Optimizing for Intel KNL - NERSC · performance is upper bound of what you get in multi-node •...

Thorsten Kurth

Optimizing Code for Intel Xeon Phi 7250 (Knight’s Landing)

NUGTraining,06/09/2017

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Multicore vs. manycore• multicore(Edison)

‣ 5000nodes

‣ 12physicalcores/CPU

‣ 24HWthreads/CPU

‣ 2.4-3.2GHz

‣ 4DPops/cycle

‣ 30MBL3cache

‣ 64GB/node

‣ 100GB/smemorybandwidth

• manycore(Cori-KNL)

‣ 9600nodes

‣ 68physicalcores/CPU

‣ 272HWthreads/CPU

‣ 1.2-1.6GHz

‣ 2x8DPops/cycle

‣ noL3cache

‣ 16GB/node(fast) 96GB/node(slow)

‣ 450GB/smemorybandwidth(fast)

Recompile and go?

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• x86-64compatible:canusecodesforolderarchitecturesorrecompile

• self-hosted:noneedforoffloading

• medianspeedupvs.Edison:1.15x

• medianspeedupvs.Haswell:0.70x

Why should I optimize my code?

• pros

• getmoreforyourbucks:makingefficientuseofexistingmanycoreHPCsystems

• fastsuccesspossible:manylowhangingfruitsinunoptimizedcodes

• investinginthefuture:heterogeneousarchitecturesareenergyefficientandthuswillstayaroundforawhile

• benefitsonmulticore:optimizationstargetingmanycorearchitecturesmostlyimproveperformanceonmulticoresystemsaswell

• cons

• effort:manymostbeneficialoptimizationsrequiresignificantcodechanges

• investinginthefuture:whatifIbetonthewronghorse?

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Optimization targets

• singlenodeperformance

• starthere:forrepresentativelocalproblemsize,singlenodeperformanceisupperboundofwhatyougetinmulti-node

• manyoptimizationopportunities,fastturnaroundtimes

• manyprofilingtoolsavailable

• multi-nodeperformance

• feweroptimizationopportunities,profiling/debuggingtedious

• IOperformance

• notmanyopportunitiesforimprovement

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Where do I start?

• gettoknowyourapplication:don’tassumeyoualreadydo!

• determinehotspots

• manualtimers:becarefulwiththreadsafety/syncbarriers

• profilingtools:NERSCoffersalot

• CrayPat(verylightweight)

• Advisor(findtime-consumingloops)

• VTune(candoalotofthingsbutalsoveryslow)

• MAP(comparablylightweight)

• foundhotspots,nowwhat?

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What architectural feature shall I target?

• KNLhasmanynewfeaturestoexplore

• manythreads

• biggervectorunits

• complexintrinsics(ISA)

• multiplememorytiers

• understandyourhotspots

• computebound:morethreads,vectorization,ISA

• memoryBWbound:memorytiers,morethreads

• memorylatencybound:morethreads,vectorization

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Prerequisites - compile and run

• recompileyourcodeforKNL:codeforolderCPUsissupportedbutthosedonotmakefulluseofnewarchitecture

• Cray(wrappers): module swap craype-haswell craype-mic-knl

• Intel: -xmic-avx512

• GNU:-march=knl

• useproperOpenMPsettings:export OMP_NUM_THREADS=64export OMP_PLACES=threadsexport OMP_PROC_BIND=spread

• usejob-script-generatoronmy.nersc.govorNERSCwebsite

• nodeconfiguration:use-C knl,quad,cacheasastart

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Prerequisites - #FLOPS

• :numberoffloatingpointoperations

• manualcalculation:

• floatadditionandmultiplication:+1

• complexmultiplication:+6(4multiplications+2additions)

• etc.

• measurewithSDE:

• usingSDEismoreprecise,becauseitaccountsformasking

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#FLOPS

Prerequisites - #BYTES

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• :numberofbytestransferredfrommainmemory

• manualcalculation(notrecommended,butgoodcheck):

• countthebytesofdatatobereadandwritteninthekernel

• doesnotaccountfordatareusethroughcaching

• measurewithVTune:

• preciselyobtainuncorecounterevents

#BYTES

What is limiting my performance?

• Rooflineperformancemodel

• arithmeticintensity

• performance

• plotPvs.AIwitharchitecturalrooflineR

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AI =#FLOPS

#BYTES

P =#FLOPS

time[s]

R(AI) = min(memory bw ·AI, peak flops)

Example roofline

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Example roofline

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memory bandwidth bound

Example roofline

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use MCDRAM

Example roofline

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compute bounduse MCDRAM

Example roofline

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use MCDRAM

utilize vectorization

Example roofline

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(possibly) memory latency bounduse MCDRAM

utilize vectorization

Example roofline

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use MCDRAM

utilize vectorization

threading, vectorization

Example roofline

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use MCDRAM

utilize vectorization

threading, vectorization

improve AI

How to improve AI?

• definitionofarithmeticintensity

• twopossibilities

• numberofflops⬆ numberofbytes➡

(notpossible/easy,choiceofalgorithmdeterminesflops)

• numberofflops ➡ numberofbytes ⬇

• reality:tradeoffbetweenboth

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AI =#FLOPS

#BYTES

Create more work/thread

• loop/kernelfusion:improvescachere-useandreduceoverhead

• collapsenestedloops:

• rearrangedatastructures:moveOpenMPout(coarsegrain)

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Loop transformations I

• looptiling:improvescachere-useandcansignificantlyimproveperformance

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Loop transformations I

• looptiling:improvescachere-useandcansignificantlyimproveperformance

• especiallyrelevantonKNLbecauseofmissingL3

• blockingtosharedL2(512KiB)usuallygood

• wasmytransformationsuccessful?checkL1,L2missrates,e.g.inVTune

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Loop transformations II

• shortloopunrolling:helpsthecompilervectorizingtherightloops

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Loop transformations II

• shortloopunrolling:helpsthecompilervectorizingtherightloops

• unrollingpragmasarehelpfultoo

• checkcompileroptimizationreports

• useIntelAdvisor

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Data alignment

• align(andpad)datato64bitwordstoimproveprefetching

• canbedoneeasilyinmajorprogramminglanguages

• FORTRAN:-align array64byte (ifort,gfortrandoesitautomagically)

• C/C++:aligned_alloc(64, <size>), __attribute__ ((aligned(64))), __declspec(align(64))

• C++trick:overloadnew operator

• advanced:manuallypaddataifarrayextentsarepowerof2tominimizecacheassociativityconflicts

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Make use of ISA

• helpthecompilertogenerateefficientintrinsics

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runtime example for app with kernel: 1.2 sec

Make use of ISA

• helpthecompilertogenerateefficientintrinsics

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runtime example for app with kernel: 1.2 sec

if condition inside loop

Make use of ISA

• helpthecompilertogenerateefficientintrinsics

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runtime example for app with kernel: 0.8 sec

1.5x speedup

Reduced precision math

• transcendentalfunctions,squareroots,etc.areexpensive

• use-fp-model fast=2 -no-prec-divduringcompilation

• replacedivisionsbyconstantswithmultiplicationswithinverse

• donotexpecttoomuch:benefitsusuallyonlyvisibleinheavilycompute-boundcodesections

• reducedprecisionmightnotalwaysbeacceptable

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Benefits of AVX-512

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• medianspeedup:1.2x

• benefitscanbelargerthan2x(probablymoreefficientprefetching)

• automaticallyenabledwhencompilingforKNLarchitecture

Use MCDRAM

• alwaysuse16GiBon-packagememory(MCDRAM)

• cacheworkswell:requestwith-C knl,cache

• codefitsinto16GiB:request-C knl,flatand prependexecutablewithnumactl -m 1

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A note on heap allocation

• KNLmemoryallocationiscomparablyslow

• avoidallocatingandde-allocatingmemoryfrequently

• removeallocations/deallocationsinloopbodiesorfunctionswhicharecalledmanytimes

• tooinvolved?poolallocatorlibraries(e.g.IntelTBBscalablememorypools)

• pros:

• overloadsnew/malloc,no/minimalsourcecodechangesnecessary

• cangivesignificantperformanceboostforcertaincodes

• takecareofthread-safety

• cons:

• memoryfootprintneedstobeknown/computedinadvance

• codemightbecomelessportable

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Multi-node optimizations

• singleKNLthreadcannotsaturateAriesinjectionrate

• usethread-levelcommunicationormultipleMPIrankspernode

• recommended:>4rankspernode

• dedicatecorestoOS:-S <ncores>insbatch(ncores=2goodchoice)

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Hugepages, DMAPP and hardware AMO

• hugepagescanreduceAriesTLBmisses

• loadcorrespondingmoduleatcompileandruntime

• canusedifferentmodulesatcompileandruntime

• MPI-collective-heavycodes:enableDMAPP(add-ldmapp) export MPICH_RMA_OVER_DMAPP=1export MPICH_USE_DMAPP_COLL=1export MPICH_NETWORK_BUFFER_COLL_OPT=1

• enablehardwareAMOforMPI-3RMAatomicsexport MPICH_RMA_USE_NETWORK_AMO=1

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Some notes on IO

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SingleCoreI/OPerformanceonCori

Rela4vePerfo

rmance(KN

L/H

SW)

0.0

0.3

0.6

0.9

1.2

WriteBa

ndwidth(M

B/s)

0

300

600

900

1200

BufferedI/O SyncI/O DirectI/O

HSWKNLKNL/HSW

Use multiple processes

• usemoreprocesses(e.g.withMPIIO)

• unfortunately,nogoodthreadedIOsolutionsavailableyet

• always:pool(writebigchunks),reducefileoperations(open,close)

• largefiles:burstbuffer

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Does it help?

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• medianspeedupvs.Edison:1.15x

• medianspeedupvs.Haswell:0.70x

Does it help?

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• medianspeedupvs.Edison:1.8x

• medianspeedupvs.Haswell:1.0x

Summary

• singlenodeperformance(goforthatonefirst)

• loopfusionandtiling

• ensuregoodvectorization

• useMCDRAM

• multi-nodeperformance

• hugepages

• DMAPP

• IOperformance

• usemultiplenodes,poolIO,reducefileoperationstominimum

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NERSC training material

• runningjobs

• process/threadbinding

• codeprofilingandtools

• measuringarithmeticintensity(AI)

• improvingOpenMPscaling

• vectorizationhelp

• howtouseMCDRAM

• NESAPcasestudies

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Thank you

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