<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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 type="cite">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">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 dir="ltr"><<a href="mailto:jonmon@utexas.edu">jonmon@utexas.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc 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="gsiftp://stor01.pads.ci.uchicago.edu:/gpfs/pads/projects/CI-CCR000013/jonmon/Swift/tests/cat_test/data.txt">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">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">swift-devel@ci.uchicago.edu</a>><br>
>>><br>
>>> Cc: Mihael Hategan Hategan <<a href="mailto:hategan@mcs.anl.gov">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>
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</div></div></blockquote></div><br><br clear="all"><br>-- <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">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></div><br></div></div></body></html>