>> It does look like an ssh problem. I am getting the same stderr and
> >>>>>> log
> >>>>>> messages on trying to communicate from Bridled to Communicado.
> >>>>>> 
> >>>>>> Ketan
> >>>>>> 
> >>>>>> On Apr 28, 2011, at 11:19 AM, Michael Wilde wrote:
> >>>>>> 
> >>>>>>> Have you already run a simple hellow-world swift test from
> >>>>>>> communicado to bridled to make sure you have ssh configured
> >>>>>>> correctly? I would do that first.
> >>>>>>> 
> >>>>>>> Im not sure if an ssh problem explains what you show below, or
> >>>>>>> not.
> >>>>>>> 
> >>>>>>> - Mike
> >>>>>>> 
> >>>>>>> ----- Original Message -----
> >>>>>>>> Thanks, I made the change. However, now, I am getting the
> >>>>>>>> following
> >>>>>>>> on
> >>>>>>>> my stderr
> >>>>>>>> 
> >>>>>>>> 
> >>>>>>>> ===========
> >>>>>>>> [ketan at bridled catsn.works]$ swift -config cf -tc.file tc
> >>>>>>>> -sites.file
> >>>>>>>> beagle-coaster-ssh-pbs.xml catsn.swift -n=1
> >>>>>>>> Swift svn swift-r4252 (swift modified locally) cog-r3088 (cog
> >>>>>>>> modified
> >>>>>>>> locally)
> >>>>>>>> 
> >>>>>>>> RunID: 20110428-1022-n9s0k0e0
> >>>>>>>> Progress:
> >>>>>>>> [ketan]
> >>>>>>>> Progress: Initializing site shared directory:1
> >>>>>>>> [ketan] Progress: Initializing site shared directory:1
> >>>>>>>> Progress: Initializing site shared directory:1
> >>>>>>>> Progress: Initializing site shared directory:1
> >>>>>>>> Progress: Initializing site shared directory:1
> >>>>>>>> Progress: Initializing site shared directory:1
> >>>>>>>> Progress: Initializing site shared directory:1
> >>>>>>>> Progress: Initializing site shared directory:1
> >>>>>>>> Progress: Initializing site shared directory:1
> >>>>>>>> Progress: Initializing site shared directory:1
> >>>>>>>> Progress: Initializing site shared directory:1
> >>>>>>>> Progress: Initializing site shared directory:1
> >>>>>>>> Progress: Initializing site shared directory:1
> >>>>>>>> Progress: Initializing site shared directory:1
> >>>>>>>> ========
> >>>>>>>> 
> >>>>>>>> And from the log it seems some network transmission has failed:
> >>>>>>>> 
> >>>>>>>> 2011-04-28 10:22:45,261-0500 INFO TransportProtocolCommon Sending
> >>>>>>>> SSH_MSG_SERVICE_REQUEST
> >>>>>>>> 2011-04-28 10:22:45,264-0500 INFO TransportProtocolCommon
> >>>>>>>> Received
> >>>>>>>> SSH_MSG_SERVICE_ACCEPT
> >>>>>>>> 2011-04-28 10:24:27,626-0500 INFO TransportProtocolCommon The
> >>>>>>>> Transport Protocol thread failed
> >>>>>>>> java.io.IOException: The socket is EOF
> >>>>>>>> at
> >>>>>>>> com.sshtools.j2ssh.transport.TransportProtocolInputStream.readBufferedData(TransportProtocolInputStream.java:183)
> >>>>>>>> at
> >>>>>>>> com.sshtools.j2ssh.transport.TransportProtocolInputStream.readMessage(TransportProtocolInputStream.java:226)
> >>>>>>>> at
> >>>>>>>> com.sshtools.j2ssh.transport.TransportProtocolCommon.processMessages(TransportProtocolCommon.java:1440)
> >>>>>>>> at
> >>>>>>>> com.sshtools.j2ssh.transport.TransportProtocolCommon.startBinaryPacketProtocol(TransportProtocolCommon.java:1034)
> >>>>>>>> at
> >>>>>>>> com.sshtools.j2ssh.transport.TransportProtocolCommon.run(TransportProtocolCommon.java:393)
> >>>>>>>> at java.lang.Thread.run(Thread.java:662)
> >>>>>>>> 
> >>>>>>>> 
> >>>>>>>> Any clues?
> >>>>>>>> Ketan
> >>>>>>>> 
> >>>>>>>> 
> >>>>>>>> On Apr 28, 2011, at 10:20 AM, Michael Wilde wrote:
> >>>>>>>> 
> >>>>>>>>> The pool name in your sites file is pads-remote-pbs-coasters-ssh
> >>>>>>>>> but
> >>>>>>>>> you used pbs in your tc.data.
> >>>>>>>>> 
> >>>>>>>>> - Mike
> >>>>>>>>> 
> >>>>>>>>> ----- Original Message -----
> >>>>>>>>>> Hello,
> >>>>>>>>>> 
> >>>>>>>>>> Some context:
> >>>>>>>>>> I am trying to submit a big run on Beagle using swift +
> >>>>>>>>>> coasters.
> >>>>>>>>>> However, a previous run is already underway on beagle. So,
> >>>>>>>>>> there
> >>>>>>>>>> are
> >>>>>>>>>> two difficulties running a new run from its login node:
> >>>>>>>>>> 
> >>>>>>>>>> 1. Running another swift from the same jvm will result in chaos
> >>>>>>>>>> on
> >>>>>>>>>> the
> >>>>>>>>>> logs (As far as I know, please correct me if this is not the
> >>>>>>>>>> case
> >>>>>>>>>> anymore)
> >>>>>>>>>> 
> >>>>>>>>>> 2. Login node is already under load because of my running
> >>>>>>>>>> previous
> >>>>>>>>>> big
> >>>>>>>>>> run.
> >>>>>>>>>> 
> >>>>>>>>>> /context
> >>>>>>>>>> 
> >>>>>>>>>> So, I am now trying to submit this big run from a remote host
> >>>>>>>>>> (bridled). I know this has been done on PADS using ssh:pbs,
> >>>>>>>>>> provider
> >>>>>>>>>> coaster. I tried the similar approach on a trial swift script
> >>>>>>>>>> but
> >>>>>>>>>> getting error.
> >>>>>>>>>> 
> >>>>>>>>>> Following is the error message:
> >>>>>>>>>> 
> >>>>>>>>>> [ketan at bridled catsn.works]$ swift -config cf -tc.file tc
> >>>>>>>>>> -sites.file
> >>>>>>>>>> beagle-coaster-ssh-pbs.xml catsn.swift -n=1
> >>>>>>>>>> Swift svn swift-r4252 (swift modified locally) cog-r3088 (cog
> >>>>>>>>>> modified
> >>>>>>>>>> locally)
> >>>>>>>>>> 
> >>>>>>>>>> RunID: 20110428-1002-c8rvqhe6
> >>>>>>>>>> Progress:
> >>>>>>>>>> The application "cat" is not available in your tc.data catalog
> >>>>>>>>>> Caused by:
> >>>>>>>>>> org.globus.cog.karajan.scheduler.NoSuchResourceException
> >>>>>>>>>> Final status: Failed:1
> >>>>>>>>>> The following errors have occurred:
> >>>>>>>>>> 1. The application "cat" is not available in your tc.data
> >>>>>>>>>> catalog
> >>>>>>>>>> 
> >>>>>>>>>> 
> >>>>>>>>>> Attached are my .swift, sites.xml and tc.data files.
> >>>>>>>>>> 
> >>>>>>>>>> Could someone indicate if what I am doing is doable and if so
> >>>>>>>>>> how
> >>>>>>>>>> can
> >>>>>>>>>> I correctly configure my sites and tc setup.
> >>>>>>>>>> 
> >>>>>>>>>> Thanks.
> >>>>>>>>>> Ketan
> >>>>>>>>>> 
> >>>>>>>>>> 
> >>>>>>>>>> 
> >>>>>>>>>> 
> >>>>>>>>>> 
> >>>>>>>>>> 
> >>>>>>>>>> 
> >>>>>>>>>> 
> >>>>>>>>>> 
> >>>>>>>>>> _______________________________________________
> >>>>>>>>>> Swift-devel mailing list
> >>>>>>>>>> Swift-devel at ci.uchicago.edu
> >>>>>>>>>> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> >>>>>>>>> 
> >>>>>>>>> --
> >>>>>>>>> Michael Wilde
> >>>>>>>>> Computation Institute, University of Chicago
> >>>>>>>>> Mathematics and Computer Science Division
> >>>>>>>>> Argonne National Laboratory
> >>>>>>>>> 
> >>>>>>> 
> >>>>>>> --
> >>>>>>> Michael Wilde
> >>>>>>> Computation Institute, University of Chicago
> >>>>>>> Mathematics and Computer Science Division
> >>>>>>> Argonne National Laboratory
> >>>>>>> 
> >>>>> 
> >>>>> --
> >>>>> Michael Wilde
> >>>>> Computation Institute, University of Chicago
> >>>>> Mathematics and Computer Science Division
> >>>>> Argonne National Laboratory
> >>>>> 
> >>> 
> >>> -- 
> >>> Michael Wilde
> >>> Computation Institute, University of Chicago
> >>> Mathematics and Computer Science Division
> >>> Argonne National Laboratory
> >>> 
> >> 
> >> _______________________________________________
> >> Swift-devel mailing list
> >> Swift-devel at ci.uchicago.edu
> >> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > 
> > 
>

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