./outputcombiner error

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./outputcombiner error

Grant, Tyler J [NREM]

Hi All,

 

I’m running batch runs on a campus server from Repast Simphony.  While running a long simulation yesterday (7 hrs), I lost connection to the server.  The simulation finished so I tried to run the outputcombiner.sh to combine the 20 instances of output files, but I got an error:

 

[tgrant@speedy2 simphony_model_1476272563950]$ ./outputcombiner.sh

Exception in thread "main" java.lang.NoClassDefFoundError: com/jcraft/jsch/JSchException

        at repast.simphony.batch.ssh.SessionBuilder.getRemote(SessionBuilder.java:25)

        at repast.simphony.batch.ssh.SessionBuilder.addInstancesToRemote(SessionBuilder.java:42)

        at repast.simphony.batch.ssh.SessionPropsParser.setRemote(SessionPropsParser.java:65)

        at repast.simphony.batch.ssh.SessionPropsParser.init(SessionPropsParser.java:43)

        at repast.simphony.batch.ssh.SessionPropsParser.parse(SessionPropsParser.java:32)

        at repast.simphony.batch.ssh.Configuration.<init>(Configuration.java:86)

        at repast.simphony.batch.ClusterOutputCombiner.createPatterns(ClusterOutputCombiner.java:60)

        at repast.simphony.batch.ClusterOutputCombiner.findOutput(ClusterOutputCombiner.java:88)

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

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

Caused by: java.lang.ClassNotFoundException: com.jcraft.jsch.JSchException

        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)

        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)

        ... 10 more

 

I’m logged in to the server (speedy2) with PuTTY and ran ./outputcombiner.sh from there. 

 

Can I use the outputcombiner to combine these 20 instances?

 

Thanks,

Tyler

 

 

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: ./outputcombiner error

srcnick
Where are you running it the outputcombiner.sh from? It expects to be in a directory above the lib directory that contains all the model etc. jars. In that lib directory you should see a jsch-0.1.48.jar that contains the missing class. 

Nick
On Oct 13, 2016, at 11:39 AM, Grant, Tyler J [NREM] <[hidden email]> wrote:

Hi All,
 
I’m running batch runs on a campus server from Repast Simphony.  While running a long simulation yesterday (7 hrs), I lost connection to the server.  The simulation finished so I tried to run the outputcombiner.sh to combine the 20 instances of output files, but I got an error:
 
[tgrant@speedy2 simphony_model_1476272563950]$ ./outputcombiner.sh
Exception in thread "main" java.lang.NoClassDefFoundError: com/jcraft/jsch/JSchException
        at repast.simphony.batch.ssh.SessionBuilder.getRemote(SessionBuilder.java:25)
        at repast.simphony.batch.ssh.SessionBuilder.addInstancesToRemote(SessionBuilder.java:42)
        at repast.simphony.batch.ssh.SessionPropsParser.setRemote(SessionPropsParser.java:65)
        at repast.simphony.batch.ssh.SessionPropsParser.init(SessionPropsParser.java:43)
        at repast.simphony.batch.ssh.SessionPropsParser.parse(SessionPropsParser.java:32)
        at repast.simphony.batch.ssh.Configuration.<init>(Configuration.java:86)
        at repast.simphony.batch.ClusterOutputCombiner.createPatterns(ClusterOutputCombiner.java:60)
        at repast.simphony.batch.ClusterOutputCombiner.findOutput(ClusterOutputCombiner.java:88)
        at repast.simphony.batch.ClusterOutputCombiner.run(ClusterOutputCombiner.java:69)
        at repast.simphony.batch.ClusterOutputCombiner.main(ClusterOutputCombiner.java:105)
Caused by: java.lang.ClassNotFoundException: com.jcraft.jsch.JSchException
        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 10 more
 
I’m logged in to the server (speedy2) with PuTTY and ran ./outputcombiner.sh from there. 
 
Can I use the outputcombiner to combine these 20 instances?
 
Thanks,
Tyler
 
 
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: ./outputcombiner error

Grant, Tyler J [NREM]

I’m running it from the right dir and I looked in lib and that .jar is not there.  I also tried find and it’s not there.  The problem is probably that I was running the simulation from the RS GUI batch runner.  I lost the connection, so I logged in with PuTTY and tried to use the outputcombiner (this is how I have to do it on a different HPC system I am also using).  So I may have to run it again?  Or I could download the 20 instances separately and combine them in R, but it would be nice if I could get the outputcombiner to work. 

 

Dr. Tyler J. Grant

Postdoctoral Associate

Department of Natural Resource Ecology and Management

Iowa State University

339 Science II

Ames, IA 50011

 

From: Nick Collier [mailto:[hidden email]]
Sent: Friday, October 14, 2016 7:57 AM
To: Grant, Tyler J [NREM] <[hidden email]>
Cc: [hidden email]
Subject: Re: [Repast-interest] ./outputcombiner error

 

Where are you running it the outputcombiner.sh from? It expects to be in a directory above the lib directory that contains all the model etc. jars. In that lib directory you should see a jsch-0.1.48.jar that contains the missing class. 

 

Nick

On Oct 13, 2016, at 11:39 AM, Grant, Tyler J [NREM] <[hidden email]> wrote:

 

Hi All,

 

I’m running batch runs on a campus server from Repast Simphony.  While running a long simulation yesterday (7 hrs), I lost connection to the server.  The simulation finished so I tried to run the outputcombiner.sh to combine the 20 instances of output files, but I got an error:

 

[tgrant@speedy2 simphony_model_1476272563950]$ ./outputcombiner.sh

Exception in thread "main" java.lang.NoClassDefFoundError: com/jcraft/jsch/JSchException

        at repast.simphony.batch.ssh.SessionBuilder.getRemote(SessionBuilder.java:25)

        at repast.simphony.batch.ssh.SessionBuilder.addInstancesToRemote(SessionBuilder.java:42)

        at repast.simphony.batch.ssh.SessionPropsParser.setRemote(SessionPropsParser.java:65)

        at repast.simphony.batch.ssh.SessionPropsParser.init(SessionPropsParser.java:43)

        at repast.simphony.batch.ssh.SessionPropsParser.parse(SessionPropsParser.java:32)

        at repast.simphony.batch.ssh.Configuration.<init>(Configuration.java:86)

        at repast.simphony.batch.ClusterOutputCombiner.createPatterns(ClusterOutputCombiner.java:60)

        at repast.simphony.batch.ClusterOutputCombiner.findOutput(ClusterOutputCombiner.java:88)

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

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

Caused by: java.lang.ClassNotFoundException: com.jcraft.jsch.JSchException

        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)

        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)

        ... 10 more

 

I’m logged in to the server (speedy2) with PuTTY and ran ./outputcombiner.sh from there. 

 

Can I use the outputcombiner to combine these 20 instances?

 

Thanks,

Tyler

 

 

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: ./outputcombiner error

srcnick
The jar is in the repast.simphony.distributed.batch lib directory (under eclipse/plugins), you could scp from there to the cluster lib directory, and try to run the outputcombiner.

Nick

On Oct 14, 2016, at 9:43 AM, Grant, Tyler J [NREM] <[hidden email]> wrote:

I’m running it from the right dir and I looked in lib and that .jar is not there.  I also tried find and it’s not there.  The problem is probably that I was running the simulation from the RS GUI batch runner.  I lost the connection, so I logged in with PuTTY and tried to use the outputcombiner (this is how I have to do it on a different HPC system I am also using).  So I may have to run it again?  Or I could download the 20 instances separately and combine them in R, but it would be nice if I could get the outputcombiner to work. 
 
Dr. Tyler J. Grant
Postdoctoral Associate
Department of Natural Resource Ecology and Management
Iowa State University
339 Science II
Ames, IA 50011
 
From: Nick Collier [[hidden email]] 
Sent: Friday, October 14, 2016 7:57 AM
To: Grant, Tyler J [NREM] <[hidden email]>
Cc: [hidden email]
Subject: Re: [Repast-interest] ./outputcombiner error
 
Where are you running it the outputcombiner.sh from? It expects to be in a directory above the lib directory that contains all the model etc. jars. In that lib directory you should see a jsch-0.1.48.jar that contains the missing class. 
 
Nick
On Oct 13, 2016, at 11:39 AM, Grant, Tyler J [NREM] <[hidden email]> wrote:
 
Hi All,
 
I’m running batch runs on a campus server from Repast Simphony.  While running a long simulation yesterday (7 hrs), I lost connection to the server.  The simulation finished so I tried to run the outputcombiner.sh to combine the 20 instances of output files, but I got an error:
 
[tgrant@speedy2 simphony_model_1476272563950]$ ./outputcombiner.sh
Exception in thread "main" java.lang.NoClassDefFoundError: com/jcraft/jsch/JSchException
        at repast.simphony.batch.ssh.SessionBuilder.getRemote(SessionBuilder.java:25)
        at repast.simphony.batch.ssh.SessionBuilder.addInstancesToRemote(SessionBuilder.java:42)
        at repast.simphony.batch.ssh.SessionPropsParser.setRemote(SessionPropsParser.java:65)
        at repast.simphony.batch.ssh.SessionPropsParser.init(SessionPropsParser.java:43)
        at repast.simphony.batch.ssh.SessionPropsParser.parse(SessionPropsParser.java:32)
        at repast.simphony.batch.ssh.Configuration.<init>(Configuration.java:86)
        at repast.simphony.batch.ClusterOutputCombiner.createPatterns(ClusterOutputCombiner.java:60)
        at repast.simphony.batch.ClusterOutputCombiner.findOutput(ClusterOutputCombiner.java:88)
        at repast.simphony.batch.ClusterOutputCombiner.run(ClusterOutputCombiner.java:69)
        at repast.simphony.batch.ClusterOutputCombiner.main(ClusterOutputCombiner.java:105)
Caused by: java.lang.ClassNotFoundException: com.jcraft.jsch.JSchException
        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 10 more
 
I’m logged in to the server (speedy2) with PuTTY and ran ./outputcombiner.sh from there. 
 
Can I use the outputcombiner to combine these 20 instances?
 
Thanks,
Tyler
 
 
Dr. Tyler J. Grant
Postdoctoral Associate
Department of Natural Resource Ecology and Management
Iowa State University
339 Science II
Ames, IA 50011
 
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most 
engaging tech sites, 
SlashDot.org! http://sdm.link/slashdot_______________________________________________
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Re: ./outputcombiner error

Grant, Tyler J [NREM]

That seems to work, thanks. 

 

Dr. Tyler J. Grant

Postdoctoral Associate

Department of Natural Resource Ecology and Management

Iowa State University

339 Science II

Ames, IA 50011

 

From: Nick Collier [mailto:[hidden email]]
Sent: Friday, October 14, 2016 10:07 AM
To: Grant, Tyler J [NREM] <[hidden email]>
Cc: [hidden email]
Subject: Re: [Repast-interest] ./outputcombiner error

 

The jar is in the repast.simphony.distributed.batch lib directory (under eclipse/plugins), you could scp from there to the cluster lib directory, and try to run the outputcombiner.

 

Nick

 

On Oct 14, 2016, at 9:43 AM, Grant, Tyler J [NREM] <[hidden email]> wrote:

 

I’m running it from the right dir and I looked in lib and that .jar is not there.  I also tried find and it’s not there.  The problem is probably that I was running the simulation from the RS GUI batch runner.  I lost the connection, so I logged in with PuTTY and tried to use the outputcombiner (this is how I have to do it on a different HPC system I am also using).  So I may have to run it again?  Or I could download the 20 instances separately and combine them in R, but it would be nice if I could get the outputcombiner to work. 

 

Dr. Tyler J. Grant

Postdoctoral Associate

Department of Natural Resource Ecology and Management

Iowa State University

339 Science II

Ames, IA 50011

 

From: Nick Collier [[hidden email]] 
Sent: Friday, October 14, 2016 7:57 AM
To: Grant, Tyler J [NREM] <[hidden email]>
Cc: [hidden email]
Subject: Re: [Repast-interest] ./outputcombiner error

 

Where are you running it the outputcombiner.sh from? It expects to be in a directory above the lib directory that contains all the model etc. jars. In that lib directory you should see a jsch-0.1.48.jar that contains the missing class. 

 

Nick

On Oct 13, 2016, at 11:39 AM, Grant, Tyler J [NREM] <[hidden email]> wrote:

 

Hi All,

 

I’m running batch runs on a campus server from Repast Simphony.  While running a long simulation yesterday (7 hrs), I lost connection to the server.  The simulation finished so I tried to run the outputcombiner.sh to combine the 20 instances of output files, but I got an error:

 

[tgrant@speedy2 simphony_model_1476272563950]$ ./outputcombiner.sh

Exception in thread "main" java.lang.NoClassDefFoundError: com/jcraft/jsch/JSchException

        at repast.simphony.batch.ssh.SessionBuilder.getRemote(SessionBuilder.java:25)

        at repast.simphony.batch.ssh.SessionBuilder.addInstancesToRemote(SessionBuilder.java:42)

        at repast.simphony.batch.ssh.SessionPropsParser.setRemote(SessionPropsParser.java:65)

        at repast.simphony.batch.ssh.SessionPropsParser.init(SessionPropsParser.java:43)

        at repast.simphony.batch.ssh.SessionPropsParser.parse(SessionPropsParser.java:32)

        at repast.simphony.batch.ssh.Configuration.<init>(Configuration.java:86)

        at repast.simphony.batch.ClusterOutputCombiner.createPatterns(ClusterOutputCombiner.java:60)

        at repast.simphony.batch.ClusterOutputCombiner.findOutput(ClusterOutputCombiner.java:88)

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

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

Caused by: java.lang.ClassNotFoundException: com.jcraft.jsch.JSchException

        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)

        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)

        ... 10 more

 

I’m logged in to the server (speedy2) with PuTTY and ran ./outputcombiner.sh from there. 

 

Can I use the outputcombiner to combine these 20 instances?

 

Thanks,

Tyler

 

 

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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engaging tech sites, 
SlashDot.org! http://sdm.link/slashdot_______________________________________________
Repast-interest mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/repast-interest

 


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