DemoModeltolaunchthedemomodelYoumayhavemoreentriesthanthesingleoneshowninthe 1httprepastsourceforgenetdownloadhtml2httpwwworaclecomtechnetworkjavajavasedownloadsindexhtml1 2NICKCOL ID: 155934
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2NICKCOLLIER,JONATHANOZIK-REPASTDEVELOPMENTTEAMscreenshot,inwhichcase,justbesuretoselectJZombies DemoModel.DonotselectZombies DemoModel. Figure1.JZombiesModelLauncher2.TheBatchRunConfigurationGUITheBatchRunCongurationGUIisusedtocongureandlaunchthebatchrun.TostartthecongurationGUI,starttheJZombiesdemomodel(seesection1)andclickonthelightningboltinthetoolbar(g.2).NotethatyoucanalsostarttheGUIasastand-aloneapplication.Seesection6.4forthedetails. Figure2.BatchRunCongurationGUILaunchTheGUIisusedtocongureabatchrun.Thiscongurationcanbesavedandthenloadedatafuturetime.ThecongurationGUIconsistsofatoolbarandfourtabbedpanels(g.3).Therstfourtoolbarbuttons areusedtocreateanewconguration,openanexistingconguration,savethecurrentconguration,andsavethecurrentcongurationinanewle.Hoveringoverthebuttonswiththemousewillshowatooltipexplainingthebuttonsfunction.Thefthbutton willreloadthepropertiesinthemodelpanelfromthecurrentmodel.Theremainingtwobuttonshavetodowithperformingthebatchrunsitself.Regardlessoftypeofbatchrun(local,distributed,andsoforth),thebatchrunrequiresenoughofRepastSimphonyaswellasthemodeltoberuninordertowork.Thesepartsarebundled 6NICKCOLLIER,JONATHANOZIK-REPASTDEVELOPMENTTEAMtherighthandside\HostProperties"displaysthepropertiesforthehostselectedonthelefthandside.Newhostscanbecreatedusingthe\AddHost" button.Acopyofanexistinghostcanbemadewiththe\CopyHost" button.Existinghostscanbedeletedbyselectingthehosttodeleteandpressingthe\DeleteHost" button. Figure5.HostsPanelTheHostPropertiesare:Type:Thetypeofhost:localorremote.User:Theusernameoftheaccountontheremotemachine.Thisisonlyusedforaremotehost.Host:Thenameoripaddressoftheremotemachine.Thisisonlyusedforaremotehost.SSHKeyFile:ThenameoftheprivateSSHkeyleusedtoauto-loginontheremotehost.Thisisonlyusedforaremotehost.Instances:Thenumberofinstancestorunonthehost.Eachinstancewillbeas-signedachunkoftheparameterspacetorun.Eachofthehostsdenedonthehostpanelwillbeusedtoperformthebatchruns.Forexample,ifonelocalhostandoneremotehostisdenedandthelocalhosthastwo REPASTSIMPHONYBATCHRUNSGETTINGSTARTED7instancesandtheremotehosthasasingleinstance,thenthebatchparameterspacewillbedividedinthirds.Two-thirdswillberunlocallyinparallel:eachinstanceonthelocalmachinewillrunathirdofthespace.Theremainingthirdwillberunontheremotemachine.Thenumberofinstancestorunonamachineshouldberoughlythenumberofhardwarethreadsavailableonthemachine.Ofcourse,yourmilagemayvary,especiallyifthemachineisperformingothercomputationallyexpensivetasks.2.3.1.LocalRuns.Localrunsaretheeasiestrunstoperform,requiringtheleastamountofexternalsetup.Tocongurealocalrun,createahost(orchoseanexistingone)andsetitstypetoLOCAL.YouwillseethehostlabeledassomethinglikeX@localhostwhereXistheusernameoftheaccountrunningtheGUI.Whenyouperformalocalrun,theGUIcopiesthearchivepayloadmentionedabovetoatemporarylocationonthemachine'shard-drive.Thispayloadisunzippedandtheparameterspaceisdividedamongtheinstancestoberunlocallyandtherunsarebegun.Oncetherunshaveended,theoutputgeneratedbyeachinstanceisconcatenatedtogetherandplacedintheoutputdirectoryspeciedinthemodelpanel.2.3.2.RemoteRuns.Remoterunsaremorecomplicatedandyoumayhavetodosomesetuponthelocalandremotemachine.Remotemachinescanbeanythingfrommiscel-laneoussparemachinesthatyoumighthaveuptoamazon'scloudcomputingservices.RemoterunsworkoverSecureShell(SSH).SSHisacryptographicnetworkprotocolforsecuredatacommunication,remoteshellservicesorcommandexecutionandothersecurenetworkservicesbetweentwonetworkedcomputersthatconnect,viaasecurechanneloveraninsecurenetwork,aserverandaclient(runningSSHserverandSSHclientprograms,respectively).AnymachinethatallowsyoutoconnecttoitviaSSHandcanrunajavavirtualmachinecanbeusedtoperformaremoterun.Seesection6onhowtosetuptheremotemachines.Onthelocalside,thatis,onthemachineyouarerunningthebatchcongurationGUIon,youwillneedtobesetuptoauto-logintotheremotemachineusingpublickeyauthentication.Thisconsistsofcreatingasshpublic/privatekeypaironyourmachine,ifthosedon'talreadyexist,copyingthatkeytotheremotemachineandthenappendingthekeytothelistofauthorizedkeysontheremotemachine.Someusefulreferencesthatdescribethisare:OSX-http://smbjorklund.no/ssh-login-without-password-using-os-xWindows-Seebelow.Linux-https://hkn.eecs.berkeley.edu/dhsu/ssh public key howto.htmlOthersitesexistaswell,google\sshpublickeyauthentication"formoreinformation.Thesituationonwindowsismorecomplicated.OSXandLinuxcomewithsshandthusthebuilt-inabilitytogeneratepublic/privatekeypairs.Unfortunately,thisisnotthecaseforWindowsandthussomesetupisrequired.ThefollowingstepsdescribeonewaytogeneratethekeypairandcopyittotheremotemachineunderWindows.(1)DownloadandinstalltheGitClientfromhttp://git-scm.com/download/win. REPASTSIMPHONYBATCHRUNSGETTINGSTARTED9nameoripaddressofthemachinetologinintoandtheSSHKeyFileistheprivatekeyleonthelocalmachineusedtoauto-logintotheremotemachine.Thisleistypicallycalledid rsaina.sshdirectoryintheuser'shomedirectory,butitmaybedi erent.Whenperformingabatchrunusingaremotehost,theactivepayloadwillbecopiedtotheaccountoftheuserspeciedinthehostproperties.Afterthat,therunoccursasitdoesinthelocalversion.Thearchiveisunzippedandtheparameterspaceisdividedamongtheinstancestoberunonthatremotehost.WhentheinstancerunshaveendedtheoutputiscopiedbacktothemachinewheretheGUIwasrun,concatenatedandwrittentotheoutputdirectory.3.PreparingYourModelforBatchRunsTherstrequirementforabatchrunisthatyourmodelmustterminateeachrun.WhenrunningthemodelviatheGUIthisistypicallydonebyclickingthestopbutton.Inthebatchruncase,youmustsetandchecksometerminationconditionandthenstopthemodelifthatconditionismet.Or,setthemodeltoterminateatsomespecictick.IntheJZombiescase,therstofthesemightlooklike:if(context.getObjects(Human.class).size()==0){RunEnvironment.getInstance().endRun();}ThischeckstoseeifthereareanymoreHumansandifnotthenitcallsRunEnvironmenttoendtherun.Contexthereisthemodel'smastercontext.Somethinglikethiscouldbescheduledtoexecuteonceeverytickeithermanuallyorviaascheduledmethodonthecontextbuilder.Thesecondoptionlookslike:RunEnvironment.getInstance().endAt(30);Thisschedulesthesimulationtoendattick30.ItcanbeplacedintheContextBuilderforyourmodel.Thesecondrequirementconcernsthemodel'sleoutput.ThebatchmechanismassumesthattheoutputiscapturedusingRepastSimphony'sFileSinksandthattheleswillbewrittensomewhereinthe\instance"directorywherethemodelruns.Thebestwaytoinsurethatthisoccurstospecifythelewithonlythelenamewithoutanypathinformation.Makesurethatthelenamedoesnotbeginwitha\/"(underOSX,Linux)or\X:n"or\n"(underwindowswhereXisanydriveletter).Thenameitselfcanbeanything.Figure7isanexampleofanacceptablele.4.BatchRunModelOutputAsmentionedabovetheoutputfromeachinstancewillbeconcatenatedandcopiedintotheoutputdirectoryspeciedintheGUI.Thelesinkoutputwilllookthesameasanormalnon-batchrunexceptthattherunnumberswilllikelynotbeinnumericordergiventhattheconcatenationmakesnoaccountfororder.Forexample,theoutputfromrun11mayappearbeforethatfromrun2. 12NICKCOLLIER,JONATHANOZIK-REPASTDEVELOPMENTTEAM Figure8.ModelPanelForRunusingthatinformation.(Inwhatfollows,thelepathshavebeenshortenedforformattingpurposes.Youwillseethefulllepath).INFO[AWT-EventQueue-0]16:55:18,582repast.simphony.batch.gui.BatchConfigMediator-Writingbatchrunconfigfileto:JZombies_Demo/output/config.propsThesecondstatusmessagesaysthatthebatch params.xmllethatwascreatedviatheGUIis\unrolled"andwrittentoatemporarydirectory.\Unrolling"herereferstoexplicitlyproducingandwritingeachindividualparametercombinationtoale.Itisthisunrolledparameterlethatisdividedanddistributedtothehostsforrunning.INFO[AWT-EventQueue-0]16:55:18,588repast.simphony.batch.gui.BatchConfigMediator-Unrollingbatchparameterfile:JZombies_Demo/batch/batch_params.xmlto/var/folders/31/yd0l22kx35zgy1wbnc8p7gbr0000gr/T/unrolledParamFile.txtThenextsectionistheoutputoftheAntscript(seehttp://ant.apache.org)thatcreatesthearchivepayload.Herewecanseethecreationofaworkingdirectoryunderneathatemporarydirectory.ThisworkingdirectorywillcontainthemodelitselfandtheRepastSimphonycodenecessarytorunthemodel.The[copy]and[jar]sectionsreportmodelcodeandlesbeingcopiedintotheworkingdirectoryandthecreationofjararchives REPASTSIMPHONYBATCHRUNSGETTINGSTARTED13 Figure9.BatchPanelForRuncontainingthenecessaryrepastcode.(I'vereplacedpartofthetemporarypathwith\..."andtruncatedthejarsectionabittoimprovethereadabilityhere.)make_zip:[delete]Deletingdirectory/private/var/folders/.../working[mkdir]Createddir:/private/var/folders/.../working[mkdir]Createddir:/private/var/folders/.../working/bin[mkdir]Createddir:/private/var/folders/.../working/scenario.rs[copy]Copying2filesto/private/var/folders/.../working[copy]Copying3resourcesto/private/var/folders/.../working[copy]Copying1resourceto/private/var/folders/.../working/binmake_pre_reqs:[mkdir]Createddir:/private/var/folders/.../working/data[mkdir]Createddir:/private/var/folders/.../working/lib...[jar]Buildingjar:/private/var/folders/.../working/lib/repast.simphony.batch.jar[jar]Buildingjar:/private/var/folders/.../working/lib/repast.simphony.statecharts.jar[copy]Copying69filesto/private/var/folders/.../working/lib[jar]Buildingjar:/private/var/folders/.../working/lib/model.jar[copy]Copying10filesto/private/var/folders/.../working/scenario.rs 14NICKCOLLIER,JONATHANOZIK-REPASTDEVELOPMENTTEAM Figure10.HostsPanelForRun[move]Moving1fileto/private/var/folders/.../working/scenario.rs[jar]Buildingjar:JZombies_Demo/output/complete_model.jar[echo]Completedbuildingmodelarchive.Thearchivepayloadisthencopiedtothelocalandremotehosts.Theprocesshereisthataziparchiveiscreatedcontainingthearchivepayloadaswellassomeadditionalcongurationdata.Thisziparchiveisnamedwiththeusernamefollowedbythehosttogetherwithatimestamp(e.g.nick localhost4106394375716993975.zip).Inthecaseofalocalhost,theziparchiveiscopiedtoalocaltemporarydirectorywhosenamebeginswithsimphony model followedbyatimestamp(e.g.simphony model 1368219324898).INFO[SwingWorker-pool-1-thread-2]16:56:26,990repast.simphony.batch.ssh.LocalSession-Copyinglocally/var/folders/.../nick_localhost4106394375716993975.zipto/var/folders/.../simphony_model_1368219324898INFO[SwingWorker-pool-1-thread-2]16:56:27,411repast.simphony.batch.ssh.LocalSession-CopyingFinished.Theremotehostworkssimilarly.Theziparchiveiscopiedtoasimphony model plustimestampdirectoryontheremotehost.Inthiscase,theziparchiveisnamedubuntu ec2-107-20-23-221.compute-1.amazonaws.com8807870753490178805.zipandtheremotedirec-toryis/simphony model 1368219324898/.INFO[SwingWorker-pool-1-thread-2]16:56:09,829 16NICKCOLLIER,JONATHANOZIK-REPASTDEVELOPMENTTEAMPolledsimphony_model_1368219324898onec2-107-20-23-221.compute-1.amazonaws.comforDONE:yesINFO[pool-3-thread-1]16:56:52,796repast.simphony.batch.ssh.RemoteDonePoller-Polledsimphony_model_1368219324898onXXX.XXX.XXX.XXXforDONE:yesIftherewaserrorduringtherun,thatshouldbereportedhereaspartofthepolling.Assumingtherewasn'tthenthelocalandremoteoutputiscopiedandconcatenatedintotheoutputdirectorythatwasspeciedintheGUI.INFO[SwingWorker-pool-1-thread-2]16:56:55,630repast.simphony.batch.ssh.RemoteSession-Findingandcopyingremoteoutputfromsshtesting@XXX.XXX.XXX.XXX:simphony_model_1368219324898to/var/folders/.../sshtesting_XXX.XXX.XXX.XXXINFO[SwingWorker-pool-1-thread-2]16:56:58,412repast.simphony.batch.ssh.RemoteSession-Findingandcopyingremoteoutputfromubuntu@ec2-107-20-23-221.compute-1.amazonaws.com:simphony_model_1368219324898to/var/folders/.../ubuntu_ec2-107-20-23-221.compute-1.amazonaws.comINFO[SwingWorker-pool-1-thread-2]16:57:00,247repast.simphony.batch.ssh.LocalSession-Findingoutputonlocalhostin/var/folders/.../simphony_model_1368219324898INFO[SwingWorker-pool-1-thread-2]16:57:00,266repast.simphony.batch.ssh.SessionsDriver-AggregatingoutputintoJZombies_Demo/outputINFO[SwingWorker-pool-1-thread-2]16:57:00,267repast.simphony.batch.ssh.SessionsDriver-Finished.ElapsedTime:1.5906 Figure11.PassphraseDialog REPASTSIMPHONYBATCHRUNSGETTINGSTARTED176.RemoteMachineSetupInordertoperformarunonaremotemachinethatmachinemustbesetuptoacceptansshconnectionandyoumusthaveanaccountontheremotemachine.Oncethere-motemachinehasbeensetupforsshlogins,youthenneedtoaddyourpublickeytoitsauthorized keysleasdescribedinsection2.3.2.TheremotemachinemusthaveJava7installedanditmustbebethedefaultJava.6.1.OSX.AllowingremoteloginsonOSXisdoneusingtheSystemPreferencesonthemachineyouwanttoremotelyloginto.StartSystemPreferencesanddoubleclickonthesharingicon.SelecttheRemoteLoginasseeningure12.Makesureyouallowaccessfortheuseryouwillbelogginginas.Youshouldnowbeabletosshintotheremotemachineandcopyyourpublickeystotheserverasdescribedinlinksgiveninsection2.3.2. Figure12.EnablingSSHDonOSX6.2.Linux/Unix.ChancesareiftheremotemachineisrunningLinuxoranotherUnixvariantitisalreadysetuptoallowsshlogins.Ifnot,followyourdistributionsinstructionsforturningonthesshdservice.Youshouldnowbeabletosshintotheremotemachineandcopyyourpublickeystotheserverasdescribedinsection2.3.2. REPASTSIMPHONYBATCHRUNSGETTINGSTARTED23Wehavecoveredtherstoftheseinsection2.TheremainingtwoallowyoutolaunchthecongurationGUIandthusbatchrunswithoutlaunchingtherepastruntime.7.1.LaunchingfromEclipse.TolaunchthebatchGUIfromtheeclipselauncher,openthelaunchersfolderinyourmodel'seclipseprojectandrightclickonthelaunchlethatbeginswith\Batch"(g20).Select\RunAs"fromthepopupmenuandthentheBatchmodelentry.ThiswilllaunchthebatchGUIandloadtheselectedmodelintoit.NotethatwhenrunningviathelaunchersomeoftheoutputthatwouldnormallybeintheBatchRunGUIConsolewillshowupinEclipse'sconsole. Figure20.EclipseLauncherforBatchRunGUI7.2.LaunchingasaStandaloneApplication.TolaunchthebatchGUIasastandaloneapplicationnavigatetowhereRepastSimphonyisinstalled.Doubleclickthebatch runner.jar.8.RunningonaClusterorHPCMachineItisalsopossibletoperformbatchrunsonaclusterorahighperformancecomputing(HPC)typemachine.Suchmachinearecomposedofmanyprocessorseachofwhichcanrunoneormorebatchruninstancesandallofwhichhaveaccesstoasharedlesystem.Cluster/HPCrunswillusethepayloadarchiveproducedbytheGUIbutarenotthemselvesrunviatheGUI.Thesebatchrunswillusethejobsubmissionparadigmthatisstandardonthesetypesofmachines.TherststepforrunningamodelonanHPCmachineistocopythepayloadcom-plete model.jartotheremotemachine.Thepayloadislocatedinthemodel'soutputdirectoryandcanbecreatedusingtheBatchCongurationGUIwiththecreatearchivebutton( ).Thetransferisoftendoneviascporsimilarsecurecopymethods.Aftercopyingthepayloadtothedesiredlocation,thenextstepistounzipthepayload:unzipcomplete_model.jar