The ABINIT Users Mailing List ( CLOSED )

[BOTTIN Francois <francois.bottin@cea.fr>]

Hi Eric,

Concerning the changes you have just to nullify the various pointers (at 
the first time) in order to
have a well defined status at the beginning.
I hope this is the origin of the problem!

For bandpp, I don't know why the link does not appear in the whole list 
of input variables.
You will see the documentation at:
http://www.abinit.org/documentation/helpfiles/for-v5.8/input_variables/vardev.html#bandpp
Its use allows to increase the size of the block without increasing the 
number of band processors.
Moreover, as said in the documentation,  "Put *bandpp*=2 when istwfk 
<http://www.abinit.org/documentation/helpfiles/for-v5.8/input_variables/vardev.html#istwfk>=2 
(the time spent in FFTs is divided by two)".
This is well suited to your case (istwfk 2), ... if your memory leak is 
removed!

Regards,
Francois

Eric J. Walter a écrit :
> Francois,
>
> I have read the link and will try implementing the changes.
> Thanks for the suggestions on the input file.  Is bandpp an input 
> variable?  Perhaps it is undocumented?  I don't see it on:
>
> http://www.abinit.org/documentation/helpfiles/for-v5.8/input_variables/keyhr.html 
>
>
> Thanks again,
>
> Eric
>
>
>
> BOTTIN Francois wrote:
> > Hi Eric and Walter,
> >
> > By setting istwfk=1, your calculations become 2 times larger and 
> > generally 2 or 3 times slower.
> > So, please, could you see if by correcting 66_wfs/prep_kg_sym_do.F90 
> > as explained in section "danger
> > with pointer" at http://www.cs.rpi.edu/~szymansk/OOF90/bugs.html, the 
> > memory doesn't increase
> > any more (using istwfk=2).
> >
> > I have strongly modified the way to do that in abinit5.9. The patch 
> > proposed above, would permit to wait
> > until a stable and production abinit6.0 release.
> >
> > Concerning your input file Eric: I suggest to use wfoptalg 14, bandpp 
> > 2 (increase your performance) and iprcch 6 (for DM).
> >
> > Regards,
> > Francois
> >
> > Eric J. Walter a écrit :
> > > Hi,
> > >
> > > I have also run a few tests and agree that the memory does not 
> > > increase when istwfk = 1 is set. Looks like you have found the 
> > > problem, Francois.  Thanks!
> > >
> > > Perhaps it is moot now, but I have not been able to determine why I 
> > > can seem to get g95 + openmpi to
> > > work with abinip.  If someone has some suggestions....
> > > Regards,
> > >
> > > Eric
> > >
> > > Winfried Lorenzen wrote:
> > > > Hi,
> > > >
> > > > I have tested it now and it works. The memory does not increase any 
> > > > more with istwfk=1.
> > > >
> > > > Are there any drawbacks from setting istwfk = 1?
> > > >
> > > > Regards,
> > > > Winfried
> > > >
> > > >
> > > > Am Donnerstag, 3. Dezember 2009 18:01:08 schrieb BOTTIN Francois:
> > > >  
> > > > > Dear Eric and Manuel,
> > > > >
> > > > > Thank you very much for your reports.
> > > > > As we can see from your graph Eric (which is very helpful; we can see
> > > > > nline, nnsclo, nstep...),
> > > > > the problem appears 1 times inside and also 1 times outside LOBPCG 
> > > > > per
> > > > > electronic STEP.
> > > > > I suspect the trouble comes from 66_wfs/prep_kg_sym_do.F90 which 
> > > > > is called
> > > > > i) 1 times/STEP through prep_getghc.F90 inside LOBPCG, and
> > > > > ii) 1 times/STEP through prep_fourwf.F90 outside LOBPCG.
> > > > > Within this routine, there are some pointers with the "save" 
> > > > > attribute
> > > > > but an undefined status (there are not nullified). In this case, I 
> > > > > think
> > > > > the "associated"
> > > > > intrinsic can't be used to check and deallocate the pointers before
> > > > > reallocation
> > > > > (see for example the section "danger with pointer" at
> > > > > http://www.cs.rpi.edu/~szymansk/OOF90/bugs.html).
> > > > > It seems that these pointers are never deallocated.
> > > > >
> > > > > One good news. This routine is only called using istwfk=2 (real
> > > > > wavefunctions).
> > > > > So, please, could you check if using istwfk=1 your memory still
> > > > > increases or not.
> > > > >
> > > > > Also, let me know if you succeed to compile and execute in 
> > > > > parallel with
> > > > > g95.
> > > > > Thanks again,
> > > > > Regards
> > > > > Francois
> > > > >
> > > > > Eric J. Walter a écrit :
> > > > >  
> > > > > > Dear Francois,
> > > > > >
> > > > > > I have put a copy of my input, output, log (called OUTFILE) and psps
> > > > > > at the following link:
> > > > > >
> > > > > > http://piezo1.physics.wm.edu/~ewalter/Abinit_memoryleak/
> > > > > >
> > > > > > NOTE:  the input file is for a different system than the one I
> > > > > > attached previously (the atom species are
> > > > > > different).  Please disregard the previous one.
> > > > > >
> > > > > > I have tried compiling with g95...  The serial code works fine, but
> > > > > > never showed the memory problem
> > > > > > anyway.  The parallel version exits right after reading the psp
> > > > > > files.  I am continuing to look into this problem.
> > > > > >
> > > > > > I have also tried compiling with pathscale v3.0, the result is the
> > > > > > same as the Intel fortran result.
> > > > > >
> > > > > > So far, my testing seems to show that the largest problem is in the
> > > > > > lobpcgwf / lobpcgccwf routine.  In my
> > > > > > test, I run for 5 iterations and output the "free-(buffers+cache)"
> > > > > > result of  "free -m" to the output file
> > > > > > (I have added call system('free -m') to various parts of the 5.8.4
> > > > > > code).  The graph is posted at the same
> > > > > > url as above (called memgraph).  You can clearly see 5 repeating
> > > > > > patterns, one for each iteration.  In the
> > > > > > serial case using wfoptalg4 (green), you can see that the memory 
> > > > > > usage
> > > > > > from iteration to iteration doesn't
> > > > > > increase.  For the parallel with the lobpcgwf routine (black) the
> > > > > > memory keeps increasing during each iteration.
> > > > > > However, when the lobpcgwf routine is commented out (red) the memory
> > > > > > increase is less quickly.
> > > > > >
> > > > > > I will continue to try and track down the problem here.
> > > > > >
> > > > > > Regards,
> > > > > >
> > > > > > Eric
> > > > > >
> > > > > > BOTTIN Francois wrote:
> > > > > >    
> > > > > > > Hi,
> > > > > > >
> > > > > > > Is it possible for you to compile abinit-5.8.4p with g95 in 
> > > > > > > order to
> > > > > > > track memory leaks?
> > > > > > > Perhaps your code will stop at a well defined line, with a tab
> > > > > > > "already allocated"!
> > > > > > > It would be very nice to get rid of this trouble.
> > > > > > >
> > > > > > > If not, could you sent your 3 pseudopotentials, output and log (of
> > > > > > > the proc 0), if this file is not too large.
> > > > > > > Regards,
> > > > > > > Francois Bottin
> > > > > > >
> > > > > > > Eric J. Walter a écrit :
> > > > > > >      
> > > > > > > > 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.h 
> > > > > > > >
> > > > > > > > tml
> > > > > > > >
> > > > > > > >
> > > > > > > > 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
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> > > > > > > >           


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Francois Bottin                    tel: 01 69 26 41 73
CEA/DIF                            fax: 01 69 26 70 77
BP 12 Bruyeres-le-Chatel         email: Francois.Bottin@cea.fr
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