[petsc-users] large PetscCommDuplicate overhead
Matthew Knepley
knepley at gmail.com
Thu Oct 6 11:03:47 CDT 2016
On Thu, Oct 6, 2016 at 10:55 AM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
> Matt,
>
> Thanks for this information. It sure looks like there is something
> seriously wrong with the MPI_Attr_get() on the cray for non-root process.
> Does any PETSc developer have access to such a machine? We need to write a
> test program that just calls MPI_Attr_get a bunch of times (no PETSc) to
> see if we can reproduce the problem and report it to Cray.
>
Barry, if you write it, we can give it to Patrick Sanan to run.
Thanks,
Matt
> Barry
>
>
>
> On Oct 6, 2016, at 10:45 AM, Matthew Overholt <overholt at capesim.com>
> wrote:
> >
> >
> > Matthew and Barry,
> >
> > 1) I did a direct measurement of PetscCommDuplicate() time by tracing
> just
> > that call (using CrayPat), and confirmed the sampling results. For 8
> > processes (n=8), tracing counted a total of 101 calls, taking ~0 time on
> the
> > root process but taking 11.78 seconds (6.3% of 188 total seconds) on
> each of
> > the other 7 processes. For 16 processes (n=16, still only 1 node),
> tracing
> > counted 102 total calls for a total of 18.42 seconds (13.2% of 139.6
> total
> > seconds) on every process except the root.
> >
> > 2) Copied below is a section of the log view for the first two solutions
> for
> > n=2, which shows the same calls as for n=8. (I can send the entire log
> files
> > if desired.) In each case I count about 44 PCD calls per process during
> > initialization and meshing, 7 calls during setup, 9 calls for the first
> > solution, then 3 calls for each subsequent solution (fixed-point
> iteration),
> > and 3 calls to write out the solution, for 75 total.
> >
> > 3) I would expect that the administrators of this machine have configured
> > PETSc appropriately. I am using their current default install, which is
> > 3.7.2.
> > https://www.nersc.gov/users/software/programming-
> libraries/math-libraries/pe
> > tsc/
> >
> > 4) Yes, I just gave the MUMPS time as a comparison.
> >
> > 5) As to where it is spending time, perhaps the timing results in the log
> > files will be helpful. The "Solution took ..." printouts give the total
> > solution time for that iteration, the others are incremental times. (As
> an
> > aside, I have been wondering why the solution times do not scale well
> with
> > process count, even though that work is entirely done in parallel PETSc
> > routines.)
> >
> > Thanks,
> > Matt Overholt
> >
> >
> > ********** -log_view -info results for n=2 : the first solution and
> > subsequent fixed-point iteration ***********
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
> > -2080374779
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
> > -2080374779
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
> > -2080374781
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > Matrix setup took 0.108 s
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
> > -2080374779
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
> > -2080374781
> > KSP PC setup took 0.079 s
> > [0] VecAssemblyBegin_MPI(): Stash has 0 entries, uses 0 mallocs.
> > [0] VecAssemblyBegin_MPI(): Block-Stash has 0 entries, uses 0 mallocs.
> > [0] MatStashScatterBegin_Ref(): No of messages: 0
> > [0] MatAssemblyBegin_MPIAIJ(): Stash has 0 entries, uses 0 mallocs.
> > [1] MatStashScatterBegin_Ref(): No of messages: 1
> > [1] MatStashScatterBegin_Ref(): Mesg_to: 0: size: 7713792 bytes
> > [1] MatAssemblyBegin_MPIAIJ(): Stash has 482112 entries, uses 5 mallocs.
> > [1] MatAssemblyEnd_SeqAIJ(): Matrix size: 599214 X 599214; storage space:
> > 1050106 unneeded,15128672 used
> > [1] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> > [1] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 27
> > [1] MatCheckCompressedRow(): Found the ratio (num_zerorows
> 0)/(num_localrows
> > 599214) < 0.6. Do not use CompressedRow routines.
> > [1] MatSeqAIJCheckInode(): Found 599214 nodes out of 599214 rows. Not
> using
> > Inode routines
> > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 621594 X 621594; storage space:
> > 1237634 unneeded,15545404 used
> > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 27
> > [0] MatCheckCompressedRow(): Found the ratio (num_zerorows
> 0)/(num_localrows
> > 621594) < 0.6. Do not use CompressedRow routines.
> > [0] MatSeqAIJCheckInode(): Found 621594 nodes out of 621594 rows. Not
> using
> > Inode routines
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > [0] VecScatterCreateCommon_PtoS(): Using MPI_Alltoallv() for scatter
> > [0] VecScatterCreateCommon_PtoS(): Using blocksize 1 scatter
> > [0] VecScatterCreate(): General case: MPI to Seq
> > [1] MatAssemblyEnd_SeqAIJ(): Matrix size: 599214 X 15700; storage space:
> > 5257543 unneeded,136718 used
> > [1] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is
> 89
> > [1] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 19
> > [1] MatCheckCompressedRow(): Found the ratio (num_zerorows
> > 582718)/(num_localrows 599214) > 0.6. Use CompressedRow routines.
> > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 621594 X 16496; storage space:
> > 5464978 unneeded,136718 used
> > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is
> 490
> > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 16
> > [0] MatCheckCompressedRow(): Found the ratio (num_zerorows
> > 605894)/(num_localrows 621594) > 0.6. Use CompressedRow routines.
> > K and q SetValues took 26.426 s
> > [0] PCSetUp(): Setting up PC for first time
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [0] VecScatterCreate(): Special case: processor zero gets entire parallel
> > vector, rest get none
> > ** Max-trans not allowed because matrix is distributed
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > [0] PCSetUp(): Leaving PC with identical preconditioner since operator is
> > unchanged
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > [0] VecScatterCreateCommon_PtoS(): Using MPI_Alltoallv() for scatter
> > [0] VecScatterCreateCommon_PtoS(): Using blocksize 1 scatter
> > [0] VecScatterCreate(): General case: Seq to MPI
> > [1] VecScatterCreate(): General case: Seq to MPI
> > Solution took 102.21 s
> >
> > NL iteration 0: delta = 32.0488 67.6279.
> > Error delta calc took 0.045 s
> > Node and Element temps update took 0.017 s
> > [0] VecAssemblyBegin_MPI(): Stash has 0 entries, uses 0 mallocs.
> > [0] VecAssemblyBegin_MPI(): Block-Stash has 0 entries, uses 0 mallocs.
> > [0] MatStashScatterBegin_Ref(): No of messages: 0
> > [0] MatAssemblyBegin_MPIAIJ(): Stash has 0 entries, uses 0 mallocs.
> > [1] MatStashScatterBegin_Ref(): No of messages: 1
> > [1] MatStashScatterBegin_Ref(): Mesg_to: 0: size: 7713792 bytes
> > [1] MatAssemblyBegin_MPIAIJ(): Stash has 482112 entries, uses 0 mallocs.
> > [1] MatAssemblyEnd_SeqAIJ(): Matrix size: 599214 X 599214; storage
> space: 0
> > unneeded,15128672 used
> > [1] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> > [1] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 27
> > [1] MatCheckCompressedRow(): Found the ratio (num_zerorows
> 0)/(num_localrows
> > 599214) < 0.6. Do not use CompressedRow routines.
> > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 621594 X 621594; storage
> space: 0
> > unneeded,15545404 used
> > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 27
> > [0] MatCheckCompressedRow(): Found the ratio (num_zerorows
> 0)/(num_localrows
> > 621594) < 0.6. Do not use CompressedRow routines.
> > [1] MatAssemblyEnd_SeqAIJ(): Matrix size: 599214 X 15700; storage space:
> 0
> > unneeded,136718 used
> > [1] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> > [1] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 19
> > [1] MatCheckCompressedRow(): Found the ratio (num_zerorows
> > 582718)/(num_localrows 599214) > 0.6. Use CompressedRow routines.
> > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 621594 X 16496; storage space:
> 0
> > unneeded,136718 used
> > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 16
> > [0] MatCheckCompressedRow(): Found the ratio (num_zerorows
> > 605894)/(num_localrows 621594) > 0.6. Use CompressedRow routines.
> > K and q SetValues took 2.366 s
> > [0] PCSetUp(): Setting up PC with same nonzero pattern
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374780
> > [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> > -2080374782
> > [0] VecScatterCreateCommon_PtoS(): Using MPI_Alltoallv() for scatter
> > [0] VecScatterCreateCommon_PtoS(): Using blocksize 1 scatter
> > [0] VecScatterCreate(): General case: Seq to MPI
> > [1] VecScatterCreate(): General case: Seq to MPI
> > Solution took 82.156 s
> >
> > -----Original Message-----
> > From: Barry Smith [mailto:bsmith at mcs.anl.gov]
> > Sent: Wednesday, October 05, 2016 4:42 PM
> > To: overholt at capesim.com
> > Cc: petsc-users at mcs.anl.gov
> > Subject: Re: [petsc-users] large PetscCommDuplicate overhead
> >
> >
> >> On Oct 5, 2016, at 2:30 PM, Matthew Overholt <overholt at capesim.com>
> wrote:
> >>
> >> Hi Petsc-Users,
> >>
> >> I am trying to understand an issue where PetscCommDuplicate() calls are
> > taking an increasing percentage of time as I run a fixed-sized problem on
> > more processes.
> >>
> >> I am using the FEM to solve the steady-state heat transfer equation
> (K.x =
> > q) using a PC direct solver, like MUMPS.
> >>
> >> I am running on the NERSC Cray X30, which has two Xeon's per node with
> 12
> > cores each, and profiling the code using CrayPat sampling.
> >>
> >> On a typical problem (1E+6 finite elements), running on a single node:
> >> -for 2 cores (1 on each Xeon), about 1% of time is PetscCommDuplicate
> (on
> > process 1, but on the root it is less), and (for reference) 9% of total
> time
> > is for MUMPS.
> >> -for 8 cores (4 on each Xeon), over 6% of time is PetscCommDuplicate (on
> > every process except the root, where it is <1%), and 9-10% of total time
> is
> > for MUMPS.
> >
> > What does PetscCommDuplicate() have to do with MUMPS? Nothing at all,
> you
> > are just giving its time for comparison?
> >
> >>
> >> What is the large PetscCommDuplicate time connected to, an increasing
> > number of messages (tags)? Would using fewer MatSetValues() and
> > VecSetValues() calls (with longer message lengths) alleviate this?
> >
> > No PetscCommDuplicate won't increate with more messages or calls to
> > XXXSetValues(). PetscCommDuplicate() is only called essentially on the
> > creation of new PETSc objects. It should also be fast since it basically
> > needs to do just a MPI_Attr_get(). With more processes but the same
> problem
> > size and code there should be pretty much the same number of objects
> > created.
> >
> > PetscSpinlockLock() does nothing if you are not using threads so it
> won't
> > take any time.
> >
> > Is there a way to see where it is spending its time inside the
> > PetscCommDuplicate()? Perhaps the Cray MPI_Attr_get() has issues.
> >
> > Barry
> >
> >
> >
> >
> >
> >
> >>
> >> For reference, the PETSc calling sequence in the code is as follows.
> >> // Create the solution and RHS vectors
> >> ierr = VecCreate(petscData->mpicomm,&mesh->hpx);
> >> ierr = PetscObjectSetName((PetscObject) mesh->hpx, "Solution");
> >> ierr = VecSetSizes(mesh->hpx,mesh->lxN,mesh->neqns); // size = # of
> > equations; distribution to match mesh
> >> ierr = VecSetFromOptions(mesh->hpx); // allow run time options
> >> ierr = VecDuplicate(mesh->hpx,&q); // create the RHS vector
> >> // Create the stiffnexx matrix
> >> ierr = MatCreate(petscData->mpicomm,&K);
> >> ierr = MatSetSizes(K,mesh->lxN,mesh->lxN,mesh->neqns,mesh->neqns);
> >> ierr = MatSetType(K,MATAIJ); // default sparse type
> >> // Do preallocation
> >> ierr = MatMPIAIJSetPreallocation(K,d_nz,NULL,o_nz,NULL);
> >> ierr = MatSeqAIJSetPreallocation(K,d_nz,NULL);
> >> ierr = MatSetOption(K,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);
> >> ierr = MatSetUp(K);
> >> // Create and set up the KSP context as a PreConditioner Only
> (Direct)
> > Solution
> >> ierr = KSPCreate(petscData->mpicomm,&ksp);
> >> ierr = KSPSetOperators(ksp,K,K);
> >> ierr = KSPSetType(ksp,KSPPREONLY);
> >> // Set the temperature vector
> >> ierr = VecSet(mesh->hpx,mesh->Tmin);
> >> // Set the default PC method as MUMPS
> >> ierr = KSPGetPC(ksp,&pc); // extract the preconditioner
> >> ierr = PCSetType(pc,PCLU); // set pc options
> >> ierr = PCFactorSetMatSolverPackage(pc,MATSOLVERMUMPS);
> >> ierr = KSPSetFromOptions(ksp);
> >>
> >> // Set the values for the K matrix and q vector
> >> // which involves a lot of these calls
> >> ierr = MatSetValues(K,mrows,idxm,ncols,idxn,pKe,ADD_VALUES);
> //
> > 1 call per matrix row (equation)
> >> ierr = VecSetValues(q,nqe,ixn,pqe,ADD_VALUES); // 1 call
> per
> > element
> >> ierr = VecAssemblyBegin(q);
> >> ierr = MatAssemblyBegin(K,MAT_FINAL_ASSEMBLY);
> >> ierr = VecAssemblyEnd(q);
> >> ierr = MatAssemblyEnd(K,MAT_FINAL_ASSEMBLY);
> >>
> >> // Solve //////////////////////////////////////
> >> ierr = KSPSolve(ksp,q,mesh->hpx);
> >> ...
> >> *Note that the code evenly divides the finite elements over the total
> > number of processors, and I am using ghosting of the FE vertices vector
> to
> > handle the vertices that are needed on more than 1 process.
> >>
> >> Thanks in advance for your help,
> >> Matt Overholt
> >> CapeSym, Inc.
> >>
> >> Virus-free. www.avast.com
> >
> >
> > ---
> > This email has been checked for viruses by Avast antivirus software.
> > https://www.avast.com/antivirus
> >
>
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20161006/5fe489da/attachment-0001.html>
More information about the petsc-users
mailing list