OK...everything is working well now and I am getting the results I expect. Much appreciated.
Saying that...I am trying to now satisfy the PC FACTOR FILL suggestion provided by the -info parameter on my sample sparse matrices. In my case I am getting: [0] MatLUFactorSymbolic_SeqAIJ(): Reallocs 3 Fill ratio:given 0 needed 2.56568 [0] MatLUFactorSymbolic_SeqAIJ(): Run with -pc_factor_fill 2.56568 or use [0] MatLUFactorSymbolic_SeqAIJ(): PCFactorSetFill(pc,2.56568); [0] MatLUFactorSymbolic_SeqAIJ(): for best performance. So I run my code with ./foo -pc_factor_fill 2.56568 but I continually get WARNING! There are options you set that were not used! WARNING! could be spelling mistake, etc! Option left: name:-pc_factor_fill value: 2.56568 Can someone suggest how I can improve performance with the pc_factor_fill parameter in my case? As my code stands there is no MatSetFromOptions() as I set everything explicitly in the code. Thanks again, Tim. Barry Smith wrote: > > For sequential codes the index set is as large as the matrix. > > In parallel the factor codes do not use the ordering, they do the > ordering > internally. > > Barry > > On Nov 14, 2007, at 10:37 AM, Tim Stitt wrote: > >> Can I just ask a question about MatLUFactorSymbolic() in this >> context? What sizes should the 'row' and 'col' index sets be? Should >> they span all global rows/columns in A? >> >> 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) >>>> >>>> >>>> >>> >>> >>> >>> >> >> >> --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) >> > -- 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)
