Hi Diana, I think the fileIn variable is useless.
The instruction:
inputFiles += (graphFile, "graphIn.graphml")
garanties you that the content of the file pointed by graphFile will be
present in the work directory of the netlogo task when it runs. At
runtime the netlogo workdirectory will contain:
OM_Metamimetic_Networks.nlogo
otherstufFromYouNetLogoWorkspace
graphIn.graphml
The graphml file will be in the same directory as the nlogo file. Do you
think that if you just call load graphIn.graphml, then netlogo will look
into the same folder as your nlogo file? If not is there a command in
netlogo that returns this path?
If not will have to find a solution on the OpenMOLE side...
Romain
Le 25/09/2015 08:13, Diana Sifuentes Munch a écrit :
> Hello Romain
>
> The file is saved in a directory which is found by an exploration task
> by listing the files. Then, through a ScalaTask I get the full name of
> the file with its location path into a string. This is the name of the
> file NetLogo, is looking for. This works on the server. Maybe it is not
> correct, would you help me figure what the name of the file should be?
>
> You can find attached the relevant pieces of code.
>
> Thank You
>
>
> val packagingPath= "rootfs/iscpif/users/sifuentes/"
> val basePath = "/iscpif/users/sifuentes/"
> val InputGraphPath = basePath + "GraphFiles/SmallWorld1000"
>
>
>
> val graphExploration =
> ExplorationTask(
> (graphFile in ListFilesDomain( InputGraphPath) zipWithName graphName)
> )
>
>
>
> /* get graphName2 */
>
>
> val getName2 = ScalaTask( "val graphName2 = graphFile.toString ") set (
> inputs += graphName,
> inputs += graphFile,
> outputs += graphFile,
> outputs += graphName,
> outputs += graphName2
> )
>
>
>
> /* NetLogo Task */
>
>
> val topology = Val[String]
> val numAgents = Val[Double]
> val connectionProbability = Val[Double]
> val initialNeighbours = Val[Double]
> val rewiringProbability = Val[Double]
> val scaleFreeExponent = Val[Double]
> val initialRandomTypes = Val[Boolean]
> val initialMaxi = Val[Double]
> val initialMini = Val[Double]
> val initialConf = Val[Double]
> val strengthOfDilemma = Val[Double]
> val inicoop = Val[Double]
> val replacement = Val[Boolean]
> val culturalConstant = Val[Double]
> val loadtopology = Val[Boolean]
> val graphNL = Val[File]
> *val filein = Val[String]*
> val seed = Val[Int]
>
> […]
>
>
> val LogoModel = NetLogo5Task( basePath +
> "metamimetic/model/OM_Metamimetic_Networks.nlogo", cmds, true) set (
> inputs += graphName,
> inputs += seed,
> topology := "MyTopology",
> numAgents := 0.0,
> connectionProbability := 0.0,
> rewiringProbability := 0.0,
> initialNeighbours := 0.0,
> scaleFreeExponent := 0.0,
> initialRandomTypes := true,
> initialMaxi := 0.0,
> initialMini := 0.0,
> initialConf := 0.0,
> culturalConstant := 2.0,
> replacement := true,
> loadtopology := true,
> *filein := "graphIn.graphml",*
> * *netLogoInputs += (topology, "Topology"),
> netLogoInputs += (numAgents, "Num-Agents"),
> netLogoInputs += (connectionProbability, "Connection-Probability"),
> netLogoInputs += (initialNeighbours, "Initial-Neighbours"),
> netLogoInputs += (rewiringProbability, "Rewiring-Probability"),
> netLogoInputs += (scaleFreeExponent, "Scale-Free-Exponent"),
> netLogoInputs += (initialRandomTypes, "Initial-Random-Types?"),
> netLogoInputs += (initialMaxi, "Initial-Maxi-%"),
> netLogoInputs += (initialMini, "Initial-Mini-%"),
> netLogoInputs += (initialConf, "Initial-Conf-%"),
> netLogoInputs += (strengthOfDilemma, "Strength-of-Dilemma"),
> netLogoInputs += (inicoop, "inicoop"),
> netLogoInputs += (replacement, "replacement?"),
> netLogoInputs += (culturalConstant, "cultural-constant"),
> netLogoInputs += (loadtopology, "Load-Topology?"),
> *netLogoInputs += ( graphName2 , "FileIn"),*
> * inputFiles += (graphFile, "graphIn.graphml"),*
> * *outputFiles += ("Rules.csv", RulesNL),
> outputFiles += ("Behavior.csv", BehaviorNL),
> outputFiles += ("Satisfaction.csv", SatisfactionNL),
> outputFiles += ("Scores.csv", ScoresNL),
> outputFiles += ("Best.csv", BestNL),
> outputFiles += ("Ages.csv", AgesNL),
> outputFiles += ("Maxi.csv", MaxiNL),
> outputFiles += ("Mini.csv", MiniNL),
> outputFiles += ("Conf.csv", ConfNL),
> outputFiles += ("Anti.csv", AntiNL),
> outputFiles += ("Global.csv", GlobalNL),
> outputs += (inicoop, strengthOfDilemma, culturalConstant ,
> graphName2, graphName, seed))
>
> [… ]
>
>
>
>> On 24 Sep 2015, at 23:07, Romain Reuillon <[email protected]
>> <mailto:[email protected]>> wrote:
>>
>> It seems like you have a problem with your nlogo file or extension which
>> is looking for a graphml on zebulon despite it is running on some other
>> computers. Is the file "ER_edges_13000_rep_24.graphml" part of the
>> design of experiments or is it the same for all model executions?
>>
>> Romain
>>
>> Le 24/09/2015 23:02, Diana Sifuentes Munch a écrit :
>>> Hello Romain, thank you very much.
>>>
>>> Apparently not finding the files (?). I had the same script working
>>> before the recent OM version update.
>>>
>>> What changed?
>>>
>>> Thank you
>>>
>>>
>>> Caused by: org.openmole.core.exception.UserBadDataError: Error while
>>> executing command Expansion(ListBuffer(UnexpandedElement(run-to-grid
>>> 2000 1490 500 250))):
>>> | org.nlogo.nvm.EngineException: Extension exception:
>>> /iscpif/users/sifuentes/GraphFiles/SmallWorld1000/ER_edges_13000_rep_24.graphml
>>> (No such file or directory)
>>> | at java.io.FileInputStream.open0(Native Method)
>>> | at java.io.FileInputStream.open(FileInputStream.java:195)
>>> | at java.io.FileInputStream.<init>(FileInputStream.java:138)
>>> | at java.io.FileInputStream.<init>(FileInputStream.java:93)
>>> | at java.io.FileReader.<init>(FileReader.java:58)
>>> | at
>>> org.nlogo.extensions.nw.jung.io.GraphMLImport$.load(GraphMLImport.scala:159)
>>> | at
>>> org.nlogo.extensions.nw.prim.jung.LoadGraphML.createTurtles(GraphML.scala:27)
>>> | at
>>> org.nlogo.extensions.nw.prim.jung.LoadGraphML.createTurtles(GraphML.scala:23)
>>> | at
>>> org.nlogo.extensions.nw.NetworkExtensionUtil$TurtleCreatingCommand$class.perform(NetworkExtensionUtil.scala:119)
>>> | at
>>> org.nlogo.extensions.nw.prim.jung.LoadGraphML.perform(GraphML.scala:23)
>>> | at org.nlogo.prim._extern.perform(_extern.java:54)
>>> | at org.nlogo.nvm.Context.stepConcurrent(Context.java:91)
>>> | at org.nlogo.nvm.ConcurrentJob.step(ConcurrentJob.java:82)
>>> | at org.nlogo.job.JobThread.org
>>> <http://org.nlogo.job.JobThread.org>$nlogo$job$JobThread$$runPrimaryJobs(JobThread.scala:143)
>>> | at
>>> org.nlogo.job.JobThread$$anonfun$run$1.apply$mcV$sp(JobThread.scala:78)
>>> | at
>>> org.nlogo.job.JobThread$$anonfun$run$1.apply(JobThread.scala:76)
>>> | at
>>> org.nlogo.job.JobThread$$anonfun$run$1.apply(JobThread.scala:76)
>>> | at scala.util.control.Exception$Catch.apply(Exception.scala:88)
>>> | at org.nlogo.util.Exceptions$.handling(Exceptions.scala:41)
>>> | at org.nlogo.job.JobThread.run(JobThread.scala:75)
>>> at org.openmole.plugin.task.netlogo.NetLogoTask$class.org
>>> <http://class.org>$
>>>
>>>
>>>> On 24 Sep 2015, at 22:40, Romain Reuillon <[email protected]
>>>> <mailto:[email protected]>> wrote:
>>>>
>>>> Hi Diana,
>>>>
>>>> there is a lot of warning. Could you execute error(env2) and send some
>>>> errors that are displayed.
>>>>
>>>> Romain
>>>>
>>>> PS: beware your grid certificate expires the 30th of septembre... you
>>>> should renew it.
>>>>
>>>> Le 24/09/2015 22:08, Diana Sifuentes Munch a écrit :
>>>>> Hello,
>>>>>
>>>>> I am trying to do some runs on a grid.
>>>>>
>>>>> Every run takes a graph file of less than 1MB and runs a NetLogo
>>>>> task. Each run takes 1.5 minutes and less than 2gb of RAM memory on
>>>>> a mid 2014 MacBook Pro.
>>>>>
>>>>> I have sent ~30K jobs to the grid two days ago and even though
>>>>> after 24 hours they started to appear to be running, none of them
>>>>> has returned the outputs.
>>>>>
>>>>> Moreover, it looks like different amounts of jobs are being run
>>>>> each time but none finish. I have run the same script on a local
>>>>> environment for fewer jobs and it works without errors.
>>>>>
>>>>> Thank you in advance for your help.
>>>>>
>>>>>
>>>>> Ready: 31504
>>>>> Running: 275
>>>>> Completed: 1927
>>>>> OpenMOLE>print(ex)
>>>>> Ready:
>>>>> 31568
>>>>>
>>>>> Running:
>>>>> 211
>>>>>
>>>>> Completed:
>>>>> 1927
>>>>> OpenMOLE>print(ex)
>>>>> Ready: 31573
>>>>> Running: 206
>>>>> Completed: 1927
>>>>> OpenMOLE>print(ex)
>>>>> Ready: 31647
>>>>> Running: 132
>>>>> Completed: 1927
>>>>> OpenMOLE>print(env2)
>>>>> Submitted: 99
>>>>> Running: 127
>>>>> Done: 61667
>>>>> Failed: 0
>>>>> 0 critical errors, 999 warning and 1 low-importance errors. Use the
>>>>> errors() function to display them.
>>>>> OpenMOLE>print(env2)
>>>>> Submitted: 128
>>>>> Running: 164
>>>>> Done: 64642
>>>>> Failed: 0
>>>>> 0 critical errors, 999 warning and 1 low-importance errors. Use the
>>>>> errors() function to display them.
>>>>> OpenMOLE>print(ex)
>>>>> Ready: 31618
>>>>> Running: 161
>>>>> Completed: 1927
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> OpenMOLE-users mailing list
>>>>> [email protected] <mailto:[email protected]>
>>>>> http://fedex.iscpif.fr/mailman/listinfo/openmole-users
>>>>>
>>>>
>>>>
>>>
>>
>>
>
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