AX=B Fortran Petsc Code

[Satish Balay]

You can use:

MatSetOption(mat,MAT_IGNORE_ZERO_ENTRIES)

So subsequent MatSetValues() will ignore these zero entries.

Satish

On Wed, 14 Nov 2007, Tim Stitt wrote:

> Matthew,
> 
> OK...I see what you are saying.
> 
> I initially set A a row at a time but for performance reasons I thought doing
> it at once would be better. I overlooked the fact that the logical 2D matrix
> input to MatSetValues() is non-zero values only. With hindsight I now remember
> that was the case for each individual row.
> 
> Thanks for pointing that out....
> 
> Regards.
> 
> Matthew Knepley wrote:
> > You appear to be setting every value in the sparse matrix. We do not
> > throw out 0 values (since sometimes they are necessary for structural
> > reasons). Thus you are allocating a ton of times. You need to remove
> > the 0 values before calling MatSetValues (and their associated
> > column entires as well).
> > 
> >   Matt
> > 
> > On Nov 14, 2007 8:13 AM, Tim Stitt <timothy.stitt at ichec.ie> wrote:
> >   
> > > Dear PETSc Users/Developers,
> > > 
> > > I have the following sequential Fortran PETSc code that I have been
> > > developing (on and off) based on the kind advice given by members of
> > > this list, with respect to solving an inverse sparse matrix problem.
> > > Essentially, the code reads in a square double complex matrix from
> > > external file of size (order x order) and then proceeds to do a
> > > MatMatSolve(), where A is the sparse matrix to invert, B is a dense
> > > identity matrix and X is the resultant dense matrix....hope that makes
> > > sense.
> > > 
> > > My main problem is that the code stalls on the MatSetValues() for the
> > > sparse matrix A. With a trivial test matrix of (224 x 224) the program
> > > terminates successfully (by successfully I mean all instructions
> > > execute...I am not interested in the validity of X right now).
> > > Unfortunately, when I move up to a (2352 x 2352) matrix the
> > > MatSetValues() routine for matrix A is still in progress after 15
> > > minutes on one processor of our AMD Opteron IBM Cluster. I know that
> > > people will be screaming "preallocation"...but I have tried to take this
> > > into account by running a loop over the rows in A and counting the
> > > non-zero values explicitly prior to creation. I then pass this vector
> > > into the creation routine for the nnz argument. For the large (2352 x
> > > 2352) problem that seems to be taking forever to set...at most there are
> > > only 200 elements per row that are non-zero according to the counts.
> > > 
> > > Can anyone explain why the MatSetValues() routine is taking such a long
> > > time. Maybe this expected for this specific task...although it seems
> > > very long?
> > > 
> > > I did notice that on the trivial (224 x 224) run that I was still
> > > getting mallocs (approx 2000) for the A assembly when I used the -info
> > > command line parameter. I thought that it should be 0 if my
> > > preallocation counts were exact? Does this hint that I am doing
> > > something wrong. I have checked the code but don't see any obvious
> > > problems in the logic...not that means anything.
> > > 
> > > I would be grateful if someone could advise on this matter. Also, if you
> > > have a few seconds to spare I would be grateful if some experts could
> > > scan the remaining logic of the code (not in fine detail)  to make sure
> > > that I am doing all that I need to do to get this calculation
> > > working...assuming I can resolve the MatSetValues() problem.
> > > 
> > > Once again many thanks in advance,
> > > 
> > > Tim.
> > > 
> > >  ! Initialise the PETSc MPI Harness
> > >   call PetscInitialize(PETSC_NULL_CHARACTER,error);CHKERRQ(error)
> > > 
> > >   call MPI_COMM_SIZE(PETSC_COMM_SELF,processes,error);CHKERRQ(error)
> > >   call MPI_COMM_RANK(PETSC_COMM_SELF,ID,error);CHKERRQ(error)
> > > 
> > >   ! Read in Matrix
> > >   open(321,file='Hamiltonian.bin',form='unformatted')
> > >   read(321) order
> > >   if (ID==0) then
> > >      print *
> > >      print *,processes," Processing Elements being used"
> > >      print *
> > >      print *,"Matrix has order ",order," rows by ",order," columns"
> > >      print *
> > >   end if
> > > 
> > >   allocate(matrix(order,order))
> > >   read(321) matrix
> > >   close(321)
> > > 
> > >   ! Allocate array for nnz
> > >   allocate(numberZero(order))
> > > 
> > >   ! Count number of non-zero elements in each matrix row
> > >   do row=1,order
> > >      count=0
> > >      do column=1,order
> > >         if (matrix(row,column).ne.(0,0)) count=count+1
> > >      end do
> > >      numberZero(row)=count
> > >   end do
> > > 
> > >   ! Declare a PETSc Matrices
> > > 
> > >   call
> > > MatCreateSeqAIJ(PETSC_COMM_SELF,order,order,PETSC_NULL_INTEGER,numberZero,A,error);CHKERRQ(error)
> > >   call
> > > MatCreateSeqAIJ(PETSC_COMM_SELF,order,order,0,PETSC_NULL_INTEGER,factorMat,error);CHKERRQ(error)
> > >   call
> > > MatCreateSeqDense(PETSC_COMM_SELF,order,order,PETSC_NULL_SCALAR,X,error);CHKERRQ(error)
> > >   call
> > > MatCreateSeqDense(PETSC_COMM_SELF,order,order,PETSC_NULL_SCALAR,B,error);CHKERRQ(error)
> > > 
> > >   ! Set up zero-based array indexing for use in MatSetValues
> > >   allocate(columnIndices(order))
> > > 
> > >   do column=1,order
> > >      columnIndices(column)=column-1
> > >   end do
> > > 
> > >   ! Need to transpose values array as row-major arrays are used.
> > >   call
> > > MatSetValues(A,order,columnIndices,order,columnIndices,transpose(matrix),INSERT_VALUES,error);CHKERRQ(error)
> > > 
> > >   ! Assemble Matrix A
> > >   call MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY,error);CHKERRQ(error)
> > >   call MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY,error);CHKERRQ(error)
> > > 
> > >   deallocate(matrix)
> > > 
> > >   ! Create Index Sets for Factorisation
> > >   call
> > > ISCreateGeneral(PETSC_COMM_SELF,order,columnIndices,indexSet,error);CHKERRQ(error)
> > >   call MatFactorInfoInitialize(info,error);CHKERRQ(error)
> > >   call ISSetPermutation(indexSet,error);CHKERRQ(error)
> > >   call
> > > MatLUFactorSymbolic(A,indexSet,indexSet,info,factorMat,error);CHKERRQ(error)
> > >   call MatLUFactorNumeric(A,info,factorMat,error);CHKERRQ(error)
> > > 
> > >   ! A no-longer needed
> > >   call MatDestroy(A,error);CHKERRQ(error)
> > > 
> > >   one=(1,0)
> > > 
> > >   ! Set Diagonal elements in Identity Matrix B
> > >   do row=0,order-1
> > >      call MatSetValue(B,row,row,one,INSERT_VALUES,error);CHKERRQ(error)
> > >   end do
> > > 
> > >   ! Assemble B
> > >   call MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY,error);CHKERRQ(error)
> > >   call MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY,error);CHKERRQ(error)
> > > 
> > >   ! Assemble X
> > >   call MatAssemblyBegin(X,MAT_FINAL_ASSEMBLY,error);CHKERRQ(error)
> > >   call MatAssemblyEnd(X,MAT_FINAL_ASSEMBLY,error);CHKERRQ(error)
> > > 
> > >   ! Solve AX=B
> > >   call MatMatSolve(factorMat,B,X,error);CHKERRQ(error)
> > > 
> > >   ! Deallocate Storage
> > >   deallocate(columnIndices)
> > > 
> > >   call MatDestroy(factorMat,error);CHKERRQ(error)
> > >   call MatDestroy(B,error);CHKERRQ(error)
> > >   call MatDestroy(X,error);CHKERRQ(error)
> > > 
> > >   call PetscFinalize(error)
> > > 
> > > --
> > > Dr. Timothy Stitt <timothy_dot_stitt_at_ichec.ie>
> > > HPC Application Consultant - ICHEC (www.ichec.ie)
> > > 
> > > Dublin Institute for Advanced Studies
> > > 5 Merrion Square - Dublin 2 - Ireland
> > > 
> > > +353-1-6621333 (tel) / +353-1-6621477 (fax)
> > > 
> > > 
> > >     
> > 
> > 
> > 
> >   
> 
> 
>