profiling PETSc code
Matt Funk
mafunk at nmsu.edu
Tue Aug 15 16:51:52 CDT 2006
Is there a limit to how big an attachment can be?
The file is 1.3Mb big. I tried to send it twice and none of the emails went
through. I also send it directly to Barry and Matthews email. I hope that got
though?
mat
On Tuesday 15 August 2006 14:44, Matthew Knepley wrote:
> I don't think it matters initially since the problem is BIG imbalances.
>
> Matt
>
> On 8/15/06, Matt Funk <mafunk at nmsu.edu> wrote:
> > Do you want me to use the debug version or the optimized version of
> > PETSc?
> >
> > mat
> >
> > On Tuesday 15 August 2006 13:56, Barry Smith wrote:
> > > Please send the entire -info output as an attachment to me. (Not
> > > in the email) I'll study it in more detail.
> > >
> > > Barry
> > >
> > > On Tue, 15 Aug 2006, Matt Funk wrote:
> > > > On Tuesday 15 August 2006 11:52, Barry Smith wrote:
> > > >>> MatSolve 16000 1.0 1.1285e+02 1.4 1.50e+08 1.4 0.0e+00
> > > >>> 0.0e+00
> > > >>
> > > >> ^^^^^
> > > >> balance
> > > >>
> > > >> Hmmm, I would guess that the matrix entries are not so well
> > > >> balanced? One process takes 1.4 times as long for the triangular
> > > >> solves as the other so either one matrix has many more entries or
> > > >> one processor is slower then the other.
> > > >>
> > > >> Barry
> > > >
> > > > Well it would seem that way at first, but i don't know how that could
> > > > be since i allocate an exactly equal amount of points on both
> > > > processor (see previous email).
> > > > Further i used the -mat_view_info option. Here is what it gives me:
> > > >
> > > > ...
> > > > Matrix Object:
> > > > type=mpiaij, rows=119808, cols=119808
> > > > [1] PetscCommDuplicateUsing internal PETSc communicator 91 168
> > > > [1] PetscCommDuplicateUsing internal PETSc communicator 91 168
> > > > ...
> > > >
> > > > ...
> > > > Matrix Object:
> > > > type=seqaij, rows=59904, cols=59904
> > > > total: nonzeros=407400, allocated nonzeros=407400
> > > > not using I-node routines
> > > > Matrix Object:
> > > > type=seqaij, rows=59904, cols=59904
> > > > total: nonzeros=407400, allocated nonzeros=407400
> > > > not using I-node routines
> > > > ...
> > > >
> > > > So to me it look s well split up. Is there anything else that
> > > > somebody can think of. The machine i am running on is all same
> > > > processors.
> > > >
> > > > By the way, i am not sure if the '[1] PetscCommDuplicateUsing
> > > > internal PETSc communicator 91 168' is something i need to worry
> > > > about??
> > > >
> > > > mat
> > > >
> > > >> On Tue, 15 Aug 2006, Matt Funk wrote:
> > > >>> Hi Matt,
> > > >>>
> > > >>> sorry for the delay since the last email, but there were some other
> > > >>> things i needed to do.
> > > >>>
> > > >>> Anyway, I hope that maybe I can get some more help from you guys
> > > >>> with respect to the loadimbalance problem i have. Here is the
> > > >>> situtation: I run my code on 2 procs. I profile my KSPSolve call
> > > >>> and here is what i get:
> > > >>>
> > > >>> ...
> > > >>>
> > > >>> --- Event Stage 2: Stage 2 of ChomboPetscInterface
> > > >>>
> > > >>> VecDot 20000 1.0 1.9575e+01 2.0 2.39e+08 2.0 0.0e+00
> > > >>> 0.0e+00 2.0e+04 2 8 0 0 56 7 8 0 0 56 245
> > > >>> VecNorm 16000 1.0 4.0559e+01 3.2 1.53e+08 3.2 0.0e+00
> > > >>> 0.0e+00 1.6e+04 3 7 0 0 44 13 7 0 0 44 95
> > > >>> VecCopy 4000 1.0 1.5148e+00 1.4 0.00e+00 0.0 0.0e+00
> > > >>> 0.0e+00 0.0e+00 0 0 0 0 0 1 0 0 0 0 0
> > > >>> VecSet 16000 1.0 3.1937e+00 1.8 0.00e+00 0.0 0.0e+00
> > > >>> 0.0e+00 0.0e+00 0 0 0 0 0 1 0 0 0 0 0
> > > >>> VecAXPY 16000 1.0 8.2395e+00 1.4 3.22e+08 1.4 0.0e+00
> > > >>> 0.0e+00 0.0e+00 1 7 0 0 0 3 7 0 0 0 465
> > > >>> VecAYPX 8000 1.0 3.6370e+00 1.3 3.46e+08 1.3 0.0e+00
> > > >>> 0.0e+00 0.0e+00 0 3 0 0 0 2 3 0 0 0 527
> > > >>> VecScatterBegin 12000 1.0 5.7721e-01 1.1 0.00e+00 0.0 2.4e+04
> > > >>> 2.1e+04 0.0e+00 0 0100100 0 0 0100100 0 0
> > > >>> VecScatterEnd 12000 1.0 1.4059e+01 9.2 0.00e+00 0.0 0.0e+00
> > > >>> 0.0e+00 0.0e+00 1 0 0 0 0 4 0 0 0 0 0
> > > >>> MatMult 12000 1.0 5.0567e+01 1.0 1.82e+08 1.0 2.4e+04
> > > >>> 2.1e+04 0.0e+00 5 32100100 0 25 32100100 0 361
> > > >>> MatSolve 16000 1.0 1.1285e+02 1.4 1.50e+08 1.4 0.0e+00
> > > >>> 0.0e+00 0.0e+00 10 43 0 0 0 47 43 0 0 0 214
> > > >>> MatLUFactorNum 1 1.0 1.9693e-02 1.0 5.79e+07 1.1 0.0e+00
> > > >>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 110
> > > >>> MatILUFactorSym 1 1.0 7.8840e-03 1.1 0.00e+00 0.0 0.0e+00
> > > >>> 0.0e+00 1.0e+00 0 0 0 0 0 0 0 0 0 0 0
> > > >>> MatGetOrdering 1 1.0 1.2250e-03 1.1 0.00e+00 0.0 0.0e+00
> > > >>> 0.0e+00 2.0e+00 0 0 0 0 0 0 0 0 0 0 0
> > > >>> KSPSetup 1 1.0 1.1921e-06 1.2 0.00e+00 0.0 0.0e+00
> > > >>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> > > >>> KSPSolve 4000 1.0 2.0419e+02 1.0 1.39e+08 1.0 2.4e+04
> > > >>> 2.1e+04 3.6e+04 21100100100100 100100100100100 278
> > > >>> PCSetUp 1 1.0 2.8828e-02 1.1 3.99e+07 1.1 0.0e+00
> > > >>> 0.0e+00 3.0e+00 0 0 0 0 0 0 0 0 0 0 75
> > > >>> PCSetUpOnBlocks 4000 1.0 3.5605e-02 1.1 3.35e+07 1.1 0.0e+00
> > > >>> 0.0e+00 3.0e+00 0 0 0 0 0 0 0 0 0 0 61
> > > >>> PCApply 16000 1.0 1.1661e+02 1.4 1.46e+08 1.4 0.0e+00
> > > >>> 0.0e+00 0.0e+00 10 43 0 0 0 49 43 0 0 0 207
> > > >>> -------------------------------------------------------------------
> > > >>>---- -- -----------------------------------------------
> > > >>>
> > > >>> ...
> > > >>>
> > > >>>
> > > >>> Some things to note are the following:
> > > >>> I allocate my vector as:
> > > >>> VecCreateMPI(PETSC_COMM_WORLD, //communicator
> > > >>> a_totallocal_numPoints[a_thisproc], //local points on this
> > > >>> proc a_totalglobal_numPoints, //total number of global points
> > > >>> &m_globalRHSVector); //the vector to be created
> > > >>>
> > > >>> where the vector a_totallocal_numPoints is :
> > > >>> a_totallocal_numPoints: 59904 59904
> > > >>>
> > > >>> The matrix is allocated as:
> > > >>> m_ierr = MatCreateMPIAIJ(PETSC_COMM_WORLD, //communicator
> > > >>> a_totallocal_numPoints[a_thisproc], //total
> > > >>> number of local rows (that is rows residing on this proc
> > > >>> a_totallocal_numPoints[a_thisproc], //total
> > > >>> number of columns corresponding to local part of parallel vector
> > > >>> a_totalglobal_numPoints, //number of global
> > > >>> rows a_totalglobal_numPoints, //number of global columns
> > > >>> PETSC_NULL,
> > > >>> a_NumberOfNZPointsInDiagonalMatrix,
> > > >>> PETSC_NULL,
> > > >>> a_NumberOfNZPointsInOffDiagonalMatrix,
> > > >>> &m_globalMatrix);
> > > >>>
> > > >>> With the info option i checked and there is no extra mallocs at
> > > >>> all. My problems setup is symmetric so it seems that everything is
> > > >>> set up so that it should be essentially perfectly balanced.
> > > >>> However, the numbers given above certainly do not reflect that.
> > > >>>
> > > >>> However, the in all other parts of my code (except the PETSc call),
> > > >>> i get the expected, almost perfect loadbalance.
> > > >>>
> > > >>> Is there anything that i am overlooking? Any help is greatly
> > > >>> appreciated.
> > > >>>
> > > >>> thanks
> > > >>> mat
> > > >>>
> > > >>> On Wednesday 02 August 2006 16:21, Matt Funk wrote:
> > > >>>> Hi Matt,
> > > >>>>
> > > >>>> It could be a bad load imbalance because i don't let PETSc decide.
> > > >>>> I need to fix that anyway, so i think i'll try that first and then
> > > >>>> let you know. Thanks though for the quick response and helping me
> > > >>>> to interpret those numbers ...
> > > >>>>
> > > >>>>
> > > >>>> mat
> > > >>>>
> > > >>>> On Wednesday 02 August 2006 15:50, Matthew Knepley wrote:
> > > >>>>> On 8/2/06, Matt Funk <mafunk at nmsu.edu> wrote:
> > > >>>>>> Hi Matt,
> > > >>>>>>
> > > >>>>>> thanks for all the help so far. The -info option is really very
> > > >>>>>> helpful. So i think i straightened the actual errors out.
> > > >>>>>> However, now i am back to the original question i had. That is
> > > >>>>>> why it takes so much longer on 4 procs than on 1 proc.
> > > >>>>>
> > > >>>>> So you have a 1.5 load imbalance for MatMult(), which probably
> > > >>>>> cascades to give the 133! load imbalance for VecDot(). You
> > > >>>>> probably have either:
> > > >>>>>
> > > >>>>> 1) VERY bad laod imbalance
> > > >>>>>
> > > >>>>> 2) a screwed up network
> > > >>>>>
> > > >>>>> 3) bad contention on the network (loaded cluster)
> > > >>>>>
> > > >>>>> Can you help us narrow this down?
> > > >>>>>
> > > >>>>>
> > > >>>>> Matt
> > > >>>>>
> > > >>>>>> I profiled the KSPSolve(...) as stage 2:
> > > >>>>>>
> > > >>>>>> For 1 proc i have:
> > > >>>>>> --- Event Stage 2: Stage 2 of ChomboPetscInterface
> > > >>>>>>
> > > >>>>>> VecDot 4000 1.0 4.9158e-02 1.0 4.74e+08 1.0 0.0e+00
> > > >>>>>> 0.0e+00 0.0e+00 0 18 0 0 0 2 18 0 0 0 474
> > > >>>>>> VecNorm 8000 1.0 2.1798e-01 1.0 2.14e+08 1.0 0.0e+00
> > > >>>>>> 0.0e+00 4.0e+03 1 36 0 0 28 7 36 0 0 33 214
> > > >>>>>> VecAYPX 4000 1.0 1.3449e-01 1.0 1.73e+08 1.0 0.0e+00
> > > >>>>>> 0.0e+00 0.0e+00 0 18 0 0 0 5 18 0 0 0 173
> > > >>>>>> MatMult 4000 1.0 3.6004e-01 1.0 3.24e+07 1.0 0.0e+00
> > > >>>>>> 0.0e+00 0.0e+00 1 9 0 0 0 12 9 0 0 0 32
> > > >>>>>> MatSolve 8000 1.0 1.0620e+00 1.0 2.19e+07 1.0 0.0e+00
> > > >>>>>> 0.0e+00 0.0e+00 3 18 0 0 0 36 18 0 0 0 22
> > > >>>>>> KSPSolve 4000 1.0 2.8338e+00 1.0 4.52e+07 1.0 0.0e+00
> > > >>>>>> 0.0e+00 1.2e+04 7100 0 0 84 97100 0 0100 45
> > > >>>>>> PCApply 8000 1.0 1.1133e+00 1.0 2.09e+07 1.0 0.0e+00
> > > >>>>>> 0.0e+00 0.0e+00 3 18 0 0 0 38 18 0 0 0 21
> > > >>>>>>
> > > >>>>>>
> > > >>>>>> for 4 procs i have :
> > > >>>>>> --- Event Stage 2: Stage 2 of ChomboPetscInterface
> > > >>>>>>
> > > >>>>>> VecDot 4000 1.0 3.5884e+01133.7 2.17e+07133.7
> > > >>>>>> 0.0e+00 0.0e+00 4.0e+03 8 18 0 0 5 9 18 0 0 14 1
> > > >>>>>> VecNorm 8000 1.0 3.4986e-01 1.3 4.43e+07 1.3 0.0e+00
> > > >>>>>> 0.0e+00 8.0e+03 0 36 0 0 10 0 36 0 0 29 133
> > > >>>>>> VecSet 8000 1.0 3.5024e-02 1.4 0.00e+00 0.0 0.0e+00
> > > >>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> > > >>>>>> VecAYPX 4000 1.0 5.6790e-02 1.3 1.28e+08 1.3 0.0e+00
> > > >>>>>> 0.0e+00 0.0e+00 0 18 0 0 0 0 18 0 0 0 410
> > > >>>>>> VecScatterBegin 4000 1.0 6.0042e+01 1.4 0.00e+00 0.0 0.0e+00
> > > >>>>>> 0.0e+00 0.0e+00 38 0 0 0 0 45 0 0 0 0 0
> > > >>>>>> VecScatterEnd 4000 1.0 5.9364e+01 1.4 0.00e+00 0.0 0.0e+00
> > > >>>>>> 0.0e+00 0.0e+00 37 0 0 0 0 44 0 0 0 0 0
> > > >>>>>> MatMult 4000 1.0 1.1959e+02 1.4 3.46e+04 1.4 0.0e+00
> > > >>>>>> 0.0e+00 0.0e+00 75 9 0 0 0 89 9 0 0 0 0
> > > >>>>>> MatSolve 8000 1.0 2.8150e-01 1.0 2.16e+07 1.0 0.0e+00
> > > >>>>>> 0.0e+00 0.0e+00 0 18 0 0 0 0 18 0 0 0 83
> > > >>>>>> MatLUFactorNum 1 1.0 1.3685e-04 1.1 5.64e+06 1.1 0.0e+00
> > > >>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 21
> > > >>>>>> MatILUFactorSym 1 1.0 2.3389e-04 1.2 0.00e+00 0.0 0.0e+00
> > > >>>>>> 0.0e+00 2.0e+00 0 0 0 0 0 0 0 0 0 0 0
> > > >>>>>> MatGetOrdering 1 1.0 9.6083e-05 1.2 0.00e+00 0.0 0.0e+00
> > > >>>>>> 0.0e+00 2.0e+00 0 0 0 0 0 0 0 0 0 0 0
> > > >>>>>> KSPSetup 1 1.0 2.1458e-06 2.2 0.00e+00 0.0 0.0e+00
> > > >>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> > > >>>>>> KSPSolve 4000 1.0 1.2200e+02 1.0 2.63e+05 1.0 0.0e+00
> > > >>>>>> 0.0e+00 2.8e+04 84100 0 0 34 100100 0 0100 1
> > > >>>>>> PCSetUp 1 1.0 5.0187e-04 1.2 1.68e+06 1.2 0.0e+00
> > > >>>>>> 0.0e+00 4.0e+00 0 0 0 0 0 0 0 0 0 0 6
> > > >>>>>> PCSetUpOnBlocks 4000 1.0 1.2104e-02 2.2 1.34e+05 2.2 0.0e+00
> > > >>>>>> 0.0e+00 4.0e+00 0 0 0 0 0 0 0 0 0 0 0
> > > >>>>>> PCApply 8000 1.0 8.4254e-01 1.2 8.27e+06 1.2 0.0e+00
> > > >>>>>> 0.0e+00 8.0e+03 1 18 0 0 10 1 18 0 0 29 28
> > > >>>>>> ----------------------------------------------------------------
> > > >>>>>>---- -- - -- -----------------------------------------------
> > > >>>>>>
> > > >>>>>> Now if i understand it right, all these calls summarize all
> > > >>>>>> calls between the pop and push commands. That would mean that
> > > >>>>>> the majority of the time is spend in the MatMult and in within
> > > >>>>>> that the VecScatterBegin and VecScatterEnd commands (if i
> > > >>>>>> understand it right).
> > > >>>>>>
> > > >>>>>> My problem size is really small. So i was wondering if the
> > > >>>>>> problem lies in that (namely that the major time is simply spend
> > > >>>>>> communicating between processors, or whether there is still
> > > >>>>>> something wrong with how i wrote the code?)
> > > >>>>>>
> > > >>>>>>
> > > >>>>>> thanks
> > > >>>>>> mat
> > > >>>>>>
> > > >>>>>> On Tuesday 01 August 2006 18:28, Matthew Knepley wrote:
> > > >>>>>>> On 8/1/06, Matt Funk <mafunk at nmsu.edu> wrote:
> > > >>>>>>>> Actually the errors occur on my calls to a PETSc functions
> > > >>>>>>>> after calling PETSCInitialize.
> > > >>>>>>>
> > > >>>>>>> Yes, it is the error I pointed out in the last message.
> > > >>>>>>>
> > > >>>>>>> Matt
> > > >>>>>>>
> > > >>>>>>>> mat
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