[Swift-devel] ext struct mapper on provider staging

Allan Espinosa aespinosa at cs.uchicago.edu
Wed Oct 27 20:06:09 CDT 2010 

Somehow when provider staging is enabled an additional "." is being
added to the path of the data objects which gives invalid path
exceptions in the jobs.  The problem does not occur in swift's normal
usage.

RunID: scratch
Progress:
Progress:  uninitialized:2  Finished in previous run:2
Progress:  uninitialized:2  Finished in previous run:2
Progress:  Selecting site:366  Stage in:1  Active:3  Finished in previous run:2
Execution failed:
        Trying to release previously released contact: 19
Exception in extract:
Arguments: [stat=LGU, extract_sgt=1, slon=-119.06587, slat=34.10819,
rupmodfile=gpfs/pads/swift/aespinosa/science/cybershake/RuptureVariations/113/4/113_4.txt.variation-s0017-h0008,
sgt_xfile=LGU/LGU_fx_664.sgt, sgt_yfile=LGU/LGU_fy_664.sgt,
extract_sgt_xfile=gpfs/pads/swift/aespinosa/science/cybershake/Results/LGU/113/4/LGU_113_4_subfx.sgt,
extract_sgt_yfile=gpfs/pads/swift/aespinosa/science/cybershake/Results/LGU/113/4/LGU_113_4_subfy.sgt]
Host: PADS
Directory: postproc-scratch/jobs/g/extract-gg6rfr0kTODO: outs
----

Caused by:
        org.griphyn.vdl.mapping.InvalidPathException: Invalid path
(..y) for org.griphyn.vdl.mapping.RootDataNode identifier
tag:benc at ci.uchicago.edu,2008:swift:dataset:20101027-2001-iexur5ud:720000026179
type Sgt with no value at dataset=sub (not closed)

log entry:
2010-10-27 20:02:07,534-0500 INFO  ExecutionContext Detailed exception:
Exception in extract:
Arguments: [stat=LGU, extract_sgt=1, slon=-119.06587, slat=34.10819,
rupmodfile=gpfs/pads/swift/aespinosa/science/cybe
rshake/RuptureVariations/113/4/113_4.txt.variation-s0017-h0008,
sgt_xfile=LGU/LGU_fx_664.sgt, sgt_yfile=LGU/LGU_fy_664
.sgt, extract_sgt_xfile=gpfs/pads/swift/aespinosa/science/cybershake/Results/LGU/113/4/LGU_113_4_subfx.sgt,
extract_sg
t_yfile=gpfs/pads/swift/aespinosa/science/cybershake/Results/LGU/113/4/LGU_113_4_subfy.sgt]
Host: PADS
Directory: postproc-scratch/jobs/g/extract-gg6rfr0kTODO: outs
----

Caused by: org.griphyn.vdl.mapping.InvalidPathException: Invalid path
(..y) for org.griphyn.vdl.mapping.RootDataNode i
dentifier tag:benc at ci.uchicago.edu,2008:swift:dataset:20101027-2001-iexur5ud:720000026179
type Sgt with no value at da
taset=sub (not closed)
Caused by: org.griphyn.vdl.mapping.InvalidPathException: Invalid path
(..y) for org.griphyn.vdl.mapping.RootDataNode i
dentifier tag:benc at ci.uchicago.edu,2008:swift:dataset:20101027-2001-iexur5ud:720000026179
type Sgt with no value at da
taset=sub (not closed)
        at org.globus.cog.karajan.workflow.nodes.functions.KException.function(KException.java:29)
        at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:27)
        at org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWith
Arguments.java:192)
        at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:32)
        at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:340)
        at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173)
        at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:181)
        at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:309)
        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:50)
        at org.globus.cog.karajan.workflow.nodes.Sequential.executeChildren(Sequential.java:26)
        at org.globus.cog.karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java:63)
        at org.globus.cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:238)
        at org.globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java:289)
        at org.globus.cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java:402)
        at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:343)
        at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173)
        at org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:44)
        at edu.emory.mathcs.backport.java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:431)
        at edu.emory.mathcs.backport.java.util.concurrent.FutureTask.run(FutureTask.java:166)
        at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:643)
        at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:668)
        at java.lang.Thread.run(Thread.java:619)
Caused by: org.griphyn.vdl.mapping.InvalidPathException: Invalid path
(..y) for org.griphyn.vdl.mapping.RootDataNode identifier
tag:benc at ci.uchicago.edu,2008:swift:dataset:20101027-2001-iexur5ud:720000026179
type Sgt with no value at dataset=sub (not closed)
Caused by: org.griphyn.vdl.mapping.InvalidPathException: Invalid path
(..y) for org.griphyn.vdl.mapping.RootDataNode identifier
tag:benc at ci.uchicago.edu,2008:swift:dataset:20101027-2001-iexur5ud:720000026179
type Sgt with no value at dataset=sub (not closed)
        at org.griphyn.vdl.karajan.lib.AppStageouts.post(AppStageouts.java:56)
        ... 22 more
Caused by: org.griphyn.vdl.mapping.InvalidPathException: Invalid path
(..y) for org.griphyn.vdl.mapping.RootDataNode identifier
tag:benc at ci.uchicago.edu,2008:swift:dataset:20101027-2001-iexur5ud:720000026179
type Sgt with no value at dataset=sub (not closed)
        at org.griphyn.vdl.mapping.AbstractDataNode.getField(AbstractDataNode.java:179)
        at org.griphyn.vdl.karajan.lib.AppStageouts.post(AppStageouts.java:40)
        ... 22 more
2010-10-27 20:02:07,538-0500 DEBUG AbstractDataNode Notifying listener
"F/org.griphyn.vdl.mapping.DataNode identifier
tag:benc at ci.uchicago.edu,2008:swift:dataset:20101027-2001-iexur5ud:720000028126
type Variation with no value at dataset=vars path=[337] (closed)"
about "org.griphyn.vdl.mapping.DataNode identifier
tag:benc at ci.uchicago.edu,2008:swift:dataset:20101027-2001-iexur5ud:720000028126
type Variation with no value at dataset=vars path=[337] (closed)"
2010-10-27 20:02:07,506-0500 DEBUG AbstractDataNode closed
org.griphyn.vdl.mapping.RootDataNode identifier
tag:benc at ci.uchicago.edu,2008:swift:dataset:20101027-2001-iexur5ud:720000029854
type VariationFile with no value at dataset=file (closed)


-- 
Allan M. Espinosa <http://amespinosa.wordpress.com>
PhD student, Computer Science
University of Chicago <http://people.cs.uchicago.edu/~aespinosa>

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