OSG All Hands Meeting 2012 Bill Marmagas zorbavbivtedu Virginia Bioinformatics Institute ACDIL Division Modeling and simulation of interactionbased coevolving technical biological and social networks in support of national policy ID: 1001735
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1. Emerging Campus Infrastructure at Virginia TechOSG All Hands Meeting 2012Bill Marmagaszorba@vbi.vt.edu
2. Virginia Bioinformatics InstituteACDIL DivisionModeling and simulation of interaction-based, co-evolving technical, biological, and social networks in support of national policyInfrastructure, immunology and disease, public health epidemiology, and national securityResearch NichesAdvancing the math & science of these simulationsIntegrating social and behavioral modelingDeveloping computational tools that leverage HPC
3. Example: DIDACTIC / EpiFastWeb-based epidemic modeling using HPC
4. Major Funders
5. Campus Infrastructure PiecesOSG Submit HostCampus Factory
6. OSG Submit HostFlocks HTPC Jobs to OSG Via EngageRENCI Configured Host DN on engage-submit3OSG Factory Also Configured to Allow AccessHost CertificateThis Host Can Be A Shared, Multi-User ResourceSubmit Host Firewall: Condor Config.HIGHPORT = 65535LOWPORT = 44536
7. Submit File Example: EpiFastuniverse = vanillaexecutable = runepifast.shRequirements = (CAN_RUN_WHOLE_MACHINE =?= TRUE)+RequiresWholeMachine = True# Put a process run on Hold if it has been running for four hours:periodic_hold = JobStatus == 2 && (CurrentTime - EnteredCurrentStatus > 14400)ShouldTransferFiles = YESwhen_to_transfer_output = ON_EXIToutput = submit.htpc.Vac-0.05_Alloc.out.$(Cluster).$(Process)error = submit.htpc.Vac-0.05_Alloc.err.$(Cluster).$(Process)log = submit.htpc.Vac-0.05_Alloc.log.$(Cluster).$(Process)#Process Run: 0transfer_input_files = ../../../bin/EpiFast, ../../../bin/mpiexec, ../../../areas/SeattleData.tgz, ../Vac-0.05_Alloc-0.0-0.0-0.0-0.0-1.0.tgzarguments = 8 Vac-0.05_Alloc-0.0-0.0-0.0-0.0-1.0queue
8. Campus FactoryEnables Flocking to Local HPC ClustersJobs Glide In To Compute NodesCan Also Be An HTPC Resourceecho "#PBS -lnodes=1:ppn=8”(/usr/libexec/condor/glite/bin/pbs_local_submit_attributes.sh)Moab NODEACCESSPOLICY=SINGLEJOB does sameSame EpiFast Jobs Run Here
9. Latest Campus Factory 0.4.3Prevents “Walltime Rogues”SHUTDOWN_GRACEFUL_TIMEOUT = 72000MAXJOBRETIREMENTTIME = 3480072000 sec. + 34800 sec. = 29 hours 40 minutes./glideinExec/glidein_startup -dyn -f -r 12001200 min. = 20 hours run time for condor_masterecho "#PBS -lwalltime=30:00:00”30 Hour Walltime is a bit more than SHUTDOWN_GRACEFUL_TIMEOUT + MAXJOBRETIREMENTTIME
10. Future WorkInfrastructureAdd Second Campus Factory ClusterIntegrate Campus Factories Into Submit HostWeb Interface Plug-In to Submit HostMore ApplicationsComputational Social Science ExampleBiochemical Network Simulation Example
11. Discrete Dynamical SystemsApplication: Model group dynamics and how a population may or may not reach a majority view.75879-node Epinions Network = 1075879 Config’sWe can look at a smaller, statistically significant setPerhaps: 100 Config’s X 50 Simulation Time StepsClusters of Muticore (Worker and Slave) Jobs0123456789increasing levels of convictionview 1 or opinion 1view 2 or opinion 2Ideology
12. COPASIA software application for simulation and analysis of biochemical networks and their dynamics.A collaboration between VBI, the University of Heidelberg, and the University of ManchesterCondor-COPASI is a web-based interface for integrating COPASI with CondorPotential good fit to flock to a dedicated Campus Factory to submit to their cluster queue
13. ReferencesTWiki: CampusGrids/InstallCondorFlockSubmitTWiki: Documentation/CampusFactoryInstallBill MarmagasSenior Systems EngineerNetwork Dynamics and Simulation Science LaboratoryVirginia Bioinformatics Institutezorba@vbi.vt.edu