Skip to Content.
Sympa Menu

forum - [abinit-forum] steady increase in memory for band parallel job

forum@abinit.org

Subject: The ABINIT Users Mailing List ( CLOSED )

List archive

[abinit-forum] steady increase in memory for band parallel job


Chronological Thread 
  • From: "Eric J. Walter" <ejwalt@wm.edu>
  • To: forum@abinit.org
  • Subject: [abinit-forum] steady increase in memory for band parallel job
  • Date: Fri, 20 Nov 2009 10:36:53 -0500


Hi,

It appears as though my jobs are suffering from the same problem outlined in this post from July of this year:

https://listes-2.sipr.ucl.ac.be/abinit.org/arc/forum/2009-07/msg00034.html

When I run the attached input file for ~14 hrs, the nodes I am using run out of memory.
I am using RHEL AS4 on dual core / dual processor Opteron 2200 with 2 GB memory per core (= 8 GB total).
I am compiling with Intel Fortran 10.1 and OpenMPI-1.2.5. This job's output file claims that the calculation
should require ~200 MB.

I have found that this increase only occurs when using band/fft parallel (kpt parallel and serial don't
have this steady increase). Besides version 5.8.4p, I have also tested versions 5.7.4 and 5.6.4, all three versions
seem to show this behavior. Version 5.4.4 does not have this problem, but is also much slower, for me at least.

I have tried changing versions of openmpi (from 1.2.5 to 1.3.3), this has no effect.

Has any progress been made on either finding the leak or another cause to this problem?
Thanks in advance for any help you can give.

Eric J. Walter
Department of Physics
College of William and Mary

---------------------------------------------------
Here is my input file:
---------------------------------------------------
ionmov 8 noseinert 5.0d5 mditemp 300 dtion 50 toldfe 1d-4 eV ntime 20 nsym 1 chkprim 0 kptopt 1 ngkpt 1 1 1 shiftk 0 0 0 occopt 3 tsmear 0.001 ecut 45 nstep 20 natom 80 ntypat 3 znucl 82 22 8 prtden 0 prtwf 0
wfoptalg 4
npfft 1 npband 26
npkpt 1
nloalg 4
fftalg 401
iprcch 4
intxc 0 fft_opt_lob 2
paral_kgb 1

typat 48*3 16*2 16*1
acell 3*20.599653
angdeg 3*56.39553912

xcart
-2.22069320900486E+00 -1.67615626136839E+00 1.02845225672214E+01
2.83216713500271E+00 -9.64895067984759E-01 1.06130211295748E+01
-3.07826006953531E-01 3.14017017198906E+00 1.02884003097039E+01
2.38571355304415E+00 1.94315354580616E+00 1.47667846684432E+01
-2.74032183791911E+00 1.44987913001174E+00 1.47058588105213E+01
4.24301353957222E-01 -3.02467161327066E+00 1.47270477618761E+01
4.37208548403877E-01 3.15701320773295E+00 1.63174232817734E+00
5.62754717842062E+00 3.65799392921832E+00 1.72482290066637E+00
2.56805130575382E+00 8.08007715450321E+00 1.75538816925331E+00
5.29946087386834E+00 6.62719979049667E+00 6.13774796347384E+00
-1.33476176608987E-01 6.02962682764747E+00 5.99150680371859E+00
3.25740331179827E+00 1.86629101076117E+00 5.92292965668993E+00
4.73721314332368E-01 -6.73544486518827E+00 1.53749001511875E+00
5.79909660316150E+00 -5.87516895113753E+00 1.52606696257784E+00
2.72661190097539E+00 -1.82547980521533E+00 1.72879478480763E+00
5.29308456737276E+00 -2.93742682967659E+00 5.98120816946857E+00
-1.02277107167427E-01 -3.47901581523419E+00 6.00815649851232E+00
3.22915540047783E+00 -7.91315859978646E+00 6.15697463378583E+00
3.20853423992771E+00 -1.70404358692119E+00 -6.97779629913824E+00
8.39651387970289E+00 -8.70615018894613E-01 -7.04102732844698E+00
5.39613269691849E+00 3.09966157186435E+00 -6.96223499113757E+00
8.17325435029689E+00 2.08765713206062E+00 -2.55251338829625E+00
2.82623828634786E+00 1.23322960474568E+00 -2.78889127839044E+00
6.11970263677967E+00 -3.17948832421889E+00 -2.34609526217649E+00
-7.91433373058299E+00 -1.81160718343090E+00 1.63075874446493E+00
-2.76694176578899E+00 -1.16579400400263E+00 1.74956240701256E+00
-5.81555263606813E+00 3.20412849389643E+00 1.72359061387011E+00
-2.79939696716810E+00 2.06735348854857E+00 6.15861322508217E+00
-8.31960266338488E+00 1.29355309750287E+00 5.93088060057318E+00
-5.10575950217045E+00 -2.98997425594191E+00 6.13900333992898E+00
-5.14327896212322E+00 3.29299293105111E+00 -7.09301147609970E+00
9.75650004473785E-02 3.78997253887449E+00 -6.91330351424288E+00
-2.92976440197528E+00 7.95211008443348E+00 -6.82517026645523E+00
-3.06355829923221E-01 6.76833507431424E+00 -2.77362691622797E+00
-5.53331641987666E+00 6.24968986891999E+00 -2.54578391594814E+00
-2.43999241882386E+00 1.80795237233396E+00 -2.67292251413726E+00
-5.14068521198933E+00 -6.68713377702076E+00 -6.86237306597303E+00
-6.12789514851627E-02 -5.98968660555720E+00 -6.97883625732929E+00
-2.99553503150223E+00 -1.83920851864552E+00 -6.83013099810669E+00
-1.80008738706434E-01 -2.89562125276255E+00 -2.65747984992241E+00
-5.56015371335734E+00 -3.55350951569161E+00 -2.53677784336301E+00
-2.23260539192524E+00 -7.88875944438475E+00 -2.59919279877736E+00
-2.31544564461024E+00 -1.60168511875929E+00 -1.57988254333016E+01
2.98206360781800E+00 -1.09336396682876E+00 -1.56367782886258E+01
-3.02653507337988E-01 3.20195569372773E+00 -1.56155029581190E+01
2.62978455935385E+00 1.90892236294971E+00 -1.12646465158811E+01
-2.74702844352294E+00 1.34758125055524E+00 -1.11329897640166E+01
3.92389502215297E-01 -3.14047927186374E+00 -1.13789217412000E+01
1.43789519936701E-01 8.95683744161872E-02 5.51308679103783E-02
3.43343139804145E-02 8.44171505400222E-02 1.31069788732053E+01
2.87456960507807E+00 4.84780682916232E+00 -8.54098683394433E+00
2.83533350827871E+00 4.91662126969937E+00 4.43850072950254E+00
2.95141488341089E+00 -4.80542390687403E+00 -8.59714703849626E+00
2.82501485426290E+00 -4.90110860896433E+00 4.40234973478692E+00
5.65634082404525E+00 -1.24851891953083E-02 -1.71524703303103E+01
5.66706037951402E+00 9.18065709228990E-02 -4.30774458733638E+00
-5.41740478793818E+00 1.03696823860055E-01 -8.46603127880005E+00
-5.52981835134213E+00 3.74816566677455E-02 4.36263803023674E+00
-2.73374622355905E+00 4.90669254100288E+00 -1.71056087884796E+01
-2.76475317059456E+00 4.97808833622533E+00 -4.26429469831174E+00
-2.71829980916229E+00 -4.81400423619281E+00 -1.71329000123123E+01
-2.78480871843135E+00 -4.79896324962904E+00 -4.16357601481035E+00
1.27116237724845E-01 5.57355728005296E-02 -2.58199597795567E+01
3.69147318259344E-02 1.01239700458947E-01 -1.28425126153755E+01
1.09315814613628E-01 2.02744841122104E-02 7.51595267544533E+00
9.28429983979248E-02 4.27836872194515E-02 2.02554355831334E+01
2.71495957648699E+00 4.91077718525781E+00 -8.53254132115559E-01
2.86538509412732E+00 4.97170584874535E+00 1.18102413232714E+01
3.09009565965701E+00 -4.82067158705315E+00 -1.15312475386682E+00
2.97965222241338E+00 -4.75118372415529E+00 1.17120712079335E+01
5.77396145656038E+00 1.07323885408925E-02 -9.98939448156541E+00
5.72978432984313E+00 -6.68544670080847E-03 3.19837381572586E+00
-5.80054029700240E+00 -3.59016258256638E-02 -1.07926803392243E+00
-5.41163712815481E+00 1.29254553589581E-01 1.16343816906280E+01
-2.62158506045681E+00 5.16922521499392E+00 -1.00544849478146E+01
-2.72015016982663E+00 4.98880486733811E+00 3.02504536215413E+00
-2.79050293194776E+00 -4.88384984087100E+00 -1.01240590641792E+01
-2.61941881955994E+00 -4.73421992471235E+00 3.07027251730700E+00
7.60779786630738E-02 2.19994741542859E-01 -1.87223237882607E+01
6.88549292157438E-02 -1.91082171805773E-02 -5.66940459435534E+00

vel
1.65929233257248E-04 -7.22899336586353E-06 2.26257574401143E-04
-4.41498838683481E-04 2.56696469185694E-05 3.31830998480140E-04
1.73881380446662E-04 -3.59274234563293E-04 2.29273421593672E-04
-7.02798094302199E-05 -2.60387333161425E-05 -2.65924872337890E-04
4.42536785165872E-04 -4.89827163710057E-04 -4.01073432982287E-04
1.95643632158351E-05 1.11653991217122E-03 -9.34094601194410E-04
-7.86319162726620E-05 1.98530438200753E-04 2.04688581300107E-04
3.00397575951297E-04 2.29731480818108E-04 -7.09537178564776E-05
-3.61460082461821E-04 2.48090453139150E-04 -5.49686708040239E-04
-8.68482177851845E-05 -1.08275834028475E-04 2.95658165452176E-05
-1.07412509904415E-04 -8.78012429709354E-05 1.54371802639068E-04
-2.09843740843053E-05 -3.01743488213807E-04 6.64260233761203E-05
-6.12496928754301E-05 1.36432817751052E-04 -9.40878503004121E-05
6.14104908278753E-04 1.68165113713754E-04 -5.12708955417303E-04
2.15443297114865E-04 -4.04241581459637E-04 2.39357619874606E-04
7.81430062976476E-05 1.59513106225212E-04 2.13405809058389E-04
-2.36012088016480E-04 1.38402390396325E-04 2.23418565305995E-04
-9.33414880283709E-05 1.20065355174723E-04 -5.40061134400772E-05
-2.80686746960019E-05 -3.62478762225168E-04 -2.99299750890718E-04
-4.40755174907394E-05 -1.32663871913867E-04 1.18770307640526E-04
-2.53558806288978E-04 4.01259820381485E-04 -2.81728409555392E-04
1.57361848603766E-04 3.41172196643058E-05 1.33022101611947E-04
4.01019710009567E-04 7.22573433787659E-07 -2.69262344059131E-04
2.99733136121017E-04 -6.68678893104353E-04 3.86496510503676E-04
3.95734899013453E-05 -2.80879543778806E-04 -2.77473937236590E-04
-2.93485746700284E-04 -1.00409592926771E-05 1.76552268367262E-04
-4.99995043152451E-04 5.34640365244488E-04 -4.16733250625040E-04
4.62540147703766E-04 2.69462418459427E-04 3.55370145754719E-04
2.11074019336284E-04 -5.09254836134716E-05 -6.07095017577757E-05
5.30486297370657E-05 -3.89516038918225E-04 4.59061055880998E-04
3.85969341185967E-05 -1.33647845375007E-04 1.45606759036967E-04
2.43990312107843E-04 1.62650517626908E-04 -1.51033371102077E-04
2.67081228198250E-04 -3.20863354500405E-04 5.19374366175999E-04
-3.10316561967053E-04 -1.85209360845414E-04 -4.03377994784274E-04
-3.01054183714974E-04 -1.79705768853539E-04 1.86267271696545E-05
2.66589291951177E-04 9.91038990779357E-04 -3.96599362099506E-04
4.08276960903040E-05 1.53432487219794E-04 1.22871735039336E-04
2.35590328814509E-04 2.76550673861414E-04 -1.90931581662904E-04
2.04967171400528E-04 -3.84948347563266E-04 1.08474133114518E-04
-6.97154912755278E-04 -4.71858129707306E-04 -3.50888447092869E-04
-1.24684436826259E-04 1.21627138377997E-04 1.68581444194268E-04
-7.70851773281092E-05 4.63714165425422E-05 1.81085183134115E-04
-3.17589866254135E-04 -5.50009675262097E-04 -4.30671530615520E-04
-1.57911296613577E-04 -4.54426250235638E-05 -4.92425558216806E-06
9.87305191973671E-06 1.80207048070693E-05 -1.79532949110393E-04
6.83671915911343E-05 -9.70105029125616E-05 1.82258963862073E-05
4.57857583174456E-04 -8.32122447198841E-05 -1.67508689699827E-04
1.94599797149855E-04 -2.23628588270493E-04 1.07780974532419E-04
-2.82971791158802E-05 4.68214184227891E-05 -8.36700118689787E-05
-4.24265368843893E-05 -3.21245875729528E-05 9.22433773212692E-05
2.51671799765403E-05 -1.77766618119046E-05 1.72494196852232E-05
6.11315117142581E-06 8.68163744077307E-05 5.67296042042437E-06
-7.70845081775687E-05 3.08561858749785E-05 1.52938314279569E-05
4.20820628111984E-05 3.70042677593407E-05 9.96812582225421E-05
1.40844649691300E-04 -7.97217755672014E-05 -1.31083237666120E-05
-5.81978615724723E-05 1.17490844352786E-04 4.40930378539056E-05
6.36078347459770E-05 6.69615793199388E-05 -8.39129585283473E-05
-6.07614472082574E-05 -4.37626480779298E-05 -4.29461393218481E-06
-6.36394987636312E-05 -3.12613972792605E-05 7.79309141070753E-05
2.39708852289351E-05 -9.39157455192732E-05 3.01944658201935E-05
-1.03662791966090E-05 3.87149926133824E-05 1.05050319203302E-04
1.10894432823969E-04 3.45992275343292E-05 -3.01976038789652E-05
-1.72253916094043E-05 3.96742670252505E-05 -5.25674305834915E-05
-8.48228304979956E-05 5.64908929641756E-05 4.47531393684651E-05
-1.47506234752193E-04 1.22556764449835E-04 -3.01480394930127E-04
-2.95445248698945E-04 -2.42094492146111E-04 2.66277938523650E-04
-7.77631153135254E-05 -1.09252568425864E-04 1.69153096659710E-04
2.60223872399644E-04 -7.70901517625762E-05 1.36621011724429E-04
4.79856202268419E-05 -3.58150632460491E-04 -1.54493852536122E-04
-7.14052845122851E-05 -2.69155466792118E-04 1.79749509700142E-04
1.45112055674323E-05 -1.80926466413756E-04 6.10956577883199E-05
9.60743159647168E-05 -1.00159903624474E-04 7.70024146584693E-05
-7.39105065049050E-05 -2.15075671717976E-04 2.20969494128146E-04
2.04020346009061E-04 1.56655746598131E-04 -1.77043062668635E-04
-4.03670312774535E-04 -5.52855555754880E-05 -1.18348120988931E-04
3.71601522478895E-04 4.88286475929969E-05 1.85192663041991E-04
4.16812192512686E-05 2.23401099965076E-04 1.46463434516355E-04
-3.25279267883869E-04 7.02921173153103E-05 1.05326094998430E-04
-6.05071951258716E-05 4.15488061404616E-04 1.16175008659989E-04
-1.93579262145139E-04 5.50540862463690E-05 4.37697584266472E-04



Archive powered by MHonArc 2.6.16.

Top of Page