GACRC User Quick Guide...All Sapelo and zcluster users, as well as all GACRC PIs, can access the...

GACRCUserQuickGuide:

MigratingfromZclustertoSapelo

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TheGACRCStaffVersion1.0

DiscussionPoints

I. RequestSapeloUserAccount

II. Systems

III. TransferFiles

IV. ConfigureSoftwareEnvironment

V. JobSubmissionWorkflow

VI. JobSubmissionScript

VII. Appendices

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Sapeloclusteruseraccount:MyID@sapelo1.gacrc.uga.edu

Note:AvalidofficialUGAMyIDisaMUSTtocreateauseraccount!

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RequestSapeloUserAccount

PIRequestUserAccount

PIVerification

NewUserTraining

UserAccount

Provisioning

WelcomeLetter

1. TheUGAPIusestheGACRConlineformhttp://help.gacrc.uga.edu/userAcct.php to

requestauseraccountforagroupmember.

2. Oncewereceivedtherequest,wewillverifyitwiththePI.

3. AfterverificationbythePI,thenewuserwillberequiredtoattendatrainingsession.

4. Aftertheuserattendedtraining,wewillprovisionaSapeloaccountfortheuser.

5. Awelcomeletterissenttotheuseronceuseraccountisready.

Systems– OverviewDiagram

TransferNodexfer.gacrc.uga.edu

LoginNodezcluster.rcc.uga.edu

LoginNodesapelo1.gacrc.uga.edu

InteractiveNode

InteractiveNode/home/abclab/userID /escratch4/userID

/home/MyID /lustre1/MyID

/project/abclab

ssh/scp

qlogin

Zcluster

Sapelo

AccessingLine

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Systems– Overview

LogontoZclusterLogin Node: ‘ssh userID@zcluster.rcc.uga.edu’(usingzclusterpassword)

OpenZclusterInteractiveNode: type‘qlogin’commandfromloginnode

ZclusterHomeDirectory: /home/abclab/userID

ZclusterGlobalScratch: /escratch4/userID (4TBquota)

Create WorkingDirectoryonZclusterGlobalScratch: type‘make_escratch’commandfromloginnode

Log onto SapeloLoginNode: ‘sshMyID@sapelo1.gacrc.uga.edu’(usingUGAMyIDpassword)

OpenSapeloInteractiveNode: type‘qlogin’ commandfromloginnode

SapeloHomeDirectory: /home/MyID(100GBquota)

SapeloGlobalScratch: /lustre1/MyID

Create WorkingDirectoryonSapeloGlobalScratch: use‘mkdir’commandin/lustre1/MyIDfrominteractivenode

LogontoGACRCTransferNode: ‘ssh MyID@xfer.gacrc.uga.edu’ (usingUGAMyIDpassword)

GroupProjectSpace: /project/abclab(“abc”areinitialsofthePI ofthegroup)

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Systems– StorageEnvironmenthttps://wiki.gacrc.uga.edu/wiki/Disk_Storage

Name Role Purpose Zcluster Sapelo

Home sshlandingspot staticdata, e.g.,scripts,software /home/abclab/userID /home/MyID

(100GBquota)

GlobalScratch

Jobworkingspace

Current Jobdatabeingused byrunningjobs

/escratch4/userID(4TBquota)

/lustre1/MyID(noquota–limitedbycapacity)

Project Activedatastorage

Non-currentactivedataforfutureanalysis

/project/abclab(1TB initialquota)

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Systems– ComputingResourcesOverviewhttps://wiki.gacrc.uga.edu/wiki/Systems

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Zcluster

150x8-core16GBRAMnodeswithIntelXeon processors(total1200cores)45x12-core48GBRAMnodeswithIntelXeon processors(total540cores)

4x8-core192GBRAMnodeswithIntelXeon processors(total32cores)10x12-core256GBRAMnodeswithIntelXeon processors(total120cores)2x32-core512GBRAMnodeswithIntelXeon processors(total64cores)

6x32-core64GBRAMnodeswithAMDOpteronprocessors(total192cores)

4x12-core96GBRAMnodeswithIntelXeonprocessors, 8NVIDIAK20XmGPUcardseach

Sapelo

112x48-core128GBRAMnodeswithAMDOpteronprocessors(total5376cores)4x48-core256GBRAMnodeswithAMDOpteronprocessors(total192cores)

6x48-core512GBRAMnodeswithAMDOpteronprocessors(total288cores)1x48-core1TBRAMnodewithAMDOpteronprocessors (total48cores)3x 28-core1TBRAMnodewithIntelXeon processors(total84cores)

2x16-core128GBRAMnodeswithIntelXeonprocessors, 8NVIDIAK40mGPUcardseach

85+buy-innodeswithvariableconfigurations

TransferofFileshttps://wiki.gacrc.uga.edu/wiki/Transferring_Files

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AllSapeloandzclusterusers,aswellasallGACRCPIs,canaccesstheGACRCtransfernodes(xfer.gacrc.uga.edu)andusingUGAMyID andMyIDpasswordtoauthenticate.

Notethatauser'shomedirectoryontransfernodeisthesameastheuser'sSapelohomedirectory,whichisnotthesameastheuser'sZclusterhomedirectory.

Transfernodescanaccessthefollowingfilesystemsusingtheirfullpaths:

SapeloHomeDirectory: cd/home/MyID

ZclusterHomeDirectory: cd/panfs/pstor.storage/home/abclab/userID

ZclusterGlobalScratch: cd/escratch4/userID

SapeloGlobalScratch: cd/lustre1/MyID

GroupProject Folder cd/project/abclab

Detailedinstructionscanbefoundatthelinkabove

FileTransferringTreehttps://wiki.gacrc.uga.edu/wiki/Transferring_Files

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scp/ssh

TransferNode

/home/MyID

/lustre1/MyID

/project/abclab

/escratch4/userID

/panfs/pstor.storage/home/abclab/userID

ü scp:Remotefiletransferringbetweenyourlocalcomputerandyourfoldersonfilesystems

ü ssh:Loggingontotransfernode.Onceloggedon,youcanusecp ormv forfiletransferbetweenfilesystems.

ConfigureSoftwareEnvironmenthttps://wiki.gacrc.uga.edu/wiki/Software

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SapeloUser issuesmodule commandstoconfigurevariouspathsfor softwarepackages

(inajobsubmissionscriptoronthecommandlineofaninteractivesession):

1. moduleavail: showallmodulesavailableoncluster2. moduleloadmoduleName/version:loadtheneededmodule“moduleName”withaversion3. modulelist:listallmodulesyoualreadyloaded

Forexample:

$moduleloadpython/2.7.8$moduleloadR/3.2.3$modulelistCurrentlyLoadedModules:1) moab/8.1.1 2)StdEnv 3)python/2.7.8 4) R/3.2.3

ZclusterUser “manually”exportsvariouspathsforsoftwarepackages(inajobsubmissionscriptoronthecommandlineofaninteractivesession),forexample:

export PATH=……:$PATH

JobSubmissionWorkflow(general)

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Zcluster Sapelo

1. Logontozclusterloginnode:

sshuserID@zcluster.rcc.uga.edu

2. Createaworkingdir onglobalscratch:

make_escratch

3. Changetoworkingdironglobalscratch:

cd/escratch4/userID/userID_mmm_dd

(mmm, dd:dateabbreviations)

4. Create azclusterjobsubmissionscript:

nano./sub.sh

5. Submitjob:

qsub-qrcc-30d./sub.sh

1. LogontoSapelologinnode:

sshMyID@sapelo1.gacrc.uga.edu

2. GotoSapelo Interactivenode:

qlogin

3. ChangetoSapeloglobalscratch:

cd/lustre1/MyID

4. Createaworkingdironglobalscratch:

mkdir./workDir

5. Changetoworkingdironglobalscratch:

cd./workDir

6. CreateaSapelojobsubmissionscript:

nano./sub.sh

7. Submitjob:

qsub./sub.sh

JobSubmissionScript(NCBIBlastasexample)

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sub.shonZcluster sub.shonSapelo

#!/bin/bash

cd`pwd`

exportPATH=/usr/local/ncbiblast/latest/bin:$PATH

blastall-pblastn-d/db/ncbiblast/latest/nt \-a4 -iQUERY\-oout.QUERY

#PBS-S/bin/bash#PBS-qbatch#PBS-NtestBlast#PBS-lnodes=1:ppn=4:AMD#PBS-lmem=20gb#PBS-lwalltime=480:00:00

cd$PBS_O_WORKDIR

moduleloadncbiblast+/2.2.26

blastall-pblastn-d/db/ncbiblast/nrte/latest/nt \-a4 -iQUERY\-oout.QUERY>outputfile2>&1

qsub-qrcc-30d-pethread4./sub.sh qsub./sub.sh

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Appendix1:

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Tasks Zcluster Sapelo

Commonfile/diroperations

ls,cd, pwd,file,cat, less,more,cpmv,mkdir,rm,rmdir,dos2unix,mac2unix,etc.

Transfer remotefiles scp, sftporSSHSecureClientFileTransfer,FileZilla,WinSCP

Openinteractivesession qlogin

Createworkingdirectoryonglobalscratch make_escratch mkdirsubdirectoryName

Edit scriptfiles nanosub.sh or vim sub.sh

Submitabatchjob qsub–qqueueName–l…–pe …sub.sh qsubsub.sh

checkjobstatus qstat

Checkdetailedjobinfo qsj jobID,qstat–jjobID,qacct–jjobID qstat–fjobID,showjobsjobID

Cancelajobfromqueue qdeljobID, qdel–uuserID qdeljobID

Appendix2:CommonCommandSummaryhttps://wiki.gacrc.uga.edu/wiki/Command_List

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Appendix3:CurrentprocessforaUGAPItorequest(re)activationorcreationofaMyIDforanexternalcollaborator

Tokeepauser'sMyIDactiveafter he/sheleavesUGA,ortocreateaMyIDforanexternalresearchcollaborator:

1. ThePIaccessestheEITShelpdeskportalathttps://uga.teamdynamix.com/TDClient/Home/

2. Click on"MyIDAccountRequest”ontherightsideofthepagein“PopularServices”section.

3. UseMyID credentialstologontheservicepage.4. IntheMyIDRequestFrom,enterhis/herinformationandselect"GACRC

RemoteCollaborator"fortheAccountTypefield.5. AfterverificationbytheGACRCDirector,EITSwillgeneratecollaborator’sMyID6. IfcollaboratorisvisitingUGAcampus,MyID canbeobtainedthroughOVPR’s

VisitingResearcher&Scholarprogram– https://research.uga.edu/visiting/

• GACRCWebsite:http://gacrc.uga.edu

• GACRCWiki:https://wiki.gacrc.uga.edu/wiki/Main_Page

• Systems: https://wiki.gacrc.uga.edu/wiki/Systems

• HowtoTransferFiles:https://wiki.gacrc.uga.edu/wiki/Transferring_Files

• CurrentSoftwareList: https://wiki.gacrc.uga.edu/wiki/Software

• HowtoSubmitaJob:https://wiki.gacrc.uga.edu/wiki/Running_Jobs_on_Sapelo

• HowtoGetHelp: http://help.gacrc.uga.edu/

• GACRCTrainingOpportunities:https://wiki.gacrc.uga.edu/wiki/Training

• HowtoregisteranewGACRCNewLab:http://help.gacrc.uga.edu/labAcct.php

• HowtoregisteranewGACRCUser:http://help.gacrc.uga.edu/userAcct.php

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Appendix4:UsefulLinks

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