r t t t r t !

t
l t t r l
Promise
of
rPerformance
hfigurable
Gomputing
I apL l t . Chao,
t . | , na t . ! A, abj . ?ad
Mnaqns Hka1L, ,
^ / ' J Gal , . r eMI
ud - r i
I
Vol..ltny K'"rratenko,
r\ r
D,h.dh BL c I I, u\i!,n, d sq,r.-" ".
SeEEl high-pertomde
@nputers now ure fietd-progr.hmabte
gate
arays as re(onfigurabte
6pre.ersor5.Theaurho6dee(ribetherwomajor.ontenporaryHpRCar.hite(urerandexptoE
theprcsand<onrofea.hGingrepresentariveappticationsfrchremoresen!in9,mote<utar
dyn.nl.r,biolniormati.r,and(yptanatyiis.
ntiepankwvr4,hish
performanec.nomDe
vcndoB have ' noduccJ nany syiems .ontain:
ins bolh micn,proe$osrnd
Gdd,pnraEmrnrhlc
"1 .".p,"^ +. .*.t " ..a.- U tc , "1 ".-.e,.
! t r h
r ddr d FPC{ . h p! . T$o or $* . - * h, * , . , h;
cr 4I Dr ud
sc A ny, r . o nr q, or , r r ; dt r n4,
nrL<\trhof rhe(l utrhsrEhhch p!.
Inaddrvn.d
Inl B..Nul t duny i ff bl hti o,s
q
Fr' 1A cJBl , p4 nL dr, su!h as H rri s rc!unhe[rJbte
. dFr r.oh ,he
,\
" Fd.e R-di .h Li bo-tu..
In al l oI thes archi rc(rrcs.
the FPCA\ rR. i s
c.procsrrsbd.ni crcproa$o(
TheDi i nappti ri -
handr . ksi et 5
r r hd. r oi s! f (
ti o' s. sud kftn.k
,rt.pi .cl l vLl an prD
htnve rpped."mpL
hr tr,hrr
oD D.di !trtrr
rpr(mfl rJ
s 6n. gnr,.d rrnr..
Fi 8ure I dtu$s dDr r trrBrr i l oni Ft.rn (ur
dunucxrunon.rdrepl i cati onon
the fr tj oDrots.
$r. n $h(h
cr rrr, n{rm mr4k- *
+rn-"
*.h,Grurc n i re!.ni aufL! pro($or
ro..r. r
the b4dop.rti on.
T. do soj the re.onnstrn6te pro
sft
rr
rs.
Thrc. such sr$ems-rh.
Chv xDt_
rh. sRc 6, ind rh. sct Al x/RAsc_arcDaril
r E.urri 8ure rhf FtcA.!n rh.
[ , . ' qh r ! r t , e, wen] ! o$qpr
ce.
puhroN
Thi s f.rrL n roa yrcLrcdb,s
runti m.
FrtN an rppl ni i i otr dAdoprent pos|ccnv.,
del el _
.ptrs.ao
drr. .he hrduai c k&nd $i Dshardwarc
?ndv.ri tos.oth(
$ i nf r i $ rttr s( of h
Lh.hkl
r;nstrrps,(h
r
sRcrorj p!,r.
.Ji ! c ri d c!tr. F,;"";, t.Nl ,.
{(dcl i l d
rtuhnotos 6, mp,,t\ c, Nttrn,{ cl l o'
^l ri onrs.
?nd Cd.xi ci r Handd
C. Tfi &c ai e tnj
I' i sh.l ekl g(phi c, pmsi j mmi na
devctoDncni i oots
j !!h
r, \ n n?pol ' 5 ,crc sr vFmi cmF;.
ssrbnJ*
twei j . \Nr x' l n. \i
' !n cei trrb,. -d Dfh" : .
rr(unl i g!Ehk
LomPf ,ns r,orbo\.
Re.' dqs drtrU coNut! Co,,rdsrs l vtarch 2007
spshl i *tr. on hi gb.pdordi nce
rcconnsrBbk
coD.
puins
ioi I
sood
okryiew of modch Ht,Rc sy*enx,
rpprra.or
aEbphmr tuots d tan.wdks,,nd
HPRC ARCHITECTURAITAXONOiIIY
Ma|y .irl,r HIRC sy$ens, such 6 dr sRc,6E ,nJ
the serbrids.
Hyp.rcompr.r.
sn hc se rr :n{he.l
potdstr.
Thse srshs sdc ds1gn.d rrohd onc
node or n' croFroc$s.^
a,d.noi hft
oi FpcAl Th.
**, *, ql l
th?daaB.D!|iB?k.U|ioroi|h.
opPlkarcaorh.r'(qaBq'lr"tb
\sdo6 .ri vrq nic ruiio ol re.onlistr-
mblc nod* m ni.roprortsoi nois to
tu6 thc diliir.fi J.mands of cu$om-
q!
lp plicd$ns.Thr n highl) dsirRbl.
ton m
(onoDic perpetiE
slu
th.
.o$ diffcrcoce bsNLm FPcls ,nd
Ei&oplo.sson,,nd tr is pxrtictrh y
on rhe downsid., havins the EcorJis
ftable lode and the microproc5sornode
Lnt mto\rr thc slured lntrco.n*tlon
ndsork ' naksthen ompd. ror ok.
lftn.y brwe.i ih. mds. In .ddition,
co&
pofuh,ftrrould b(om Nnsue
.v.n rvnhii ihe slnt typeofradine
if tl'r. 6 I chrnst n rh. iatio bemen
thr ni.npm..$or nodcs 3nd ihe FPCA
A Eprescnbiivc rrrnplr ol ilt
UNNS n ihe sRC 6/SRC 7, whi.l, cor.
' ni.rop' o.csor n' bs]$ems, one or
nore MA l' Econlisu(hl. subrrrtds,
and
elobal
<' mmon mcnory
iccM)
n.ds ofshircd mrmorr sp.cc. Thse
srbsy$sns : a inerconD(ed thbugh
R Hi' Bar s{it.h comnuDllxin Iry.r.
The micDr!,.c$.! 6.r!ds r{h in ld.
sois rnd xre conDected to the Hi' Bar
sRith nroush a SNAI incllatc. Th.
SNAPca.d
oluss
jni,
tbc durlin lin.
frdnorv nrduh doi on th. micropD.
c6so nodHboard ro proide highs
E)
;
1S
( I
tuet.
Mtu%@a bes@qd hbtuohdtd tuss: Ic)nttomnode
No nod$ sere .orr(Ed ,llrcal* wnh.,ft r krl,bh
Hcrc N. d. not 2ddnss ihts .Jlv ,iMchcd proftsor
sFrnsbrilo.a$re.don$rl lepadlklslnos.uch
s thc Cry xDl,SRC-6, and SGI Altix/RASC rs \tll
N re.on6sumbh [cowulr clu*.u. Th6. ,rhirtcrDrcs
can
serenllybe
dktinsui$cd 6r Nhfther e,ch node in
ttu q..E h h.m.s.n6d
Gnironn)
or hctcrogcneous
{nonunifo!n).rA
uii{.rn n.de n ihis conxt.ont?ins
oi. ryp. oI po($lrschmn-fordamph, onlv micD.
psrtsos or rrcAs. ENed on thisdistlndi{,!,m.Jrtn
Hl,RCs can be groupd into Mo major.lass, miiorn
nodc nonuni6D synchs end noibildnr troJc m,lom
Unit rn nod nonuniform 3ystms
In UNNSS, shown in Fistrre 2a, nodes $ictlr hrd
dlhtrFPGASor mi.roproe$otr ald arulink d 2,n
interconnedon nebvork to
elobal
(CSM),Exanplcsoliu.hsrs.nsincldcthcSRC-6and
.h.Alir/R,\sc.Th.Diioid\anosEof UNNSSisthat
d,h thnsto rxtcs bdwe.n the bolrds than the k$ dh
dent bn commoD psiphcGL.onp
lPCll
solution. Th. su{rin.d mns
ri.ropnasorboldrdrLcMArprocesoisis 1,400
Thc MAP Ssies C p.o.esor con5nb olon! contln
fl' GA ind t{o tr$r FrcAs. all xili
4s. AdditionalLy,{ch MAPunit..itriissixint nertd
bin[s oronho l nmory
loBM)
w
of21 Mby6. Tl1. ndjn(n iggrs,te ditr tu,,ufer mre
lmong rLL FPGAS rtrd OBM is {,!00 MSps. The usr
FPc,\srrc.onhstrrcd nrch ihit onc is in mstcr m.dc
andtheofh{isinslivemodc.AhlidBLFrtdiE.
r..n
re6a MAPts. FPGi.. Fuiih... N
be con.ed
yn
r chrjn poft ro cre,ie ,n FPGA ,i*
Nonuniform node uniform systems
NNUss.s[own inll8uie2]r, Nonlyonetvpeof iodq
rhN i[e sysem leveln unifom. H
.onhins both
ryps
or rcn,ulrs, a
ndcd dlrcny td ih. ni.opnrtsoc i' Bide rhe nod..
8", , *,
\il1
Exmples of nrh sy*ems arc ihc CEy xDl rnd
rcconfuuiable clu*trs. N NUSI main drNbrk
r rhar 6xed niio of FPCAS b mi.n,pr.csois,
Rhich mishtnotsunrh(tudnionrl \qdoFbuys
coioni.nodcl. H.wcv.r, tlEycr{in r$EighF
lorw,idmyrothesinsk.prqnm,muhiph darr
ISFMD)
modd dxt no$ paralldlproe n' ni"s
pxrd1gN embmc.. Furhr, ds hM.y bdkdl
de micrcproeso! rnd its rPGA .oprcesor can
bc lou, and rtu b,nd$idrh berueen lhem Njll 6.
dcdicrcJ this.d ' nern hish pdformane ror
hlny
drh
inensive appl'c*ionr
A rprc$nbrive examplcorrtu NNUS is the
crry xDl. who* direccconncftd proce$or
IDCP)
rrchit(nrc hames$ multjrl!
|lr.!i$o$
tuoasinsle,trni6edsFcm.Tl' . hN dnirMcha'
sis, with trpb lzcha$is
pc.rlbin.,. one.hasis
houssrixcoEfur.i!ds,.rhof uhrch coniains
nrc 2.4 GH: AlvlD optenn micrcproccs$* rnd
one ar rwo RrpidAriry lrocssoE IRAPS)
th,i
hrndle.omntrni.ation.Ther!. opt rcn n' i.ro
prasos are conn(td via AMDl HlperTrin!
potrchnologr {nh r b,idnidd, of i.2 CRps
nrning r iwo wa) svNn{ric mul.ip!.tsiis lslvlPl
clu$cr. Erd XDl ch?siscan bc(onigurd wiih!x
applicition-accclcErion
pro.esors brsd on Xilinx
vniq ll rro or vrrex 4 FPGAS. \vnh nvo R]\Ps p.r
boird, r b,ndwidth ofSCBps 1.1CBps bidne.ioml)
beNeen bo.rds sreihbG vja r RlpidAiny swirch.
Halfofthis $vlEh\ 43 links n nmr
.onpur 60,idswiiILndr.hasis,vhiLetheothe6.an
vc lNc ukd ihe sRc 6I snd SRC.6 sl$chl i. inks
rigtrr. iodc hvcl pdormanc. of H PRC rrch itcdurts in
prortsnrg remotc scnsinsr and nol..trLxr dvnrrtrsl
applicationr Th$e nudics included the trs ofoptinri.
za.i.n erhniltu.s su.h $ pip.lininsand dati r?nsr-
orqlipping { iih co'npu rinon to e
t' nposl,ndspatial panlkLkmolsuch appltltions
H) peqccnal dimdrion rdu. on' isrcprcsenh.\
of remoE snsj's rpplicdoc wnh ftsped to nod! ps
f.drnrt. vnh FPCA as oprc(soBlbr the njcrcprc
.dsor,strbnrtirl ddr in this,lae' itucnsiy.rpplic,iioi
mD$ mov brck and forth bes(n r
nenoryand thc FPCA.nhorrd mcnrry. Vhile dt
bandwidth fo. such ransl* n on ihe oidtr ofCBps,
$e iEnsfc6 aa an Jd.d okhcrd rnd repftsnt i ch:|.
Gnsconrft sRc 6 givendeliniresizeof nsOBNI.
Thh ovshcxd can b. avoided ilto8*h( throush
iI. sh,rins afnemor) banks, o! tlc hlnJwiJrI c]tr
be rneasd io hke adYantas dr FP
proccsins sr@d. OvtLappinc monory mnsfes-thrt
F
b!t.
3. tutu r
prtti*
ot tv
p.
rpa re
*u ta r.i n2 on sfl c-6 E.
@
tob t eE.r | tu d n, a r sc-6
i5, *rcrn1ng beNs, nE$ two p!..B!ing .l.n.nts
md' h.computaiions rlsocan hclr.A
sud, rindc6
1I/o
fu d,nd srir. optrr,iont hkeoDl)
3 p{ant ofth.,pplniion execurion tlnE on a 1.3
92 pment is sp.nt oi tonpm,' o.s.
As Figtrrc 3b showi th. rnncen*Iion sRc.6E
achi.!* r signili.rnr spftdup ovd the mi.roproa$orl
11.03x wiihout*fe.minsaod rl 21
H owcvc. the computation tjD! n o
of rh. ovcEll.xftutioi inc.I' , rh. aoLLou{' p SRC' 6,
thc 6andwidtL bd{*i t|r mrcrop.
nuclscs ftom i30 NlBps
lsu*aincdl
to la GBps
lsusrinedl.
As ljisu' c 3. $.v!, th
a 24.06x speedup
hrnhod
*ie,nins) md a r2.0Jx
spcldup
(wnhsturi' ing) ovd ih. n' crcprocesei
Th.s r.suhs cleliLr denontrrat. tlat 6rndridilt
[rw. dr mi.ropro.ssor and thL FPCA nqs be
intreNed to sup.rt nor. dn lircnsvc lppLmtions-
an area the rhi.J
g.n.nrcn sRc 7 ,s likely to a,ldE$.
li should 6. iond, how.ve. t|[r in no* HIRC5 todiy,
ramle6 bdw.en dr nicroprccessor an,l FPCA a(
cxplnii. ftrihn compli.rtins pmgummins modcls.
Th*e iwo 'nemorv subsy*cms s hou ld .ii [d b. au$d
i'to one or intesmted ;to a hLErthr wlih de obiedfle
of rcduclrsd dininari' rg drisokrhcad{ndnakinsth
Nrmscal. Dolecular drnamics
(NA\,{DI' is rtpre
s.nirtive of floriins.point appli.d.ns {iih nsp.c,,o
mde perlornancs A rctcit.1s r
yhcn
podng su.l' hshly oprnnized code, a sensible
.pproarhnb se*veialdsisn itdations,shrtingwnh
,.,' *' -' qll
dE si ples, no* $nishtfoNrd implemei.itjon aod
smdtrally
addins io ii nntilachieylns thc hc$!,lmion
o. runnins out of FI,CA Esourc$.'
Thc*udy! tinaldun FPCA brsd imolnlibiion
sas.nly$rt(im*INdthrn' roris;ml.od..\(u
otr. Ths. rtsuhs, howder, are datu d.pardent. for I
hlgtrctrtoffmdius, th. origimlCPU codc cxecftes in
more tlEn 300 seonds xhlh n,e.ljPCA x<uiD tinc
n un.hai&d, which Nou d <Dnnu
Th. nr.d m ftnshr dru bdween rhe cr+ drb somsr
' h..hrnnir 1nd dr slstutrr d.lintd MiP/FPGA dr.{
$onge xrchii(Ne rcqurcd co ridcmb . dev.lopmcnt
elfofr. When creatinscode i.oF s!
FPCA archienft, a prosmmmqwould inpllDsDt
rhe dti *onse ' nechanisms comptibh bcnvcLa thr
CPU ind FPCA f rom rhc l4inoins,
hsrha n Etulr th..*. nr.\is
insq)dcandadJrn) ft amouitol
uolk rc'ttrircd ro port dr cod..
AltLoush ihe official bench.
m?rk' k{nd mplovs doubLe pre
.isidn floltiig poi r.nhnfrn, $.
NAMD rseirh$ applied ileo
riihmic optimDRtion iechniqns
rnd ifrpl.mddl th.i! kdnd udng
mcti. tor atom loc.iors ard rl.btr
"n
y
arhie' c
sood
p{n.-"' .".' h!i
thr unddLrids
I.IPRC rrthndu( supp.ns kitur
oroldhppiis.srra' niigc h.uhli.d6v,ichtrddrcs
ihrt,ie.hm.rcnzed by h
Eh
I/O brndwidth xnd/or tighr
.ouplinB ofrPc,As with asociftd D,i{oprces$s. Nsv
promkingcxamphs oIth5cft DCParhitdurs5u.h
a5 A]\'ID.s TorEna iliririY| ifi
ry
i! s(ll i5 Inrlk
QtrtrlIsN
tehnology suppoius tan
sdrb' siABlsysems.Lrgeenough rrcmorbrndsidth
r odE equllv inporiinr iiaue.
B] memor
y
ban widrh rc mcan ilft rhe memory sys
tlmhrsslri.i$tnuldpknvrv.llrspftd.{id' ,or
dlprhkt.. hoth{{orJJ,6(.u$FPCA5lanpr,{lu.(
ind ff$Dc dra at a high ilqft. ofpral|.|nn, th.
,l soh*ti i .,turl degft of n ri
dnn!.
smpN pr, a hlge ntrhiple
of meDorY b.nks Ni th nrowword
l cnsth or l ol aL FPCA n!mo' r, QD
h! morL u5crul !, mooq bouod
rnd wi dft nH,ori es sth fesd
inils{ a.nhmctic rr rorcs. Coos
d6isn o.cups nos iv.l ?ble dices
197
percnil.d
filtxrion oI on .hip ine' nor! |]liks
1a0
pft..n) md
hmdsiie mtrltiplns
(23 pefend is Los. lhe f.ct thxr rhe
dice LimnNr reached bdore iny oiher Fsof..e lim 6
bdrrriliroiherrvidrbk csotr($. otr. po$$lesolr
rion is io orerl.p calculiioDs lvith datl tansfer Ior rLr
D3xr,ih*tbtr$DoEryriLiblcoFdrlpnrcmor*
DsDnc th! rdatndv ' nodst soelduo achiclcJ, d!
NAMD $udv.L.i y,lhtsr,ia rl1. pomr rLofHPRC
ichnolosy.FrcA.odedevdopDentmdromllrbegft
\viihsftingsde k inpkmcnG tr trxtbook aLsoithm,
NnhIitnc.!Di)o' iim' ition' vhcnPo(ingsuchufuP'
tiniu.d oJr b ai HPRC
drfrn
and bljiscn n,
l00x speedup. ln .onrN, {. h.g1nvnhd..ld. olJ
cod. oprDu rd ro rur oi ,hc cPU bx$d
d' dorq
s.h
codesu.c$sftrlly.ompdsstrh i$r|' GA.portedcooi
e.prrt. rr is impoftantio kep ir m nd rhit the $ndrt
hsur.hmlogy grdsrh.tr.vrrlDr cPUs."
Optim;ation iechniqu$ sudr $ ov{hpdrrg diia
icnsrqs bNeD the m oopro.e$o6 and IPCA: Nirh
bonnd ,pplrrions. HorBer, srcl rpplicrtiois, nclud
ds uith imnspirc( n.nsf{s oI dita benveen FPCAS
ind mnropro!6so^
b
lDregft ngiLe nicrcprocesor
chy vodor providedrtmsp.rtnttinstes.u.nhrn.e
pcrforman( bvstrr:nte.ing tft no(dfi .ienttiansfd
mddcsL' thcunddllingrL orD T
lom on tsornh' ni. optiniz.iioisth,i.m 6cn.1i th.
rppLi.rion uDde. i' Nsnsarion Hhd,hii dm tixns
ft a or dnribrt on. k ilso crn improve prodrctiv,*
v.h,v.us.d rsRc 6 md c rxDl srnrns to
i' N$igitc slscm-L.kl
ftrbnnrirt
of HPRC,rhi
&cnr 3shbbi nnt r n. . i . s' aDdcr ypkni l vssN, ! l ppl i
crlons Thse ipplic:tjons prcvlde i neFpndic?l
up|.r h.uDJ.i HPRCp.rtn l p.,f.rnancc s {dl
* in5iFht inn, 5yf d lrEr pfl )gEmmhirnrand prfo.
m,m issDNxpri, fron rl' os.$s..ii *nhg.iml
hrsh pdonnrre.oDp$ea. They u* iftegd rnhne
ric, r, r.a $htre HPRCS excel, ar
wnh l,trs or<,Druhtior aod ar Doch dak innsfcr
bdwlcD lhc rPCAs and Djnopnlcsso6. and;h{it
6orh spitirl ind rnpoal plirl.lnh.
vI. dniiibuftd the N.rllo,d .f hoth trpLr oI appli
.itiotrs o\rr iLL noda usng dEns
ii.e(ivll,l). I' , rhe.rsolDNA d porm,l.vsis.we
broidca$ r dliiba* of rcfercnce *qu cs md$atter
dNtjlied matching
s.ors l..,llf 1nd thrn glthdd th.h t.gdh{. [&l
F* " "
b oidcr( rlt.ipli.re\r r ndls nr.orrsNndillg
o.
ni.\i:uron hnd os rh.l.!. r Norlc' iodc *nt ir
lor.\rtrsd3slftllnpdrsftrseordlccuPs)rdr
nr onshprr n,d,i. r NdlN h.onrrtrr. sr(drp o{r
nrxDl haJanldvint?F!0!.rh!s
sp*dL pDnfl doarh.e\ped.d erj,sp*dtrpdr.osso-
pd.dr Jli.i(od. on rh( orhq hanJ, cichrq&5 oo nr!
\rdi! rlno ollttn
(
, eh !r!J r 69jx !nc!Jur r*c,J
olr|tr;p{rd 73sx sp..Jur dur b inkr]Jrd)nr
riu, .i riJ lro ordu . Tl' ( rthi!!(J
$!!Jtrr,
ilr
olhr .r8i,rs/.hip Nr l,7e4i Lns.ld oirlf -imred
trdeir) of 4.i1!\ dtre b rlrir inknod
rln. sJi(d, dsllrJlrh ] iir(ro& riJ i' r n,J(
. crls r HPRCS
h,gt.or6gritridx n gh ntr b. n.di.
r h. r r t , DNhs s i Gt r 6. dkr r i i r Tr I c! ] r i Ll l , . i t u
cri nore!n.onrigirrs,*re. i r' srne(rNrpdrrior
his.rn o\rrolsLcid \\r' $.hcI\h Ln(yN.D ni r
o' d,|t .bpnr$or ]sD, r l 1 cl lz ooiooo
\ h . r r ! ( j r r ! xDr i . hi . knl D. r 6r \ \ r l Jqr Tl r
ipr nrid,s srhb,lnr srlDon d{1.
hr r | [ c. s! or Ac
( r v
Xl ) r . nn
3ht oNi r d, \ l l ' l
, r ul j l r i oor $f Li nul nsr r a! L$ Honr \ r . i r n !
D oi YoN mi ! r .
hi J n, i trtr dtr rfu Di .' .ri !.$nrr, trfJ,l i ! 5rnun l ,
n,*mhLL+ *!i .nrj o rd$cr.rd, m noprort$or
^odi r!1rr,Drc<$or Bcau$thesrrc 6 $sLnni .dh
N)a(\orri Di fhl rs rnri q{L dMb.nnred.fl i
h. er . ThnNr t r
l l do.scoerr r nr sl nen l evd-nrnl l ,. !Nr-s
**, *, ul i
SPNi D prcsnmmi Dts prad,sn\. T
!urcnt i .!hn.l d$ l ri l LTd i hi tu$rl i smrb c
l )n)rso6
r.oprort$oE i orl ]e m.n l ,on pr
si ngh trndrrcd .oD,muni !*i oo dr
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Tri but e t o Honor Ji m Gray
The rEEE Computer Sociely, ACM, and UC
BerkeLey wi
lon
the ramry and coleasues
ol Jim Gray n hosrnq a tibure td the
egenoary compuier scnc proneer.
missng al sea since 2a Jan 2007
uc Berke ey
htlpt/ww eecs.berkeley.edu/
proljlmgraytrirrule