Output Combiner error

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Output Combiner error

Grant, Tyler J [NREM]

Hi all,

 

I’m running my monarch model on a large USGS HPC cluster.  The outputcombiner.sh worked the first time, but I got an error the second time.  I deleted all the old instance folders and combined_output folder, but still getting this error:

 

INFO  [main] 07:46:02,611 repast.simphony.batch.ClusterOutputCombiner - Finding output on localhost in .

repast.simphony.batch.ssh.StatusException: java.nio.file.FileSystemLoopException: /home/tjgrant/monarch/./instance_2/data/data

        at repast.simphony.batch.ssh.LocalOutputFinder.findOutputFiles(LocalOutputFinder.java:56)

        at repast.simphony.batch.ssh.LocalOutputFinder.run(LocalOutputFinder.java:72)

        at repast.simphony.batch.ClusterOutputCombiner.findOutput(ClusterOutputCombiner.java:95)

        at repast.simphony.batch.ClusterOutputCombiner.run(ClusterOutputCombiner.java:69)

        at repast.simphony.batch.ClusterOutputCombiner.main(ClusterOutputCombiner.java:105)

Caused by: java.nio.file.FileSystemLoopException: /home/tjgrant/monarch/./instance_2/data/data

        at java.nio.file.FileTreeWalker.walk(FileTreeWalker.java:149)

        at java.nio.file.FileTreeWalker.walk(FileTreeWalker.java:199)

        at java.nio.file.FileTreeWalker.walk(FileTreeWalker.java:199)

        at java.nio.file.FileTreeWalker.walk(FileTreeWalker.java:69)

        at java.nio.file.Files.walkFileTree(Files.java:2602)

        at repast.simphony.batch.ssh.LocalOutputFinder.findOutputFiles(LocalOutputFinder.java:54)

        ... 4 more

 

Dr. Tyler J. Grant

Postdoctoral Associate

Department of Natural Resource Ecology and Management

Iowa State University

339 Science II

Ames, IA 50011

 


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Re: Output Combiner error

Grant, Tyler J [NREM]

I figured out this problem.  In case anyone else has the same problem: the outputcombiner apparently checks to make sure the output files in all the instances are from the same simulation.  So you have to delete all instance folders, AND the data folder or link to the data folder.  So after I ran these commands the output combiner worked fine and the combined output files were correct:

 

rm -r instance_*

rm -r combined_data

rm -rf data/data

 

 

Dr. Tyler J. Grant

Postdoctoral Associate

Department of Natural Resource Ecology and Management

Iowa State University

339 Science II

Ames, IA 50011

 

From: Grant, Tyler J [NREM] [mailto:[hidden email]]
Sent: Monday, August 08, 2016 9:06 AM
To: [hidden email]
Subject: [Repast-interest] Output Combiner error

 

Hi all,

 

I’m running my monarch model on a large USGS HPC cluster.  The outputcombiner.sh worked the first time, but I got an error the second time.  I deleted all the old instance folders and combined_output folder, but still getting this error:

 

INFO  [main] 07:46:02,611 repast.simphony.batch.ClusterOutputCombiner - Finding output on localhost in .

repast.simphony.batch.ssh.StatusException: java.nio.file.FileSystemLoopException: /home/tjgrant/monarch/./instance_2/data/data

        at repast.simphony.batch.ssh.LocalOutputFinder.findOutputFiles(LocalOutputFinder.java:56)

        at repast.simphony.batch.ssh.LocalOutputFinder.run(LocalOutputFinder.java:72)

        at repast.simphony.batch.ClusterOutputCombiner.findOutput(ClusterOutputCombiner.java:95)

        at repast.simphony.batch.ClusterOutputCombiner.run(ClusterOutputCombiner.java:69)

        at repast.simphony.batch.ClusterOutputCombiner.main(ClusterOutputCombiner.java:105)

Caused by: java.nio.file.FileSystemLoopException: /home/tjgrant/monarch/./instance_2/data/data

        at java.nio.file.FileTreeWalker.walk(FileTreeWalker.java:149)

        at java.nio.file.FileTreeWalker.walk(FileTreeWalker.java:199)

        at java.nio.file.FileTreeWalker.walk(FileTreeWalker.java:199)

        at java.nio.file.FileTreeWalker.walk(FileTreeWalker.java:69)

        at java.nio.file.Files.walkFileTree(Files.java:2602)

        at repast.simphony.batch.ssh.LocalOutputFinder.findOutputFiles(LocalOutputFinder.java:54)

        ... 4 more

 

Dr. Tyler J. Grant

Postdoctoral Associate

Department of Natural Resource Ecology and Management

Iowa State University

339 Science II

Ames, IA 50011

 


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