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Research ComputingUSCViterbiSchoolofEngineering

NewFacultyOrienta:onPresenta:onAugust16,2017

ErinShaw,Presenter

AdvancedCyberinfrastructureResearch&Educa:onFacilitator(ACI-REF)USCCenterforHigh-PerformanceCompu:ng(HPC)

Information Technology Services (ITS) Research Computing Initiative

§  So)ware•  Campus-wideso)ware

§  Storage•  Datastorageop9ons

§  High-PerformanceCompu9ng(HPC)•  Resourcesandpurchaseop9ons•  Researchsupportandfacilita9on

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ITS Research Computing Management

CarolLiFleBuilding(CAL)

DouglasShookUSCCIO

MaureenDoughertyHPCDirector

RandolphHallUSCVPofResearch&HPCFacultyExecu=ve

Director**TheHPCFacultyAdvisoryCommiFeeadvisestheCIOaboutthefaculty’sresearchneedsrelatedtotheuniversity’sHPCresources.

SoftwareComprehensivelistatsoOware.usc.edu

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Statistical Computing Software

§  Campus-widelicenses•  SAS,SPSS,STATA&JMP-  Availablefordownloadatlow-cost/no-cost

•  SAS&STATA-  InstalledonHPCandavailableforfreewithanHPCaccount

§  OpensourceonHPC-  ThesesoHwarepackagesarepre-installedonHPC

•  RSta9s9calcompu9ngso)ware

•  Pythonscien9ficcompu9ngpackages

Technical Computing Software

§  Technicalso)wareavailablefordownload

•  MATLAB•  Mathema9ca

§  GISandremotesensing•  ArcGISandCityEngine•  TerrSetConstella9on•  Data/Geoportal

§  So)wareavailableonHPC•  MATLABandMathema9ca•  Compilers:Gnu,Intel,PGI•  NumericalLibraries:mpich,

Openmpi,CUDA,Sw,petsc•  MolecularSimula9on:NAMD,

Gromacs,Amber•  QuantumChemistry:Gaussian,

Qchem,MnovaNMR

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Bioinformatics Software (nml.usc.edu/bioinformatics/#software)

§  Comprehensivefunc9onalanalysis&advancedliterature/datamining•  PartekGenomicsSuite•  PartekFlow•  Galaxy•  VectorNTIAdvance•  MicroarrayRUS

§  Sta9s9calanalysisofhigh-throughputdataandDNA/proteinsequenceanalysis•  IngenuityPathwayAnalysis•  BIOBASE•  Nextbio•  Oncomine•  Geneves9gator•  Quetzal

Research & Research Management Software

§  Cita9onmanagement•  RefWorks,Mendeley,EndNote,

andZotero-  libraries.usc.edu/research/cita=on-management

§  Projectmanagement•  RedCap-  redcap.sc-ctsi.org

§  Surveydatacollec9on•  Qualtrics

§  Qualita9vedataanalysis•  ATLAS.9•  NVivo

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UNIX Computing Utilities

§  UNIXdocumenta9on-  itservices.usc.edu/unix

§  UNIXcompu9ngu9li9es•  Secureshell-  X-Win32(Preconfiguredwithconnec=onstoHPCheadnodesandotherUSCnetworks)

•  Securefiletransfer-  scp,FileZilla,Fetch(thirdparty)

§  Virtualprivatenetworking•  vpn.usc.edu•  CiscoAnyConnectVPN

Storage

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Cloud Data Storage

§  MSOffice365/OneDriveforBusiness•  5TBcapacity•  Approvedforstoringsomerestrictedinforma9on,includingHIPAA-and

FERPA-relatedinforma9on-  AllfacultyandstaffwithITS-supportedO365accountsreceiveaccess-  Graduatestudentsthatneedaccessshouldinquirewiththeirrespec=veschools

§  GoogleDrive•  Unlimitedcapacity•  NotapprovedforstoringHIPAA-relatedinforma9on-  Allfaculty,staff,andstudentsreceiveaccess

USC Data Storage

§  USCDigitalRepository-  repository.usc.edu

•  Fee-basedstorage,40PBoftotalcapacity-  High-speed,high-performancediskstorage,andlow-demandtapestorage-  AvailableforWindows,Mac,andLinux(includingHPC)-  Highlysecureandencryptedcloudstorage(ApprovedforHIPAA-relatedinforma=on)

§  USCDrive-  itservices.usc.edu/uscdrive

•  Free50GBhigh-speedstorageperresearcher-  NotapprovedforstoringHIPAA-relatedinforma=on-  Addi=onalstoragecanbepurchased

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HPC Data Storage

§  HPC“PI”scanrequestupto2TB*ofdiskspaceperproject•  Backedupdaily

§  Usershaveaccesstoa328TB/stagingdirectory•  Nodatabackup•  Cleanedduringsemi-annualdown9mesorwhencapacityreached

§  HPCisnowapprovedforstoringHIPAAdata•  HPCSecureDataAccounts(HSDA)applica9onsareavailable•  Dataisencryptedandprocessedinavirtualenvironment

*Notofficial

HPC Condo Data Storage

HPCallowsPIswithac9veHPCaccountstopurchasestorageinitscondominium-stylecomputeenvironment.

•  HPCobtainsapprovedvendorquotesforstoragearraysbasedonuserneeds.

•  Allstoragerequiresamandatoryminimum3-yearMOUwith3yearsofvendorsupport.

•  HPCprovideslimitedbackupofdata(upto100TB)atnocosttothecondoowner.

•  ThecondostorageisonlyavailableontheHPCcluster;thefilesystemisnotsharedoutsideofHPC.

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High-Performance Computing

High-Performance Computing (HPC)

HPCadvancesUSC’smissionbyprovidingtheinfrastructureandsupportnecessaryforresearchcompu9ng

•  ManyofHPC’sresourcesareavailableatnochargetoUSCfaculty,staff,graduatestudents,andiVIPcollaborators

•  AsapartofUSC’sInforma9onTechnologyServices(ITS)division,HPCishousedwithintheITSdatacenterandismonitoredaround-the-clockbyITSstaff

World-classsuper-compu9ngcenter•  LINPACKbenchmarking,publishedbyTop500Supercomputers•  12thfastestacademicsupercomputerinU.S.,June2016lis9ng

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HPC Resources

§  Computenodes(~2700runningCentOS7)§  Networkedstorage(disksarrays,fileservers)§  Twolow-latencynetworks

•  Infiniband56-gigabit(1,025nodes)•  Myricom10-gigabit(1,741nodes)

§  Regularlyupgraded•  Everyfallando)enalsoinspring,HPCinstalls

newnodes,upgradesandpatches•  HPCresourcesareunavailableduringthisweek

Condo Compute Nodes

HPCallowsPIswithac9veHPCaccountstopurchasecomputenodesinitscondominium-stylecomputeenvironment

•  CondonodescanbepurchasedthroughHPCatany9me,aslongasnodesareavailableinourexis9ngpoolofnodes-  OnlyHPC-purchasednodesareavailableforcondo

•  CondonodesarepricedattheamountthatHPCpurchasedthem,includingtaxes-  Thisisaone=mefee-  Condofeesdonotincludeinfrastructure,whichiscoveredbyHPC

•  Contacthpc@usc.eduforcurrentconfigura9onandpricinginforma9on

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HPC Research Support and Facilitation

HPC Research Support

§  ProposalSupport•  Helpbuildstartuppackages,providequotesforcondopurchases,and

writeleFersofsupportforgrantsubmissions•  Provideadescrip9onofACIresourcesandsupportforproposals-  hpcc.usc.edu/files/2016/01/Support-for-Grant-Applica=ons1.pdf

§  Collabora9on•  CollaboratesonHPCprojectswithresearchersonallUSCcampuses

§  Research•  HPCdirectorisco-PIofNSF-sponsored,6-universitygrant-  Advancingscien=ficdiscoverythroughana=onalnetworkofAdvancedCyberinfrastructureResearchandEduca=onFacilitators(ACI-REFs)

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HPC Facilitation

OutreachandEduca9on•  Newfacultypresenta9ons•  Classroompresenta9ons•  Workshops-  IntroLinux,IntrotoHPC,-  AdvancedHPC,ParallelMATLAB-  InstallingSoHware,PegasusWMS

•  Guesttrainingevents-  Mathworks,NVIDIA

•  ITSdatacentertours

DirectAssistance•  Help9ckets(hpc@usc.edu)•  Officehours-  Tuesdays@2:30(UPCLVL)-  TBD(HSCNML)

•  Consulta9ons-  Labconsulta=ons-  Individualmee=ngs-  Remoteconferencing

ThankyouforyouraXen:on

Forinforma9onaboutHPC,pleaseseehpcc.usc.eduoremailhpc@usc.edu.Ialsogiveanin-depthtalkonHPC.