provisioning complex software environments for scientific ...dthain/talks/ccl-cvmfs-2018.pdfnative...

ProvisioningComplexSoftwareEnvironments

forScientificApplicationsProf.DouglasThain,UniversityofNotreDame

http://www.nd.edu/~dthaindthain@nd.edu@ProfThain

TheCooperativeComputingLab•  Wecollaboratewithpeoplewhohavelargescalecomputingproblemsinscience,engineering,andotherfields.

•  WeoperatecomputersystemsontheO(10,000)cores:clusters,clouds,grids.

•  Weconductcomputerscienceresearchinthecontextofrealpeopleandproblems.

•  Wedevelopopensourcesoftwareforlargescaledistributedcomputing.

2

http://ccl.cse.nd.edu

ParrotVirtualFileSystem

UnixAppl

ParrotVirtualFileSystem

Local iRODS Chirp HTTP CVMFS

Capture System Calls via ptrace

/home=/chirp/server/myhome/software=/cvmfs/cms.cern.ch/cmssoft

Custom Namespace

File Access Tracing Sandboxing User ID Mapping . . .

Douglas Thain, Christopher Moretti, and Igor Sfiligoi, Transparently Distributing CDF Software with Parrot, Computing in High Energy Physics, pages 1-4, February, 2006.

Parrot+CVMFS

wwwserver

CMSTask

Parrot

squidproxysquidproxysquidproxy

CVMFSLibrarymetadata

data

data

data

metadata

data

data

CAS Cache

CMS Software 967 GB

31M files

Content Addressable

Storage

Bui

ld C

AS

HTTP GET HTTP GET

Jakob Blomer, Predrag Buncic, Rene Meusel, Gerardo Ganis, Igor Sfiligoi and Douglas Thain, The Evolution of Global Scale Filesystems for Scientific Software Distribution, IEEE/AIP Computing in Science and Engineering, 17(6), pages 61-71, December, 2015. DOI: 10.1109/MCSE.2015.111

Howdoweruncomplexworkflowsondiversecomputingresources?

6

Makeflow=Make+Workflow

Makeflow

Local HTCondor Torque WorkQueue

•  Providesportabilityacrossbatchsystems.•  Enablesparallelism(butnottoomuch!)•  Faulttoleranceatmultiplescales.•  Dataandresourcemanagement.•  Transactionalsemanticsforjobexecution.

http://ccl.cse.nd.edu/software/makeflow

Amazon

7

Makeflow=Make+Workflow

Makeflow

Local HTCondor Torque WorkQueue

•  Providesportabilityacrossbatchsystems.•  Enablesparallelism(butnottoomuch!)•  Faulttoleranceatmultiplescales.•  Dataandresourcemanagement.•  Transactionalsemanticsforjobexecution.

http://ccl.cse.nd.edu/software/makeflow

AmazonMesosKuber-netes

Charles Zheng (czheng2@nd.edu)

Example:SpeciesDistributionModeling

FullWorkflow:12,500speciesx15climatescenariosx6experimentsx500MBperprojection=1.1Mjobs,72TBofoutput Small Example: 10 species x 10 expts

www.lifemapper.org

MoreExamples

http://github.com/cooperative-computing-lab/makeflow-examples

WorkflowLanguageEvolution

output.5.txt : input.txt mysim.exe mysim.exe –p 10 input.txt > output.5.txt

{ "command" : "mysim.exe –p 10 input.txt > output.5.txt", "outputs" : [ "output.5.txt" ], "inputs" : [ "input.dat", "mysim.exe" ] }

{ "command" : "mysim.exe –p " + x*2 + " input.txt > output." + x + " .txt", "outputs" : [ "output" + x + "txt" ], "inputs" : [ "input.dat", "mysim.exe" ] } for x in [ 1, 2, 3, 4, 5 ]

Classic "Make" Representation

JSON Representation of One Job

JX (JSON + Expressions) for Multiple Jobs

Tim Shaffer (tshaffe1@nd.edu)

ElaboratingJobswithWrappers

Nick Hazekamp (nhazekam@nd.edu)

Taskinput

inputoutput Original Job

strace

Task

input

input

output

logfile Add Debug Tool

Singularity

rhel6.img

input

input

strace

Task

output

logfile

Add Container Environment

Local Files and Programs

Work Queue Architecture

WorkerProcess

Cache Dir

A

C B

WorkQueueMaster

4-core machine

Task.1 Sandbox

A

BT

2-core task

Task.2 Sandbox

C

AT

2-core task

Send files

A B C

Submit Complete

Send tasks

NationalComputingResource

CampusHTCondor

Pool

PublicCloud

Provider

PrivateCluster

MakeflowMaster

LocalFilesandPrograms

Makeflow+WorkQueue

W

W

W

ssh

WW

WW

torque_submit_workers

W

W

W

condor_submit_workers

W

W

W

ThousandsofWorkersinaPersonalCloud

submittasks

Problem:SoftwareDeployment•  Gettingsoftwareinstalledonanewsiteisabigpain!Theuser(probably)knowsthetoplevelpackage,butdoesn'tknow:– Howtheysetupthepackage(sometimelastyear)– Dependenciesofthetop-levelpackage.– Whichpackagesaresystemdefaultvsoptional– HowtoimportthepackageintotheirenvironmentviaPATH,LD_LIBRARY_PATH,etc.

•  Manyscientificcodesarenotdistributedviarpm,yum,pkg,etc.(anduserisn'troot)

EvenBiggerDifferences:•  HardwareArchitecture

–  X86-64,KNL,BlueGene,GPUs,FPGAs,...•  OperatingSystem

–  GreenAvocadoLinux,BlueDolphinLinux,RedRashLinux,...•  BatchSystemorResourceManager

–  HTCondor,PBS,Torque,Cobalt,Mesos,...

•  ContainerTechnology–  None,Docker,Singularity,CharlieCloud,Shifter,…

•  RunningServices–  FUSE,CVMFS,HTTPProxy,Frontier,...

•  NetworkConfiguration–  Public/Private,Incoming/Outgoing,Firewalls

OurApproach:•  Providetoolsthatmakeaflexiblemappingbetweentheuser'sintentandthelocalsite:– "IneedOSRHEL6"

•  Checkifalreadypresent,otherwiserunincontainer.– "IneedcontainerX.img"

•  TryDocker,trySingularity,tryCharlieCloud.– "Ineed/cvmfs/repo.cern.ch"

•  Lookfor/cvmfs;activateFUSE;build/runparrot.

– "IneedsoftwarepackageX"•  LookforXinstalledlocally,elsebuildfromrecipe.

DeliveringPlatformswithRunOS

"runosslc6– mysim.exe"

SiteA SiteCSiteB

slc6 rhel7 debian45

docker singularity charliecloudmysim.exe

slc6

mysim.exe

slc6

mysim.exeKyle Sweeney (ksweene3@nd.edu)

DeliveringSoftwarewithVC3-Builder

TypicalUserDialogInstallingBLAST

"I just need BLAST." "Oh wait, I need Python!" "Sorry, Python 2.7.12" "Python requires SSL?" "What on earth is pcre?" "I give up!"

MAKERBioinformaticsPipeline

SealedPackage

VC3-BuilderArchitecture

UpstreamSources

Builder

CachedSources

InstallTree

Task

Task Sandbox A B

C D

SoftwareRecipes

CachedRecipes

A B

C DRecipe

Archival or Disconnected Operation

PATH PYTHONPATH LD_LIBRARY_PATH

..Plan: ncbi-blast => [, ]

..Try: ncbi-blast => v2.2.28

....Plan: perl => [v5.008, ]

....Try: perl => v5.10.0

....could not add any source for: perl v5.010 => [v5.8.0, ]

....Try: perl => v5.16.0

....could not add any source for: perl v5.016 => [v5.8.0, ]

....Try: perl => v5.24.0

......Plan: perl-vc3-modules => [v0.001.000, ]

......Try: perl-vc3-modules => v0.1.0

......Success: perl-vc3-modules v0.1.0 => [v0.1.0, ]

....Success: perl v5.24.0 => [v5.8.0, ]

....Plan: python => [v2.006, ]

....Try: python => v2.6.0

....could not add any source for: python v2.006 => [v2.6.0, ]

....Try: python => v2.7.12

......Plan: openssl => [v1.000, ] ……………….. Downloading 'Python-2.7.12.tgz' from http://download.virtualclusters.org/builder-files details: /tmp/test/vc3-root/x86_64/redhat6/python/v2.7.12/python-build-log processing for ncbi-blast-v2.2.28 preparing 'ncbi-blast' for x86_64/redhat6 Downloading 'ncbi-blast-2.2.28+-x64-linux.tar.gz' from http://download.virtualclusters.org… details: /tmp/test/vc3-root/x86_64/redhat6/ncbi-blast/v2.2.28/ncbi-blast-build-log

"vc3-builder–requirencbi-blast"(New Shell with Desired Environment)

bash$ which blastx /tmp/test/vc3-root/x86_64/redhat6/ncbi-blast/v2.2.28/bin/blastx bash$ blastx –help USAGE blastx [-h] [-help] [-import_search_strategy filename] . . . bash$ exit

Problem:LongBuildonHeadNode•  Manycomputingsiteslimittheamountofworkthatcanbedoneontheheadnode,soastomaintainqualityofserviceforeveryone.

•  Solution:Movethebuildjobsouttotheclusternodes.(Whichmaynothavenetworkconnections.)

•  Idea:Reducetheproblemtosomethingwealreadyknowhowtodo:Workflow!

•  Buthowdowebootstraptheworkflowsoftware?Withthebuilder!

vc3-builder--requiremakeflow--requirencbi-blast--makeflow–Tcondorblast.mf

HeadNode

BootstrappingaWorkflow

UpstreamSources

Builder

SoftwareRecipes Worker

Nodes

Makeflow Makeflow

BuildTask

BuildTask

BuildTask

BuildTask

BuildTask

BuildTask

Build Makeflow

Build BLAST

BLAST

BLASTTask

BLASTTask

BLASTTask

BLASTTask

BLASTTask

BLASTTask

ExampleApplications

MAKER Octave Benjamin Tovar, Nicholas Hazekamp, Nathaniel Kremer-Herman, and Douglas Thain, Automatic Dependency Management for Scientific Applications on Clusters, IEEE International Conference on Cloud Engineering (IC2E) , April, 2018.

DeliveringServiceswithVC3-Builder

..Plan: cvmfs => [, ]

..Try: cvmfs => v2.0.0

....Plan: parrot => [v6.0.16, ]

....Try: parrot => v6.1.1

......Plan: cctools => [v6.1.1, ]

......Try: cctools => v6.1.1

........Plan: zlib => [v1.002, ]

........Try: zlib => v1.2.8

........Success: zlib v1.2.8 => [v1.2.0, ]

......Fail-prereq: cctools-v6.1.1

........Plan: perl => [v5.010.000, v5.010001]

........Try: perl => v5.10.0

..........Plan: perl-vc3-modules => [v0.001.000, ]

..........Try: perl-vc3-modules => v0.1.0

..........Success: perl-vc3-modules v0.1.0 => [v0.1.0, ]

........could not add any source for: perl v5.010 => [v5.10.0, v5.10001.0]

........Try: perl => v5.16.0

..........Plan: perl-vc3-modules => [v0.001.000, ]

..........Try: perl-vc3-modules => v0.1.0

..........Success: perl-vc3-modules v0.1.0 => [v0.1.0, ]

........could not add any source for: perl v5.016 => [v5.10.0, v5.10001.0]

........Try: perl => v5.24.0

..........Plan: perl-vc3-modules => [v0.001.000, ]

..........Try: perl-vc3-modules => v0.1.0

..........Success: perl-vc3-modules v0.1.0 => [v0.1.0, ]

........Success: perl v5.24.0 => [v5.10.0, v5.10001.0]

"vc3-builder–requirecvmfs"

(New Shell with Desired Environment) bash$ ls /cvmfs/oasis.opensciencegrid.org atlas csiu geant4 ilc nanohub osg-software auger enmr glow ligo nova sbgrid cmssoft fermilab gluex mis osg snoplussnolabca . . . bash$ exit

PuttingitAllTogether

Submit Batch Jobs

NativeRHEL7Machines

RunOS"rhel6"

SingularityContainer

VC3Builder

Parrot+CVMFS

Factory

Request 128 nodes of16 cores, 4G RAM, 16G disk with RHEL6 operating system, CVMFS and Maker software installed:

Worker

128X

BatchSystem

Makeflow

Sandbox

Task

VC3:VirtualClustersforCommunityComputation

DouglasThain,UniversityofNotreDameRobGardner,UniversityofChicago

JohnHover,BrookhavenNationalLab

http://virtualclusters.org

YouhavedevelopedalargescaleworkloadwhichrunssuccessfullyataUniversitycluster.

Now,youwanttomigrateandexpandthatapplicationtonational-scaleinfrastructure.(Andallowotherstoeasilyaccessandrunsimilarworkloads.)

TraditionalHPCFacility DistributedHTCFacility CommercialCloud

TraditionalHPCFacility DistributedHTCFacility CommercialCloud

Concept:VirtualCluster•  200nodesof24coresand64GBRAM/node•  150GBlocaldiskpernode•  100TBsharedstoragespace•  10Gboutgoingpublicinternetaccessfordata•  CMSsoftware8.1.3andpython2.7

VirtualClusterService

VirtualClusterFactory

DeployServices DeployServices DeployServices

VirtualClusterFactory

VirtualCluster

VirtualClusterFactory

VirtualClusterFactory

VirtualClusterFactory

SomeThoughts:•  Makesoftwaredependenciesmoreexplicit.

– Proposed:Nothingshouldbeavailablebydefault,allsoftwareshouldrequirean"import"step.

•  Layertoolswithcommonabstractions:–  Factory->HTCondor->Singularity->Builder->Worker–  Provision->Schedule->Contain->Build->Execute

•  Needbetter,portable,waysofexpressing:– Whatsoftwareenvironmenttheuserwants.– Whatenvironmentthesiteprovides.

•  Theabilitytonestenvironmentsiscritical!

Acknowledgements

DE-SC0015711 VC3: Virtual Clusters for Community Computation

ACI-1642409 SI2-SSE: Scaling up Science on Cyberinfrastructure with the Cooperative Computing Tools

Notre Dame CMS: Kevin Lannon Mike Hildreth Kenyi Hurtado Univ. Chicago: Rob Gardner Lincoln Bryant Suchandra Thapa Benedikt Riedel Brookhaven Lab: John Hover Jose Caballero

http://ccl.cse.nd.edu

@ProfThain