Slow assembly

Mon Oct 29 05:53:10 CDT 2007

Yes, the stash holds entries for other processes which are sent during Assembly.

   Matt

On 10/29/07, John R. Wicks <jwicks at cs.brown.edu> wrote:
> Although I have the malloc problem fixed, I'm wondering about the number of
> messages during assembly:
> [0] MatStashScatterBegin_Private(): No of messages: 0
> [0] MatAssemblyBegin_MPIAIJ(): Stash has 0 entries, uses 0 mallocs.
> [1] MatStashScatterBegin_Private(): No of messages: 1
> [1] MatStashScatterBegin_Private(): Mesg_to: 0: size: 272
> [1] MatAssemblyBegin_MPIAIJ(): Stash has 33 entries, uses 0 mallocs.
> [3] MatStashScatterBegin_Private(): No of messages: 3
> [3] MatStashScatterBegin_Private(): Mesg_to: 0: size: 360
> [3] MatStashScatterBegin_Private(): Mesg_to: 1: size: 328
> [3] MatStashScatterBegin_Private(): Mesg_to: 2: size: 360
> [3] MatAssemblyBegin_MPIAIJ(): Stash has 128 entries, uses 0 mallocs.
> [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 11 X 11; storage space: 0
> unneeded,11 used
> [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
> [6] MatStashScatterBegin_Private(): No of messages: 6
> [6] MatStashScatterBegin_Private(): Mesg_to: 0: size: 184
> [6] MatStashScatterBegin_Private(): Mesg_to: 1: size: 168
> [6] MatStashScatterBegin_Private(): Mesg_to: 2: size: 184
> [6] MatStashScatterBegin_Private(): Mesg_to: 3: size: 184
> [6] MatStashScatterBegin_Private(): Mesg_to: 4: size: 152
> [6] MatStashScatterBegin_Private(): Mesg_to: 5: size: 168
> [6] MatAssemblyBegin_MPIAIJ(): Stash has 124 entries, uses 0 mallocs.
> [2] MatStashScatterBegin_Private(): No of messages: 2
> [2] MatStashScatterBegin_Private(): Mesg_to: 0: size: 96
> [2] MatStashScatterBegin_Private(): Mesg_to: 1: size: 88
> [2] MatAssemblyBegin_MPIAIJ(): Stash has 21 entries, uses 0 mallocs.
> [2] MatAssemblyEnd_SeqAIJ(): Matrix size: 11 X 11; storage space: 0
> unneeded,11 used
> [2] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> [2] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
> [5] MatStashScatterBegin_Private(): No of messages: 5
> [5] MatStashScatterBegin_Private(): Mesg_to: 0: size: 360
> [5] MatStashScatterBegin_Private(): Mesg_to: 1: size: 328
> [5] MatStashScatterBegin_Private(): Mesg_to: 2: size: 360
> [5] MatStashScatterBegin_Private(): Mesg_to: 3: size: 360
> [5] MatStashScatterBegin_Private(): Mesg_to: 4: size: 296
> [5] MatAssemblyBegin_MPIAIJ(): Stash has 208 entries, uses 0 mallocs.
> [5] MatAssemblyEnd_SeqAIJ(): Matrix size: 10 X 10; storage space: 0
> unneeded,10 used
> [5] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> [5] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
> [6] MatAssemblyEnd_SeqAIJ(): Matrix size: 10 X 10; storage space: 0
> unneeded,10 used
> [6] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> [6] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
> [1] MatAssemblyEnd_SeqAIJ(): Matrix size: 10 X 10; storage space: 0
> unneeded,10 used
> [1] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> [1] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
> [4] MatStashScatterBegin_Private(): No of messages: 4
> [4] MatStashScatterBegin_Private(): Mesg_to: 0: size: 184
> [4] MatStashScatterBegin_Private(): Mesg_to: 1: size: 168
> [4] MatStashScatterBegin_Private(): Mesg_to: 2: size: 184
> [4] MatStashScatterBegin_Private(): Mesg_to: 3: size: 184
> [4] MatAssemblyBegin_MPIAIJ(): Stash has 86 entries, uses 0 mallocs.
> [3] MatAssemblyEnd_SeqAIJ(): Matrix size: 11 X 11; storage space: 0
> unneeded,11 used
> [3] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> [3] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
> [4] MatAssemblyEnd_SeqAIJ(): Matrix size: 9 X 9; storage space: 0 unneeded,9
> used
> [4] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> [4] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
> [7] MatStashScatterBegin_Private(): No of messages: 7
> [7] MatStashScatterBegin_Private(): Mesg_to: 0: size: 184
> [7] MatStashScatterBegin_Private(): Mesg_to: 1: size: 168
> [7] MatStashScatterBegin_Private(): Mesg_to: 2: size: 184
> [7] MatStashScatterBegin_Private(): Mesg_to: 3: size: 184
> [7] MatStashScatterBegin_Private(): Mesg_to: 4: size: 152
> [7] MatStashScatterBegin_Private(): Mesg_to: 5: size: 168
> [7] MatStashScatter[6] PetscCommDuplicate(): Using internal PETSc
> communicator 1140850689 -2080374784
> [6] PetscCommDuplicate():   returning tag 2147483643
> [5] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> -2080374784
> [5] PetscCommDuplicate():   returning tag 2147483643
> [2] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> -2080374784
> [2] PetscCommDuplicate():   returning tag 2147483643
> [6] PetscCommDuplicate():   returning tag 2147483643
> [5] PetscCommDuplicate():   returning tag 2147483643
> [2] PetscCommDuplicate():   returning tag 2147483643
> Begin_Private(): Mesg_to: 6: size: 168
> [7] MatAssemblyBegin_MPIAIJ(): Stash has 144 entries, uses 0 mallocs.
> [7] MatAssemblyEnd_SeqAIJ(): Matrix size: 8 X 8; storage space: 4 unneeded,4
> used
> [7] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> [7] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
> [1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> -2080374784
> [1] PetscCommDuplicate():   returning tag 2147483643
> [7] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> -2080374784
> [7] PetscCommDuplicate():   returning tag 2147483643
> [3] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> -2080374784
> [3] PetscCommDuplicate():   returning tag 2147483643
> [7] PetscCommDuplicate():   returning tag 2147483643
> [1] PetscCommDuplicate():   returning tag 2147483643
> [3] PetscCommDuplicate():   returning tag 2147483643
> [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> -2080374784
> [0] PetscCommDuplicate():   returning tag 2147483643
> [0] MatSetUpMultiply_MPIAIJ(): Using block index set to define scatter
> [0] PetscCommDuplicate():   returning tag 2147483643
> [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
> -2080374784
> [0] PetscCommDuplicate():   returning tag 2147483642
> [0] PetscCommDuplicate():   returning tag 2147483642
> [0] PetscCommDuplicate():   returning tag 2147483637
> [0] VecScatterCreateCommon_PtoS(): Using blocksize 1 scatter
> [0] VecScatterCreate(): General case: MPI to Seq
> [0] MatSetOption_Inode(): Not using Inode routines due to
> MatSetOption(MAT_DO_NOT_USE_INODES
> [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 11 X 8; storage space: 0
> unneeded,14 used
> [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 2
>
> What is this "stash"?  Does this mean that it is sending matrix entries
> between processes (b/c I should be only setting entries local to each
> process), or some other kind of meta-information?
>
> > -----Original Message-----
> > From: owner-petsc-users at mcs.anl.gov
> > [mailto:owner-petsc-users at mcs.anl.gov] On Behalf Of Barry Smith
> > Sent: Friday, October 26, 2007 7:54 PM
> > To: petsc-users at mcs.anl.gov
> > Subject: RE: Slow assembly
> >
> >
> >
> >   The sorting does not matter.
> >
> >   Under normal conditions the MatAssembly should take a
> > fraction of a second. The only cause that we know that slows
> > it down to the extreme you have is that it is sending a huge
> > amount of data across processes (the -info option Satish
> > suggested will tell us if that is true).
> >
> >   Are you only call MatAssemblyBegin/End() once? You should,
> > don't call it
> > multiple times.
> >
> >   The sorting is not important (in fact it takes advantage of
> > it automatically and does not need to be set).
> >
> >    Barry
> >
> >
> > On Fri, 26 Oct 2007, John R. Wicks wrote:
> >
> > > I have confirmed that I am calling MatSetValues() for local
> > rows only
> > > and am only setting each value exactly once.
> > >
> > > Because of how the matrix was partitioned for another non-Petsc
> > > program, each partition is partitioned (by columns) into 32 blocks
> > > (corresponding to the row partitions).  I enter the data for each
> > > block one row at a time, i.e., for any one SetValues call,
> > the entries
> > > are sorted by increasing column index.  Does that mean I can use
> > > MatrixSetOption(A,MAT_COLUMNS_SORTED).  Should that help?
> > >
> > > P.S.: I tried it, and it still seems to be taking quite a long time.
> > >
> > > > -----Original Message-----
> > > > From: owner-petsc-users at mcs.anl.gov
> > > > [mailto:owner-petsc-users at mcs.anl.gov] On Behalf Of Satish Balay
> > > > Sent: Friday, October 26, 2007 3:04 PM
> > > > To: petsc-users at mcs.anl.gov
> > > > Subject: Re: Slow assembly
> > > >
> > > >
> > > > On Fri, 26 Oct 2007, John R. Wicks wrote:
> > > >
> > > > > I am working on computing PageRank for a web scale graph
> > > > which uses a
> > > > > square matrix which is 1.2x10^8 dimensional with about 10^9
> > > > entries.
> > > > > I have partitioned the matrix for 32 processors myself
> > into my own
> > > > > ascii format, and I know the memory allocation, so I:
> > > > >
> > > > > 1) create the matrix with "A = MatCreateMPIAIJ(*n, *n, *N,
> > > > *N, 0, nnz,
> > > > > 0, onnz)",
> > > > > 2) load the entries by repeatedly calling
> > > > > "MatSetValues(A,1,&row,links,cols,vals,INSERT_VALUES)", and
> > > > >
> > > > > 3) call MatAssemblyBegin/End.
> > > > >
> > > > > Steps 1 and 2 complete in a couple minutes, but step 3 is taking
> > > > > several hours.  What is going on?  Is there a way to speed
> > > > up matrix
> > > > > assembly?
> > > >
> > > > Are you makeing sure that you call MatGetOwnershipRange() -
> > > > and calling MatSetValues() for mostly local rows only?
> > > >
> > > > Also can you confirm that multiple processes [for eg: proc-0
> > > > and proc-1 etc..]  are not setting the same value [i.e both
> > > > of them calling MatSetValues(row=0,col=0)]
> > > >
> > > > Satish
> > > >
> > >
> > >
> >
>
>

-- 
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