<div dir="ltr"><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">Swift Users,<br><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">Finally back to trying out swift after a delay -- thanks for all your help so far.<br>
</div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">I've got a functional swift script up and running, and am now trying to configure my sites.xml to get it running on 4 remote clusters. I've gotten it working on 2, so 2 more to go!<br>
<br></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">Let's focus on one first. This cluster is running PBS and I'm trying to access it using coasters, via provider="ssh-cl:pbs". Unfortunately, it seems like swift can't boot up the coaster service for some reason, which I haven't been able to figure out. Maybe someone can help me debug this, or at least know where to start poking around! <br>
<br>Here's the site xml entry:<br><br> <span style="font-family:courier new,monospace"> <pool handle="biox3"><br><br> <execution provider="coaster" jobmanager="ssh-cl:pbs" url="<a href="http://biox3.stanford.edu">biox3.stanford.edu</a>"/><br>
<br> <profile namespace="globus" key="maxWalltime">00:30:00</profile><br><br> <profile namespace="globus" key="lowOverAllocation">100</profile><br> <profile namespace="globus" key="highOverAllocation">100</profile><br>
<profile namespace="globus" key="maxtime">3600</profile><br><br> <profile namespace="globus" key="queue">batch</profile><br> <profile namespace="globus" key="slots">10</profile><br>
<profile namespace="globus" key="maxnodes">1</profile><br> <profile namespace="globus" key="nodeGranularity">1</profile><br><br> <profile namespace="globus" key="jobsPerNode">1</profile><br>
<br> <profile namespace="karajan" key="jobThrottle">1.0</profile><br> <profile namespace="karajan" key="initialScore">10000</profile><br> <br> <!--<br>
<profile namespace="env" key="SWIFT_GEN_SCRIPTS">1</profile><br> --><br><br> <workdirectory>/home/tjlane/swiftwork</workdirectory><br><br> </pool><br></span><br>
</div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">and here's what gets printed when I try and run a very basic "hello cluster" swift script:<br><br><span style="font-family:courier new,monospace">tjlane@vspm42 ~/swift_hello<br>
$ swift -sites.file ~/opt/swift-0.94/etc/sites.xml -tc.file ~/opt/swift-0.94/etc/tc.data -config swift.properties uname.swift<br>Swift started<br>Swift 0.94 swift-r6492 cog-r3658<br><br>RunID: 20130615-1512-h2fskgme<br>Progress: time: Sat, 15 Jun 2013 15:12:32 -0700<br>
Progress: time: Sat, 15 Jun 2013 15:12:34 -0700 Submitted:1<br>Execution failed:<br> Exception in uname:<br> Arguments: [-a]<br> Host: biox3<br> Directory: uname-20130615-1512-h2fskgme/jobs/a/uname-aan4rzal<br>
<br>Caused by:<br> Could not submit job<br>Caused by:<br> Could not start coaster service<br>Caused by:<br> Task ended before registration was received. <br><br>Failed to start coaster service<br>java.lang.NullPointerException<br>
at java.net.URI.compareTo(libgcj.so.10)<br> at java.net.URI.compareTo(libgcj.so.10)<br> at java.util.TreeMap.compare(libgcj.so.10)<br> at java.util.TreeMap.put(libgcj.so.10)<br> at java.util.TreeSet.addAll(libgcj.so.10)<br>
at org.globus.cog.abstraction.coaster.service.job.manager.Settings.setCallbackURIs(Settings.java:403)<br> at org.globus.cog.abstraction.coaster.service.job.manager.JobQueue.<init>(JobQueue.java:41)<br> at org.globus.cog.abstraction.coaster.service.CoasterService.start(CoasterService.java:148)<br>
at org.globus.cog.abstraction.coaster.service.CoasterService.main(CoasterService.java:382)<br>java.lang.NullPointerException<br> at java.net.URI.compareTo(libgcj.so.10)<br> at java.net.URI.compareTo(libgcj.so.10)<br>
at java.util.TreeMap.compare(libgcj.so.10)<br> at java.util.TreeMap.put(libgcj.so.10)<br> at java.util.TreeSet.addAll(libgcj.so.10)<br> at org.globus.cog.abstraction.coaster.service.job.manager.Settings.setCallbackURIs(Settings.java:403)<br>
at org.globus.cog.abstraction.coaster.service.job.manager.JobQueue.<init>(JobQueue.java:41)<br> at org.globus.cog.abstraction.coaster.service.CoasterService.start(CoasterService.java:148)<br> at org.globus.cog.abstraction.coaster.service.CoasterService.main(CoasterService.java:382)<br>
<br><br> uname, uname.swift, line 12</span><br><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">Finally, here's part of what gets dumped to my log file:<br><span style="font-family:courier new,monospace"><br>
<snip><br>2013-06-15 14:54:22,350-0700 INFO BootstrapService [/<a href="http://171.67.106.68:39309">171.67.106.68:39309</a>] GET /coaster-bootstrap.jar HTTP/1.0<br>2013-06-15 14:54:22,713-0700 INFO ServiceManager Service task Task(type=JOB_SUBMISSION, identity=urn:cog-1371333260175) terminated. Removing service.<br>
2013-06-15 14:54:22,713-0700 INFO ServiceManager Service does not appear to be registered with this manager<br>2013-06-15 14:54:22,713-0700 INFO ServiceManager Coaster service ended. Reason: null<br> stdout: <br>
stderr: Failed to start coaster service<br>java.lang.NullPointerException<br> at java.net.URI.compareTo(libgcj.so.10)<br> at java.net.URI.compareTo(libgcj.so.10)<br> at java.util.TreeMap.compare(libgcj.so.10)<br>
at java.util.TreeMap.put(libgcj.so.10)<br> at java.util.TreeSet.addAll(libgcj.so.10)<br> at org.globus.cog.abstraction.coaster.service.job.manager.Settings.setCallbackURIs(Settings.java:403)<br> at org.globus.cog.abstraction.coaster.service.job.manager.JobQueue.<init>(JobQueue.java:41)<br>
at org.globus.cog.abstraction.coaster.service.CoasterService.start(CoasterService.java:148)<br> at org.globus.cog.abstraction.coaster.service.CoasterService.main(CoasterService.java:382)<br>java.lang.NullPointerException<br>
at java.net.URI.compareTo(libgcj.so.10)<br> at java.net.URI.compareTo(libgcj.so.10)<br> at java.util.TreeMap.compare(libgcj.so.10)<br> at java.util.TreeMap.put(libgcj.so.10)<br> at java.util.TreeSet.addAll(libgcj.so.10)<br>
at org.globus.cog.abstraction.coaster.service.job.manager.Settings.setCallbackURIs(Settings.java:403)<br> at org.globus.cog.abstraction.coaster.service.job.manager.JobQueue.<init>(JobQueue.java:41)<br> at org.globus.cog.abstraction.coaster.service.CoasterService.start(CoasterService.java:148)<br>
at org.globus.cog.abstraction.coaster.service.CoasterService.main(CoasterService.java:382)<br><br><br>2013-06-15 14:54:22,714-0700 INFO NotificationManager <a href="http://biox3.stanford.edu">biox3.stanford.edu</a><br>
2013-06-15 14:54:22,771-0700 INFO RuntimeStats$ProgressTicker Submitted:1<br>2013-06-15 14:54:22,775-0700 DEBUG swift APPLICATION_EXCEPTION jobid=uname-d77eqzal - Application exception: Caused by: Could not submit job<br>
Caused by: Could not start coaster service<br>Caused by: Task ended before registration was received. <br><br>Failed to start coaster service<br>java.lang.NullPointerException<br> at java.net.URI.compareTo(libgcj.so.10)<br>
at java.net.URI.compareTo(libgcj.so.10)<br> at java.util.TreeMap.compare(libgcj.so.10)<br> at java.util.TreeMap.put(libgcj.so.10)<br> at java.util.TreeSet.addAll(libgcj.so.10)<br> at org.globus.cog.abstraction.coaster.service.job.manager.Settings.setCallbackURIs(Settings.java:403)<br>
at org.globus.cog.abstraction.coaster.service.job.manager.JobQueue.<init>(JobQueue.java:41)<br> at org.globus.cog.abstraction.coaster.service.CoasterService.start(CoasterService.java:148)<br> at org.globus.cog.abstraction.coaster.service.CoasterService.main(CoasterService.java:382)<br>
java.lang.NullPointerException<br> at java.net.URI.compareTo(libgcj.so.10)<br> at java.net.URI.compareTo(libgcj.so.10)<br> at java.util.TreeMap.compare(libgcj.so.10)<br> at java.util.TreeMap.put(libgcj.so.10)<br> at java.util.TreeSet.addAll(libgcj.so.10)<br>
at org.globus.cog.abstraction.coaster.service.job.manager.Settings.setCallbackURIs(Settings.java:403)<br> at org.globus.cog.abstraction.coaster.service.job.manager.JobQueue.<init>(JobQueue.java:41)<br> at org.globus.cog.abstraction.coaster.service.CoasterService.start(CoasterService.java:148)<br>
at org.globus.cog.abstraction.coaster.service.CoasterService.main(CoasterService.java:382)<br></span></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><span style="font-family:courier new,monospace"><snip></span><br>
</div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><br><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">Any help or advice on how to resolve this issue, much much appreciated!<br>
<br>Thanks,<br><br>TJ<br></div></div>