<html><head><base href="x-msg://40/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">I am starting to believe that this maybe a bug. I have this line in the log.<div><div><br></div><div>2011-07-13 16:17:50,835+0000 DEBUG vdl:dostageinfile FILE_STAGE_IN_START file=data.txt srchost=gridftp.pads.ci.uchicago.edu:2811 srcdir=/gpfs/pads/projects/CI-CCR000013/jonmon/Swift/tests/cat_test srcname=data.txt desthost=localhost destdir=script-20110713-1617-lzk6sxj3/shared/gpfs/pads/projects/CI-CCR000013/jonmon/Swift/tests/cat_test provider=gsiftp policy=DEFAULT</div><div><br></div><div>The desthost is localhost. That is correct. But why does the destdir have /gpfs in it? My localhost is VM. It does not have access to gpfs.</div><div><br></div><div>The files for this run are in ~jonmon/run.0002 on the ci machines.</div><div><br></div><div><div>On Jul 13, 2011, at 9:13 AM, Michael Wilde wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><div style="font-family: 'Times New Roman'; font-size: 12pt; color: rgb(0, 0, 0); ">I was going to suggest that same as Sarah pointed out, suspecting that the short-form of single_file_mapper is not correctly parsing the GSIFTP URI. If thats the case, please file it as a bug, Jon.<div><br></div><div>Can you try both forms of the mapper syntax with a known-good URI?</div><div><br></div><div>Thanks,</div><div><br></div><div>- Mike</div><div><br><br><hr id="zwchr"><blockquote style="border-left-width: 2px; border-left-style: solid; border-left-color: rgb(16, 16, 255); margin-left: 5px; padding-left: 5px; ">Thanks. I just verified that something maybe wrong with the path. I could not globus-url-copy that URI so I will continue to investigate<div><br><div><div><div>On Jul 12, 2011, at 4:59 PM, Sarah Kenny wrote:</div><br class="Apple-interchange-newline"><blockquote>i've used this successfully in the past:<br><br>file mybrain<single_file_mapper; file="gsiftp://<a href="http://calero.bsd.uchicago.edu/gpfs/pads/projects/stroke_recovery/dude.mgz" target="_blank">calero.bsd.uchicago.edu/gpfs/pads/projects/stroke_recovery/dude.mgz</a>")>;<br><br>it's been a while though...haven't tested with the latest swift...<br><br><div class="gmail_quote">On Tue, Jul 12, 2011 at 1:59 PM, Jonathan Monette<span class="Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:jonmon@utexas.edu" target="_blank">jonmon@utexas.edu</a>></span><span class="Apple-converted-space"> </span>wrote:<br><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; ">How does this syntax look when mapping with the GSIURI? How does it work? I am still getting errors when trying to map a file with a GSIURI. It says file not found. Maybe I have a different understanding on how it works.<br><br>The files and the logs are in ~jonmon/run.0001 on the ci machines.<br><div><div></div><div class="h5"><br>On Jul 12, 2011, at 2:16 AM, Mihael Hategan wrote:<br><br>> You have a colon after the host name but no port. Either remove the<br>> colon or put a number after it.<br>><br>> On Mon, 2011-07-11 at 22:45 -0500, Jonathan Monette wrote:<br>>> I actually meant to send this to swift-devel.<br>>><br>>><br>>> Here is the background to the problem. I have data on PADS, I am<br>>> executing Swift on a VM, and I want to use OSG to compute with the<br>>> data. Before Mike left for vacation he said that you can map data in<br>>> Swift using the GSIURI scheme but he did not tell me how. What I did<br>>> below is<br>>><br>>><br>>> file<br>>> data<"<a href="about:blank" target="_blank">gsiftp://stor01.pads.ci.uchicago.edu:/gpfs/pads/projects/CI-CCR000013/jonmon/Swift/tests/cat_test/data.txt</a>">;<br>>><br>>><br>>> This does not seem to work in release 0.92.1 as the error below<br>>> shows. How do you map data in Swift using the GSIURI scheme?<br>>><br>>> Begin forwarded message:<br>>><br>>>> From: Jonathan Monette <<a href="mailto:jonmon@utexas.edu" target="_blank">jonmon@utexas.edu</a>><br>>>><br>>>> Date: July 11, 2011 2:30:34 PM CDT<br>>>><br>>>> To: swift-devel Devel <<a href="mailto:swift-devel@ci.uchicago.edu" target="_blank">swift-devel@ci.uchicago.edu</a>><br>>>><br>>>> Cc: Mihael Hategan Hategan <<a href="mailto:hategan@mcs.anl.gov" target="_blank">hategan@mcs.anl.gov</a>><br>>>><br>>>> Subject: NumberFormatException<br>>>><br>>>><br>>>> Mihael,<br>>>> I am getting this error using release 0.92.1.<br>>>><br>>>> 2011-07-11 19:24:44,395+0000 INFO unknown RUNID<br>>>> id=run:20110711-1924-c944yl9c<br>>>> 2011-07-11 19:24:44,508+0000 DEBUG VDL2ExecutionContext vdl:new @<br>>>> script.kml, line: 69: java.lang.RuntimeException:<br>>>> java.lang.NumberFormatException: For input string: ""<br>>>> java.lang.RuntimeException: java.lang.NumberFormatException: For<br>>>> input string: ""<br>>>> Caused by: java.lang.RuntimeException:<br>>>> java.lang.NumberFormatException: For input string: ""<br>>>> at org.griphyn.vdl.mapping.AbsFile.exists(AbsFile.java:109)<br>>>> at<br>>>> org.griphyn.vdl.mapping.file.SingleFileMapper.existing(SingleFileMapper.java:24)<br>>>> at<br>>>> org.griphyn.vdl.mapping.RootDataNode.checkInputs(RootDataNode.java:97)<br>>>> at<br>>>> org.griphyn.vdl.mapping.RootDataNode.checkInputs(RootDataNode.java:75)<br>>>> at<br>>>> org.griphyn.vdl.mapping.RootDataNode.innerInit(RootDataNode.java:61)<br>>>> at org.griphyn.vdl.mapping.RootDataNode.init(RootDataNode.java:37)<br>>>> at org.griphyn.vdl.karajan.lib.New.function(New.java:126)<br>>>> at org.griphyn.vdl.karajan.lib.VDLFunction.post(VDLFunction.java:68)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:32)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:340)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:181)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:309)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.user.UserDefinedElement.childCompleted(UserDefinedElement.java:290)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.user.SequentialImplicitExecutionUDE.childCompleted(SequentialImplicitExecutionUDE.java:85)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:32)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:340)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:181)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:309)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.functions.Argument.post(Argument.java:45)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:32)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:340)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:181)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:309)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.functions.Map_Map.post(Map_Map.java:55)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:50)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.Sequential.childCompleted(Sequential.java:44)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:32)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:340)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:181)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:309)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)<br>>>> at org.globus.cog.karajan.workflow.nodes.Each.post(Each.java:31)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:32)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:340)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:181)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:309)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:28)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:50)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.Sequential.executeChildren(Sequential.java:26)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java:63)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:238)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java:289)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java:402)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:343)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173)<br>>>> at<br>>>> org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:44)<br>>>> at edu.emory.mathcs.backport.java.util.concurrent.Executors<br>>>> $RunnableAdapter.call(Executors.java:431)<br>>>> at<br>>>> edu.emory.mathcs.backport.java.util.concurrent.FutureTask.run(FutureTask.java:166)<br>>>> at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor<br>>>> $Worker.runTask(ThreadPoolExecutor.java:643)<br>>>> at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor<br>>>> $Worker.run(ThreadPoolExecutor.java:668)<br>>>> at java.lang.Thread.run(Thread.java:636)<br>>>> Caused by: java.lang.NumberFormatException: For input string: ""<br>>>> at<br>>>> java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)<br>>>> at java.lang.Integer.parseInt(Integer.java:493)<br>>>> at java.lang.Integer.parseInt(Integer.java:514)<br>>>> at<br>>>> org.globus.cog.abstraction.impl.common.task.ServiceContactImpl.parse(ServiceContactImpl.java:90)<br>>>> at<br>>>> org.globus.cog.abstraction.impl.common.task.ServiceContactImpl.<init>(ServiceContactImpl.java:27)<br>>>> at org.griphyn.vdl.mapping.AbsFile.getFileResource(AbsFile.java:84)<br>>>> at org.griphyn.vdl.mapping.AbsFile.exists(AbsFile.java:99)<br>>>> ... 63 more<br>>>><br>>>> The files needed for this run are located in ~jonmon/run.0000 on the<br>>>> ci machines.<br>>><br>>><br>><br>><br>> _______________________________________________<br>> Swift-devel mailing list<br>><span class="Apple-converted-space"> </span><a href="mailto:Swift-devel@ci.uchicago.edu" target="_blank">Swift-devel@ci.uchicago.edu</a><br>><span class="Apple-converted-space"> </span><a href="https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel" target="_blank">https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel</a><br><br>_______________________________________________<br>Swift-devel mailing list<br><a href="mailto:Swift-devel@ci.uchicago.edu" target="_blank">Swift-devel@ci.uchicago.edu</a><br><a href="https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel" target="_blank">https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel</a><br></div></div></blockquote></div><br><br clear="all"><br>--<span class="Apple-converted-space"> </span><br>Sarah Kenny<br>Programmer<br>University of Chicago, Computation Institute<br>University of California Irvine, Dept. of Neurology<br>773-818-8300<br><br>_______________________________________________<br>Swift-devel mailing list<br><a href="mailto:Swift-devel@ci.uchicago.edu" target="_blank">Swift-devel@ci.uchicago.edu</a><br><a href="https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel" target="_blank">https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel</a><br></blockquote></div><br></div></div><br>_______________________________________________<br>Swift-devel mailing list<br><a href="mailto:Swift-devel@ci.uchicago.edu">Swift-devel@ci.uchicago.edu</a><br><a href="https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel">https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel</a><br></blockquote><br><span><br><br>--<span class="Apple-converted-space"> </span><br><span name="x"></span>Michael Wilde<br>Computation Institute, University of Chicago<br>Mathematics and Computer Science Division<br>Argonne National Laboratory<br><span name="x"></span><br></span></div></div></div></blockquote></div><br></div></body></html>