[Swift-user] Block task failed: Connection to worker lost

Ozik, Jonathan jozik at anl.gov
Thu Dec 4 14:58:38 CST 2014 

Thank you all,

The job is queued up now. I’ll update on the results.

Jonathan

> On Dec 4, 2014, at 1:33 PM, Michael Wilde <wilde at anl.gov> wrote:
> 
> We should (and will) add a getcwd( ) library function to eliminate this 
> particular need for java( ), though.
> 
> - Mike
> 
> 
> On 12/4/14 1:23 PM, Yadu Nand Babuji wrote:
>> Hi Jonathan,
>> 
>> I rebuilt the trunk package with Mihael's fixes, and you can get it from
>> here :
>> http://users.rcc.uchicago.edu/~yadunand/swift-trunk-latest.tar.gz
>> 
>> -Yadu
>> 
>> On 12/04/2014 01:01 PM, Mihael Hategan wrote:
>>> Hi Jonathan,
>>> 
>>> I fixed this in GIT. Yadu, can you compile the latest GIT please?
>>> 
>>> Mihael
>>> 
>>> On Thu, 2014-12-04 at 18:33 +0000, Ozik, Jonathan wrote:
>>>> Hi Yadu,
>>>> 
>>>> I’ve tried running with trunk and am getting a strange Java error this time:
>>>> No method: getProperty in java.lang.System with parameter types[class java.lang.String]
>>>> swiftscript:java @ repast, line: 267
>>>> 
>>>> at org.griphyn.vdl.karajan.lib.swiftscript.Java.getMethod(Java.java:192)
>>>> at org.griphyn.vdl.karajan.lib.swiftscript.Java.function(Java.java:162)
>>>> at org.griphyn.vdl.karajan.lib.SwiftFunction.runBody(SwiftFunction.java:77)
>>>> at org.globus.cog.karajan.compiled.nodes.InternalFunction.run(InternalFunction.java:175)
>>>> at org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:110)
>>>> at org.globus.cog.karajan.compiled.nodes.InternalFunction.run(InternalFunction.java:165)
>>>> at org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:110)
>>>> at org.globus.cog.karajan.compiled.nodes.InternalFunction.run(InternalFunction.java:165)
>>>> at org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:110)
>>>> at org.globus.cog.karajan.compiled.nodes.Sequential.run(Sequential.java:41)
>>>> at org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:110)
>>>> at org.globus.cog.karajan.compiled.nodes.UParallel$1.run(UParallel.java:91)
>>>> at k.thr.LWThread.run(LWThread.java:247)
>>>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>>> at java.lang.Thread.run(Thread.java:745)
>>>> 
>>>> Execution failed:
>>>> Error attempting to use: java.lang.System
>>>> swiftscript:java @ repast, line: 267
>>>> 
>>>> I think this is being triggered by the call:
>>>> string s = strcat(java("java.lang.System","getProperty","user.dir"),"/“);
>>>> 
>>>> Which worked just fine with 0.95 RC5.
>>>> 
>>>> Any thoughts?
>>>> 
>>>> Jonathan
>>>> 
>>>> On Dec 4, 2014, at 11:14 AM, Yadu Nand Babuji <yadunand at uchicago.edu<mailto:yadunand at uchicago.edu>> wrote:
>>>> 
>>>> Hi Jonathan,
>>>> 
>>>> If your config file is named swift.conf and is in the current directory, it will be automatically selected and you needn't specify
>>>> the file on the commandline, otherwise specify the config file using the -config option:
>>>> swift -config <path_to_config> <your_script.swift>
>>>> 
>>>> To resume from the log, say the restart.log in your run001 folder specify the restart.log using the -resume option:
>>>> swift -resume run001/restart.log  ...
>>>> The restart log is from an 0.95 run, and I'm not quite sure if it will work correctly with trunk.
>>>> 
>>>> There is no trunk module available on Midway, since we rebuild from source to keep up to date with changes in the codebase.
>>>> 
>>>> Generally you can always get the latest trunk builds here, (atmost a week older than last commit):
>>>> http://users.rcc.uchicago.edu/~yadunand/swift-trunk-latest.tar.gz
>>>> 
>>>> Thanks,
>>>> Yadu
>>>> 
>>>> On 12/04/2014 10:48 AM, Jonathan Ozik wrote:
>>>> Thanks Yadu,
>>>> 
>>>> I have a few questions.
>>>> - How do I invoke swift and pass it the new swift.conf?
>>>> - What is the “restart” procedure?
>>>> - Is there a module I can load to use the latest swift trunk?
>>>> 
>>>> Jonathan
>>>> 
>>>> On Dec 3, 2014, at 7:03 PM, Yadu Nand Babuji <yadunand at uchicago.edu<mailto:yadunand at uchicago.edu>> wrote:
>>>> 
>>>> Hi Jonathan,
>>>> 
>>>> I believe some of the issues related to timeouts seen in your logs are fixed/less likely in trunk
>>>> and would recommend that you try a run with that. I've also converted your swift.properties to
>>>> the new swift.conf format. You can get a tested .conf file along with a small test case from here:
>>>> 
>>>> http://users.rcc.uchicago.edu/~yadunand/test_configs_package.tar.gz<http://users.rcc.uchicago.edu/%7Eyadunand/test_configs_package.tar.gz>
>>>> 
>>>> Here are some changes I've made to the conf:
>>>> lazyErrors: true and executionRetries: 0 so that long running jobs are not retried.
>>>> staging set to direct, since you are running on the shared FS.
>>>> added worker logging and an app definition for debug.
>>>> 
>>>> You can get the latest trunk build from here : http://users.rcc.uchicago.edu/~yadunand/swift-trunk-latest.tar.gz<http://users.rcc.uchicago.edu/%7Eyadunand/swift-trunk-latest.tar.gz>
>>>> 
>>>> Thanks,
>>>> Yadu
>>>> 
>>>> On 12/03/2014 01:16 PM, Jonathan Ozik wrote:
>>>> Hi Yadu,
>>>> 
>>>> The tar.gz archive is here: https://www.dropbox.com/s/tt3ewapzaf0ygac/run001.tar.gz?dl=0
>>>> I’m also attaching the swift.properties file that I used below.
>>>> 
>>>> Thank you,
>>>> 
>>>> Jonathan
>>>> 
>>>> On Dec 3, 2014, at 11:04 AM, Yadu Nand Babuji <yadunand at uchicago.edu<mailto:yadunand at uchicago.edu>> wrote:
>>>> 
>>>> Hi Jonathan,
>>>> 
>>>> The issue you are seeing sounds pretty close to what David reported a
>>>> while back.
>>>> Could you send us a tar ball of your run directory from a failed run ?
>>>> 
>>>> Could you also check if you've set lowOverAllocation and
>>>> highOverAllocation in your sites definition ?
>>>> 
>>>> Thanks,
>>>> Yadu
>>>> 
>>>> On 12/03/2014 10:50 AM, Ozik, Jonathan wrote:
>>>> Hi all,
>>>> 
>>>> I’m trying to run a large set of simulations on Midway using Swift 0.95-RC5.
>>>> 768 of the 2187 tasks completed successfully and then I got the exception:
>>>> 
>>>> exception @ swift-int.k, line: 530
>>>> Caused by: Block task failed: Connection to worker lost
>>>> org.globus.cog.coaster.TimeoutException: Channel timed out. lastTime=141203-145449.325, now=141203-145649.844, channel=TCPChannel [type: server, contact: 1202-5410010-000072-000000]
>>>> at org.globus.cog.coaster.channels.AbstractCoasterChannel.checkTimeouts(AbstractCoasterChannel.java:133)
>>>> at org.globus.cog.coaster.channels.AbstractCoasterChannel$1.run(AbstractCoasterChannel.java:124)
>>>> at java.util.TimerThread.mainLoop(Timer.java:555)
>>>> at java.util.TimerThread.run(Timer.java:505)
>>>> 
>>>> Progress: Wed, 03 Dec 2014 14:59:51+0000  Submitted:651  Failed:6  Finished successfully:768  Failed but can retry:762
>>>> Progress: Wed, 03 Dec 2014 14:59:52+0000  Submitted:651  Failed:44  Finished successfully:768  Failed but can retry:724
>>>> 
>>>> And the process seems to have stopped.
>>>> 
>>>> What log file would be helpful for diagnosing this?
>>>> 
>>>> Jonathan
>>>> 
>>>> 
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>>>> 
>>>> 
>>>> 
>>>> 
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> 
> -- 
> Michael Wilde
> Mathematics and Computer Science          Computation Institute
> Argonne National Laboratory               The University of Chicago
> 
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