June 2015 - swift-bugs - mailman3.cels.anl.gov

[Bug 1423] New: clarification on toXXX functions
by bugzilla-daemon＠mcs.anl.gov 13 Aug '15

13 Aug '15

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=1423 Summary: clarification on toXXX functions Product: Swift Version: 0.96 Platform: All OS/Version: All Status: NEW Severity: normal Priority: P2 Component: Documentation AssignedTo: hategan(a)mcs.anl.gov ReportedBy: ketan(a)mcs.anl.gov Relaying from user Max Hutchinson: The documentation defines toInt, toFloat, etc. as operating on strings only. toFloat(int) seems to work; However, toInt(float) does not work. If it is polymorphic, it would help if that was in the docs. -- Configure bugmail: http://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are watching all bug changes.

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[Bug 1141] New: Null pointer exception if foreach array is empty
by bugzilla-daemon＠mcs.anl.gov 30 Jul '15

30 Jul '15

https://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=1141 Summary: Null pointer exception if foreach array is empty Product: Swift Version: 0.94 Platform: PC OS/Version: Mac OS Status: ASSIGNED Severity: normal Priority: P2 Component: SwiftScript language AssignedTo: hategan(a)mcs.anl.gov ReportedBy: wilde(a)mcs.anl.gov Example below. Note that the null array is desired here, as the array may be set dynamically and an empty array should result in zero iterations of the foreach. login1$ swift e1.swift WARNING: Empty array constant Swift 0.94.1 swift-r7114 cog-r3803 RunID: 20131123-1240-v2j459gd Progress: time: Sat, 23 Nov 2013 12:40:31 -0600 Execution failed: java.lang.NullPointerException Caused by: java.lang.NullPointerException at org.griphyn.vdl.karajan.lib.CreateArray.function(CreateArray.java:57) at org.griphyn.vdl.karajan.lib.VDLFunction.post(VDLFunction.java:81) at org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.completed(AbstractSequentialWithArguments.java:194) at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:214) at org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58) at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:28) at org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:29) at org.globus.cog.karajan.workflow.nodes.Sequential.executeChildren(Sequential.java:20) at org.globus.cog.karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java:63) at org.globus.cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:139) at org.globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java:197) at org.globus.cog.karajan.workflow.FlowElementWrapper.start(FlowElementWrapper.java:227) at org.globus.cog.karajan.workflow.events.EventBus.start(EventBus.java:103) at org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:40) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:722) login1$ cat e1.swift int i[] = [1,3,5,7,9]; foreach j in [] { trace(j); } login1$ -- Configure bugmail: https://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are watching all bug changes.

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[Bug 945] New: coaster.service.job.manager.SortedJobSet NoSuchElementException
by bugzilla-daemon＠mcs.anl.gov 30 Jul '15

30 Jul '15

https://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=945 Summary: coaster.service.job.manager.SortedJobSet NoSuchElementException Product: Swift Version: trunk Platform: PC OS/Version: Mac OS Status: NEW Severity: normal Priority: P2 Component: General AssignedTo: hategan(a)mcs.anl.gov ReportedBy: davidk(a)ci.uchicago.edu I am seeing this error on Beagle: CoasterService fatal error: Exception caught in block processor java.util.NoSuchElementException at org.globus.cog.abstraction.coaster.service.job.manager.SortedJobSet$1.next(SortedJobSet.java:182) at org.globus.cog.abstraction.coaster.service.job.manager.SortedJobSet$1.next(SortedJobSet.java:162) at org.globus.cog.abstraction.coaster.service.job.manager.BlockQueueProcessor.allocateBlocks(BlockQueueProcessor.java:609) at org.globus.cog.abstraction.coaster.service.job.manager.BlockQueueProcessor.updatePlan(BlockQueueProcessor.java:734) at org.globus.cog.abstraction.coaster.service.job.manager.BlockQueueProcessor.run(BlockQueueProcessor.java:139) Exception caught in block processor java.util.NoSuchElementException at org.globus.cog.abstraction.coaster.service.job.manager.SortedJobSet$1.next(SortedJobSet.java:182) at org.globus.cog.abstraction.coaster.service.job.manager.SortedJobSet$1.next(SortedJobSet.java:162) at org.globus.cog.abstraction.coaster.service.job.manager.BlockQueueProcessor.allocateBlocks(BlockQueueProcessor.java:609) at org.globus.cog.abstraction.coaster.service.job.manager.BlockQueueProcessor.updatePlan(BlockQueueProcessor.java:734) at org.globus.cog.abstraction.coaster.service.job.manager.BlockQueueProcessor.run(BlockQueueProcessor.java:139) The full log is at http://www.ci.uchicago.edu/~davidk/logs/modis-20130130-1819-jrybzslc.log -- Configure bugmail: https://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are watching all bug changes.

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[Bug 1425] New: Support file rename (move)
by bugzilla-daemon＠mcs.anl.gov 03 Jul '15

03 Jul '15

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=1425 Summary: Support file rename (move) Product: Swift Version: unspecified Platform: All OS/Version: All Status: NEW Severity: normal Priority: P2 Component: Design Decision AssignedTo: wozniak(a)mcs.anl.gov ReportedBy: maxhutch(a)uchicago.edu I have an app that names checkpoint files implicitly. If I invoke it with the name "job0" it produces a checkpoint file named something like "job0-0.checkpoint". Then, if I want to resume from that checkpoint in "job1", I need to rename "job0-0.check" to "job1-0.check". Swift is happy to copy it, but it doesn't seem like there is a way to rename/move it. This is important because the checkpoint files are very large, both slowing a serial copy and requiring more disk space. -- Configure bugmail: http://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are watching all bug changes.

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[Bug 1427] New: wrapperParameterMode=files causes java.lang.UnsupportedOperationException
by bugzilla-daemon＠mcs.anl.gov 25 Jun '15

25 Jun '15

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=1427 Summary: wrapperParameterMode=files causes java.lang.UnsupportedOperationException Product: Swift Version: trunk Platform: Other OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Runtime AssignedTo: wozniak(a)mcs.anl.gov ReportedBy: maxhutch(a)uchicago.edu CC: ketan(a)mcs.anl.gov I'm staging lots of files, so argument lists are overflowing. Switching wrapperParameterMode to files causes errors on the first job (below). This seems related, but wasn't addressed on the mailing list: http://lists.ci.uchicago.edu/pipermail/swift-devel/2014-July/010858.html [maxhutch@cetuslac1 nek-swift]$ ./cet Swift trunk git-rev: 1d512cbda070d363e8ec3cf16e77dfcddc6e66cb heads/master 6377 RunID: run001 Progress: Wed, 17 Jun 2015 15:46:59+0000 Progress: Wed, 17 Jun 2015 15:47:00+0000 Initializing site shared directory:1 Execution failed: java.lang.UnsupportedOperationException sys:file:write @ swift-int.k, line: 322 swiftStaging:execute2 @ swift.k, line: 138 executeSelect @ swift.k, line: 206 Caused by: java.lang.UnsupportedOperationException at org.globus.cog.karajan.analyzer.ChannelRef$Return.set(ChannelRef.java:108) at org.globus.cog.karajan.compiled.nodes.FileWrite.runBody(FileWrite.java:81) 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.Sequential.run(Sequential.java:41) at org.globus.cog.karajan.compiled.nodes.If.run(If.java:184) 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.user.Function.runBody(Function.java:117) at org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.runBody(InvocationWrapper.java:287) at org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.run(InvocationWrapper.java:89) 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.If.run(If.java:184) 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.user.Function.runBody(Function.java:117) at org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.runBody(InvocationWrapper.java:287) at org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.run(InvocationWrapper.java:89) 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.grid.AllocateHost.runBody(AllocateHost.java:99) 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.Sequential.run(Sequential.java:41) at org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:110) at org.globus.cog.karajan.compiled.nodes.Try.run(Try.java:71) 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.Sequential.run(Sequential.java:41) at org.globus.cog.karajan.compiled.nodes.RestartOnErrorNode.runBody(RestartOnErrorNode.java:81) 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.SetVarK.run(SetVarK.java:70) 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.Sequential.run(Sequential.java:41) at org.griphyn.vdl.karajan.lib.Throttled.run(Throttled.java:54) 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.Try.run(Try.java:71) 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.If.run(If.java:184) 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.If.run(If.java:184) 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.user.Function.runBody(Function.java:117) at org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.runBody(InvocationWrapper.java:287) at org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.run(InvocationWrapper.java:89) 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.user.Function.runBody(Function.java:117) at org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.runBody(InvocationWrapper.java:287) at org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.run(InvocationWrapper.java:89) 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.If.run(If.java:191) 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.user.Function.runBody(Function.java:117) at org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.runBody(InvocationWrapper.java:287) at org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.run(InvocationWrapper.java:89) at org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:110) at org.globus.cog.karajan.compiled.nodes.UParallel$1.run(UParallel.java:91) at k.thr.LWThread.run(LWThread.java:247) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:906) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:929) at java.lang.Thread.run(Thread.java:761) k:assign @ swift.k, line: 173 swift:execute @ nek, line: 226 app_genrun_new @ nek, line: 26 genrun @ nek, line: 18 -- Configure bugmail: http://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are watching all bug changes.

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[Bug 1431] New: NPE at service registration
by bugzilla-daemon＠mcs.anl.gov 25 Jun '15

25 Jun '15

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=1431 Summary: NPE at service registration Product: Swift Version: trunk Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: General AssignedTo: hategan(a)mcs.anl.gov ReportedBy: yadunandb(a)ci.uchicago.edu I'm seeing this issue only when the client is running on workflow.iu.xsede.org and attempts to run coasters remotely with ssh-cl. This was tested with 0.96.0 and 0.96.1. Java version is 1.7.0_51. I've set TCP_RANGE to 50000-55000, and from the coaster logs I see that the bootstrap.jar was downloaded, so this doesn't look like a firewall issue. Local coaster jobs work fine as well. All logs are here: http://users.rcc.uchicago.edu/~yadunand/part04/ Here's the error message I see : Failed to start coaster service java.lang.RuntimeException: Failed to register service at org.globus.cog.abstraction.coaster.service.CoasterService.start(CoasterService.java:271) at org.globus.cog.abstraction.coaster.service.CoasterService.main(CoasterService.java:524) Caused by: org.globus.cog.coaster.channels.ChannelException: Failed to start channel GSSChannel[client, https://149.165.228.156:50000] at org.globus.cog.coaster.channels.GSSChannel.connect(GSSChannel.java:166) at org.globus.cog.coaster.channels.GSSChannel.start(GSSChannel.java:105) at org.globus.cog.coaster.ChannelFactory.newChannel(ChannelFactory.java:76) at org.globus.cog.coaster.Client.connect(Client.java:119) at org.globus.cog.coaster.Client.newClient(Client.java:83) at org.globus.cog.coaster.Client.getClient(Client.java:60) at org.globus.cog.coaster.channels.ChannelManager.openChannel(ChannelManager.java:205) at org.globus.cog.coaster.channels.ChannelManager.openChannel(ChannelManager.java:200) at org.globus.cog.abstraction.coaster.service.CoasterService.start(CoasterService.java:259) ... 1 more Caused by: java.lang.NullPointerException at COM.claymoresystems.cert.X509Cert.checkSignatureKey(X509Cert.java:293) at COM.claymoresystems.cert.X509Cert.verify(X509Cert.java:323) at COM.claymoresystems.cert.X509Cert.verifyCertChain(X509Cert.java:411) at COM.claymoresystems.ptls.SSLHandshake.recvCertificate(SSLHandshake.java:292) at COM.claymoresystems.ptls.SSLHandshakeClient.processTokens(SSLHandshakeClient.java:128) at COM.claymoresystems.ptls.SSLHandshake.processHandshake(SSLHandshake.java:135) at org.globus.gsi.gssapi.GlobusGSSContextImpl.initSecContext(GlobusGSSContextImpl.java:510) at org.globus.gsi.gssapi.net.GssSocket.authenticateClient(GssSocket.java:107) at org.globus.gsi.gssapi.net.GssSocket.startHandshake(GssSocket.java:145) at org.globus.gsi.gssapi.net.GssSocket.getInputStream(GssSocket.java:177) at org.globus.cog.coaster.channels.AbstractTCPChannel.setSocket(AbstractTCPChannel.java:62) at org.globus.cog.coaster.channels.GSSChannel.connect(GSSChannel.java:158) -- Configure bugmail: http://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are watching all bug changes.

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[Bug 714] New: Give more information for "could not convert" error message
by bugzilla-daemon＠mcs.anl.gov 19 Jun '15

19 Jun '15

https://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=714 Summary: Give more information for "could not convert" error message Product: Swift Version: 0.93 Platform: PC OS/Version: Mac OS Status: NEW Severity: normal Priority: P2 Component: SwiftScript language AssignedTo: davidk(a)ci.uchicago.edu ReportedBy: wilde(a)mcs.anl.gov Swift dies with the following message: Execution failed: Could not convert value to number: nan Provide at least the built-in function name and ideally the line number of the failing operation. -- Configure bugmail: https://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are watching all bug changes.

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[Bug 1417] New: NullPointer exception when an undefined site is requested
by bugzilla-daemon＠mcs.anl.gov 19 Jun '15

19 Jun '15

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=1417 Summary: NullPointer exception when an undefined site is requested Product: Swift Version: 0.96 Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: General AssignedTo: hategan(a)mcs.anl.gov ReportedBy: yadunandb(a)ci.uchicago.edu If an site with no corresponding site definition in the config is requested, Swift throws a NullPointerException. It would be nice to have an error message saying the site requested is not defined. I tried this on Rev 6274, 6280 and 6307(latest). The same bug pops up if I specify the sites on the command-line or in the swift.conf sites attribute. [yadunand@midway001 part05]$ swift -config xsede.conf -sites badsite p5.swift 2015-04-01 16:17:56,633+0000 DEBUG Loader Detailed exception: java.lang.NullPointerException at org.globus.cog.karajan.util.ContactSet.addContact(ContactSet.java:43) at org.globus.swift.catalog.site.SwiftContactSet.addContact(SwiftContactSet.java:57) at org.griphyn.vdl.util.SwiftConfig.build(SwiftConfig.java:420) at org.griphyn.vdl.util.SwiftConfig.load(SwiftConfig.java:256) at org.griphyn.vdl.karajan.Loader.loadConfig(Loader.java:598) at org.griphyn.vdl.karajan.Loader.main(Loader.java:148) Could not start execution: java.lang.NullPointerException -- Configure bugmail: http://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are watching all bug changes.

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[Bug 1421] New: concurrent mapper
by bugzilla-daemon＠mcs.anl.gov 19 Jun '15

19 Jun '15

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=1421 Summary: concurrent mapper Product: Swift Version: 0.96 Platform: All OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: General AssignedTo: hategan(a)mcs.anl.gov ReportedBy: ketan(a)mcs.anl.gov Files mapped via concurrent mapper does not show up in _concurrent directory. For example, after running the following code, the _concurrent directory is created but is empty: type file; app (file _out, file _err) dosed (file _in, float _val){ sed strcat("s/cc/", _val, "/") stdin=@_in stdout=@_out stderr=@_err; } file infile <"x.txt">; float val=0.01; foreach i in [0:9]{ file o<concurrent_mapper; prefix="out-", suffix=".txt">; file e<concurrent_mapper; prefix="err-", suffix=".txt">; (o, e) = dosed (infile, val); } Logs attached. -- Configure bugmail: http://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are watching all bug changes.

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[Bug 1429] New: Documentation for worker logging configuration options
by bugzilla-daemon＠mcs.anl.gov 19 Jun '15

19 Jun '15

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=1429 Summary: Documentation for worker logging configuration options Product: Swift Version: trunk Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Documentation AssignedTo: hategan(a)mcs.anl.gov ReportedBy: yadunandb(a)ci.uchicago.edu The trunk userguide is missing any documentation on workerLoggingLevel and workerLoggingDirectory config options. -- Configure bugmail: http://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are watching all bug changes.

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