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Research ComputingInforma(onforNewandJuniorFaculty,ResearchersandGraduateStudents

August,2016

ErinShawAdvancedCyberinfrastructure,Research&Educa(onFacilitator(ACI-REF)

USCCenterforHigh-PerformanceCompu(ng

Information Technology Services (ITS)

ITSDataCenter

DouglasShookUSCCIO

MaureenDoughertyHPCDirector

RandolphHallUSCVPofResearch&FacultyExecu=veDirector,HPC*

*TheHPCFacultyAdvisorycommiEeeadvisestheCIOaboutthefaculty’sresearchneedsrelatedtotheuniversity’sHPCresources.

ITS Research Computing Initiative

§  SoKware•  Campus-widesoKwarelicenses

§  Storage•  DatastorageopNons

§  High-PerformanceCompuNng•  Overviewandresources

§  HPCSupportandOutreach•  Facultysupport,outreach,andeducaNon

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Software

Statistical Computing Software 


§  Campus-widelicensesitservices.usc.edu/stats

•  SAS,SPSS,STATA&JMP-  Availableforlow/no-costthroughUSCcampus-widelicenses

•  SASandSTATAinstalledonHPC-  AvailableforfreethroughyourHPCaccount

§  OpensourceonHPC•  RStaNsNcalcompuNngsoKware

•  PythonscienNficcompuNngpackages-  ThesesoKwarepackagesarepre-installedonHPC

Technical Computing Software 


§  TechnicalsoKwareavailablefordownload

•  MATLAB-  itservices.usc.edu/matlab

•  MathemaNca-  itservices.usc.edu/mathemaNca

§  GISandremotesensingsoKware

-  spaNal.usc.edu/index.php/soKware•  ArcGISandCityEngine•  TerrSetConstellaNon•  Data/Geoportal

§  SoKwareavailableonHPC •  MATLABandMathemaNca•  Compilers:Gnu,Intel,PGI•  NumericalLibraries:mpich,Openmpi,CUDA,FKw,Petsc

•  MolecularSimulaNon:NAMD,Gromacs,Amber

•  QuantumChemistry:Gaussian‘03,QChem

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Qualitative Data Analysis Software

§  DataanalysissoKware.usc.edu•  ATLAS.N•  NVivo

§  DatacollecNonitservices.usc.edu/qualtrics•  Qualtrics

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

§  ComprehensivefuncNonalanalysisandadvancedliterature/datamining•  PartekGenomicsSuite•  PartekFlow•  Galaxy•  VectorNTIAdvance•  MicroarrayRUS

§  StaNsNcalanalysisofhigh-throughputdataandDNA/proteinsequenceanalysis•  IngenuityPathwayAnalysis•  BIOBASE•  Nextbio•  Oncomine•  GenevesNgator•  Quetzal

Research Management Software 
(Available through other sources to USC community)

§  CitaNonmanagement•  RefWorks,Mendeley,EndNote,andZotero-  libraries.usc.edu/research/citaNon-management

-  norris.usc.libguides.com/CitaNonManagement

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

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UNIX Computing Utilities 
(itservices.usc.edu/sftp, itservices.usc.edu/unix)

§  UNIXcompuNnguNliNes•  Securefiletransfer-  FileZilla,Fetch,SCP

•  Secureshell-  XWin-32(Pre-configuredwithconnecNonstoUSCnetworks,includingHPC)

§  UNIXdocumentaNon•  Accounts,loggingin,tutorials,etc.-  itservices.usc.edu/unix

Storage

Cloud Data Storage

§  MSOffice365/OneDriveforBusiness•  5TBcapacity•  ApprovedforstoringsomerestrictedinformaNon,includingHIPAA-

andFERPA-relatedinformaNon-  AllfacultyandstaffwithITS-supportedO365accountsreceiveaccess-  GraduatestudentsthatneedaccessshouldinquirewiththeirrespecNveschools

§  GoogleDrive•  Unlimitedcapacity•  NotapprovedforstoringHIPAA-relatedinformaNon

-  Allfaculty,staff,andstudentsreceiveaccess

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USC Data Storage§  USCDigitalRepository

-  repository.usc.edu•  40PBoftotalstoragecapacity

-  High-speed,high-performancediskstorage,andlow-demandtapestorage-  AvailableforWindows,Mac,andLinux(includingHPC)-  Highlysecureandencryptedcloudstorage(ApprovedforstoringHIPAA-

relatedinformaNon)•  Fee-basedusagepolicy

§  USCDrive-  itservices.usc.edu/uscdrive

•  High-speedstoragethatallowsuserstouploadlargedatafilesquickly•  Forfacultyandgraduatestudents•  IniNalstoragespaceof50GBperperson

-  AddiNonalstoragecanbepurchased•  NotapprovedforstoringHIPAA-relatedinformaNon

HPC Data Storage

§  Groupprojectscanrequestupto2TBofdiskspace•  Backedupdaily

§  Usershaveaccesstoa328TB/stagingdirectory•  Nodatabackup•  Cleanedduringsemi-annualdownNmesorwhencapacityreached

§  Usersalsohaveaccesstotemporarydirectories•  /tmpand/scratchwhilerunningjoboncomputenode(s)•  Clearedatendofeachjob

§  HPCisnotapprovedforstoringHIPAAinformaNonbutcompliancyisunderdevelopment

HPC Condo Data Storage

HPCallowsPIswithacNveHPCaccountstopurchasestorageonitscondominium-stylecomputeenvironment.

•  HPCobtainsapprovedvendorquotesforstoragearraysbasedonuserneeds.

•  Allstoragerequiresamandatoryminimum3-yearMOUwith3yearsofvendorsupport.

•  HPCprovideslimitedbackupofdata(upto100TB)atnocosttothecondoowner.

•  ThecondostorageisonlyavailableontheHPCcluster;thefilesystemisnotsharedoutsideofHPC.

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High-Performance Computing

High-Performance Computing (HPC)

HPCadvancesUSC’smissionbyprovidingtheinfrastructureandsupportnecessaryforresearchcompuNng

•  ManyofHPC’sresourcesareavailableatnochargetoUSCfaculty,researchers,andgraduatestudents

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

World-classsuper-compuNngcenter•  LINPACKbenchmarking,publishedbyTop500Supercomputers•  12thfastestacademicsupercomputerinU.S.,June2016lisNng

Electrical Engineering, 11%

Aerospace and Mechanical Engineering, 8%

Computer Science, 7%

Preventive Medicine, 7%

Chemistry, 5%

Chemical Engineering and Materials Science, 5%

Computational Biology and Bioinformatics, 5%Biological Sciences, 4%Physics and Astronomy, 4%Information Sciences Institute, 3%

Economics, 3%

Biomedical Engineering, 2%

Center for Regenerative Medicine & Stem Cell Research, 2%

Civil and Environmental Engineering, 2%

Finance and Business Economics, 2%

Other Keck School of Medicine, 11%

Other Dornsife College of Letters, Arts and Science, 6%

Other Marshall School of Business, 3%

Other Viterbi School of Engineering, 2%

Other, 8%

FY16 Department BreakdownHPC Users as of March 2016

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HPC Resources

§  Computecyclesontwolow-latencybandwidthLinuxclusters

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

§  Diskarrays•  Partofastorageareanetworkpresentedvianetworkedfilesystems

frommulNplefileservers§  Dataanddiskresources

•  Limitedstorageofresearchdataandoutputfromcluster-runjobs§  Availabletofaculty,researchers,gradstudents,andiVIPs

Condo Compute Nodes

HPCallowsPIswithacNveHPCaccountstopurchasecomputenodesonitscondominium-stylecomputeenvironment

•  CondonodescanbepurchasedthroughHPCatanyNme,aslongasnodesareavailableinourexisNngpoolofnodes-  OnlyHPC-purchasednodesareavailableforcondo

•  CondonodesarepricedattheamountthatHPCpurchasedthem,includingtaxes-  ThisisaoneNmefee-  Condofeesdonotincludeinfrastructure,whichiscoveredbyHPC

•  Contacthpc@usc.eduforcurrentconfiguraNonandpricinginformaNon

HPC Support and Outreach

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HPC Support, Facilitation, and Collaboration

§  ProposalSupport•  Helpbuildstartuppackages,providequotesforcondopurchases,

andwriteleEersofsupportforgrantsubmissions•  ProvideadescripNonofACIresourcesandsupportforproposals

-  hpcc.usc.edu/files/2016/01/Support-for-Grant-ApplicaNons1.pdf

§  ACI-REF(FacilitaNon)•  HPCdirectorisco-PIofNSF-sponsored,6-universitygrant

-  AdvancingscienNficdiscoverythroughanaNonalnetworkofAdvancedCyberinfrastructureResearchandEducaNonFacilitators(ACI-REFs)

§  CollaboraNon•  CollaboratesonHPCprojectswithresearchersonallUSCcampuses

HPC Outreach, Education, and Assistance

OutreachandEducaNon•  NewfacultypresentaNons•  ClassroompresentaNons•  Workshops

-  IntroLinux,IntrotoHPC-  AdvancedHPC,ParallelMatlab-  Pegasusworkflows

•  Sponsorguesttalks-  Mathworks,NVIDIA

•  ITSdatacentertours

DirectAssistance•  Emailhpc@usc.edu•  AEendofficehours

-  Tuesdays@2:30(UPCLVL)

-  Mondays@2:30(HSCNML)

•  RequestconsultaNon-  LabconsultaNons-  IndividualmeeNngs