You should not need to call any preallocation routines when using MatLoad()
How did you generate the file? Are you sure it has the correct information for the matrix? Barry > On Mar 31, 2015, at 11:05 PM, Steena M <[email protected]> wrote: > > Thanks Matt. I'm still getting the malloc error > > [0]PETSC ERROR: Argument out of range! > [0]PETSC ERROR: New nonzero at (2,18) caused a malloc! > > and > > a new incorrect matrix file error: > > [0]PETSC ERROR: Unexpected data in file! > [0]PETSC ERROR: not matrix object! > > Maybe the order of calls is mixed up. This is the code snippet: > > if (rank ==0) > { > PetscPrintf (PETSC_COMM_WORLD,"\n On rank %d ", rank); > > CHKERRQ(MatSetSizes(A, 15, PETSC_DETERMINE, 20, 20)); > CHKERRQ(MatSetType(A, MATMPIBAIJ)); > CHKERRQ( MatMPIBAIJSetPreallocation(A,1,1,NULL,1,NULL)); > CHKERRQ( MatLoad(A,fd)); > CHKERRQ(MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE)); > } > > else > { > PetscPrintf (PETSC_COMM_WORLD,"\n On rank %d ", rank); > > CHKERRQ( MatSetSizes(A, 5, PETSC_DETERMINE, 20, 20) ); > CHKERRQ(MatSetType(A, MATMPIBAIJ)); > CHKERRQ( MatMPIBAIJSetPreallocation(A,1,1,NULL,1,NULL)); > CHKERRQ(MatLoad(A,fd)); > CHKERRQ(MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE)); > } > > Is there something I'm missing? > > Thanks, > Steena > > > > > > On Tuesday, March 31, 2015 6:10 PM, Matthew Knepley <[email protected]> wrote: > > > On Tue, Mar 31, 2015 at 6:51 PM, Steena M <[email protected]> wrote: > Thanks Barry. I'm still getting the malloc error with NULL. Is there a way to > distribute the matrix without explicit preallocation? Different matrices will > be loaded during runtime and assigning preallocation parameters would mean an > additional preprocessing step. > > 1) MatSetOption(MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) > > 2) Note that this is never ever ever more efficient than making another pass > and preallocating > > Thanks, > > Matt > -------------------------------------------- > On Sun, 3/29/15, Barry Smith <[email protected]> wrote: > > Subject: Re: [petsc-users] Unequal sparse matrix row distribution for MPI > MatMult > To: "Steena M" <[email protected]> > Cc: "Matthew Knepley" <[email protected]>, [email protected] > Date: Sunday, March 29, 2015, 9:26 PM > > > > On > Mar 29, 2015, at 11:05 PM, Steena M <[email protected]> > wrote: > > > > Thanks > Matt. I used PETSC_DETERMINE but I'm now getting an > allocation-based error: > > > > [0]PETSC ERROR: --------------------- > Error Message ------------------------------------ > > [0]PETSC ERROR: Argument out of range! > > [0]PETSC ERROR: New nonzero at (2,18) > caused a malloc! > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > > > > I tried > preallocating on each rank for the diagonal and off diagonal > section of the matrix as the next step My current > approximations for preallocation > > > > CHKERRQ( > MatMPIBAIJSetPreallocation(A,1,5,PETSC_DEFAULT,5,PETSC_DEFAULT)); > > > These > arguments where you pass PETSC_DEFAULT are expecting a > pointer not an integer. You can pass NULL in those > locations. Though it is better to provide the correct > preallocation rather than some defaults. > > Barry > > > > > are throwing segmentation errors. > > > > [0]PETSC ERROR: > Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > > > Any insights into what I'm doing > wrong? > > > > Thanks, > > Steena > > > > > > > > On Sun, 3/29/15, Matthew Knepley <[email protected]> > wrote: > > > > Subject: > Re: [petsc-users] Unequal sparse matrix row distribution for > MPI MatMult > > To: "Steena M" > <[email protected]> > > Cc: "Barry Smith" <[email protected]>, > [email protected] > > Date: Sunday, March 29, 2015, 10:02 PM > > > > On Sun, Mar 29, 2015 > at > > 9:56 PM, Steena M <[email protected]> > > wrote: > > Hi > > Barry, > > > > > > > > I am trying to partition a 20 row and 20 > col sparse matrix > > between two procs > such that proc 0 has 15 rows and 20 cols > > and proc 1 has 5 rows and 20 cols. The > code snippet: > > > > > > > > > > > > > > > > > CHKERRQ(MatCreate(PETSC_COMM_WORLD,&A)); > // > > at runtime: -matload_block_size 1 > > > > > > > > > > > > > if (rank ==0) > > > > { > > > > > CHKERRQ( MatSetSizes(A, 15, 20, 20, > > 20) ); //rank 0 gets 75% of the rows > > > > > CHKERRQ( MatSetType(A, MATMPIBAIJ) > > ); > > > > CHKERRQ( > MatLoad(A,fd) ); > > > > } > > > > > > > > else > > > > > { > > > > > CHKERRQ( MatSetSizes(A, 5, > 20, 20, > > 20) ); //rank 1 gets 25% of the > rows > > > > > CHKERRQ( MatSetType(A, MATMPIBAIJ) > > ); > > > > CHKERRQ( > MatLoad(A,fd) ); > > > > } > > > > > > > > > This throws the following error (probably > from psplit.c): > > > > > [1]PETSC ERROR: --------------------- Error Message > > ------------------------------------ > > > > [1]PETSC ERROR: > Nonconforming object sizes! > > > > [1]PETSC ERROR: Sum of local lengths 40 > does not equal > > global length 20, my > local length 20 > > > > likely a call to > VecSetSizes() or MatSetSizes() is > > > wrong. > > > > See > http://www.mcs.anl.gov/petsc/documentation/faq.html#split! > > > > > > > > This error printout > doesn't quite make sense to me. > > > I'm trying to specify a total matrix size of 20x20... > I > > haven't yet figured out where the > '40' comes > > from in the error > message. > > > > > > > > Any thoughts on what > might be going wrong? > > > > Its the column specification. Just > > use PETSC_DETERMINE for the local columns > since all our > > sparse matrixformats are > row divisions > > anyway. > > > > Thanks, > > > > Matt > > Thanks in advance, > > > > > Steena > > > > > > > > > > > > > > > > > -------------------------------------------- > > > > On Sun, 3/22/15, > Barry Smith <[email protected]> > > wrote: > > > > > > > > Subject: Re: [petsc-users] Unequal > sparse matrix row > > distribution for MPI > MatMult > > > > To: > "Steena M" <[email protected]> > > > > Cc: [email protected] > > > > Date: Sunday, > March 22, 2015, 3:58 PM > > > > > > > > > > > > > > > > Steena, > > > > > > > > I am > > > > > a little unsure of your question. > > > > > > > > > 1) > you can create a MPIBAIJ > > > > matrix with any distribution of block > rows per process > > you > > > > want, just set the > local row size for each process to > > > be > > > > what you > like. Use MatCreateVecs() to get > > > correspondingly > > > > > laid out vectors. > > > > > > > > > > or 2) if you have a MPIBAIJ > > > > matrix with > "equal" row layout and you want a > > new > > > > one with uneven row layout you can > simply use > > > > > MatGetSubMatrix() to create that new matrix. > > > > > > > > Barry > > > > > > > > Unless you have > another reason to have the > > > > matrix with an equal number row layout I > would just > > generate > > > > the matrix with > the layout you want. > > > > > > > > > > > > > On Mar 22, 2015, at 5:50 PM, Steena > M > > > > <[email protected]> > > > > wrote: > > > > > > > > > > Hello, > > > > > > > > > > I need to > distribute > > > > a > sparse matrix such that each proc owns an unequal > > number > > > > of blocked rows before I proceed with > MPI MatMult. My > > > > > initial thoughts on doing this: > > > > > > > > > > 1) Use MatGetSubMatrices() on the > test > > > > MATMPIBAIJ > matrix to produce a new matrix where each > > proc > > > > has an unequal number of rows. > > > > > > > > > > 2) Provide > scatter context for vector X > > > > (for MatMult )using IS iscol from > MatGetSubMatrices() > > while > > > > creating the > vector X. > > > > > > > > > > > 3) > Call MatMult() > > > > > > > > > > > Will > MatMult_MPIBAIJ continue to scatter > > > > this matrix and vector such that each > proc will own an > > equal > > > > number of matrix > rows and corresponding diagonal vector > > > > > elements? Should I write my own > MPIMatMult function to > > > > retain my redistribution of the matrix > and vector? > > > > > > > > > > > > Thanks in > > > > > advance, > > > > > > Steena > > > > > > > > > > > > > > -- > > 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 > > > > > > > > -- > 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 > >
