> On Fri, Jan 20, 2012 at 6:55 PM, Xuefei (Rebecca) Yuan <xyuan at lbl.gov> > wrote: > Hello Matt, > > I tried several times for 3.1-p8 and dev version by putting MatSetOption > > Are you sure your entries are exactly 0.0? >
Yes, because I have looked at the output, they are 0.00000000000000e+00. R > Matt > > 1) right after creation of the matrix: > > #ifdef petscDev > ierr = DMCreateMatrix(DMMGGetDM(dmmg), MATAIJ, > &jacobian);CHKERRQ(ierr); > #else > ierr = DAGetMatrix(DMMGGetDA(dmmg), MATAIJ, &jacobian);CHKERRQ(ierr); > #endif > ierr = MatSetOption(jacobian, MAT_IGNORE_ZERO_ENTRIES, > PETSC_TRUE);CHKERRQ(ierr); > > 2) at the beginning of the FormJacobianLocal() routine: > > PetscFunctionBegin; > ierr = MatSetOption(jacobian, MAT_IGNORE_ZERO_ENTRIES, > PETSC_TRUE);CHKERRQ(ierr); > > 3) before calling MatAssemblyBegin() in FormJacobianLocal() routine: > > ierr = MatSetOption(jacobian, MAT_IGNORE_ZERO_ENTRIES, > PETSC_TRUE);CHKERRQ(ierr); > ierr = MatAssemblyBegin(jacobian, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); > ierr = MatAssemblyEnd(jacobian, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); > > None of those works. What is wrong here? > > Thanks, > > R > > > On Jan 20, 2012, at 4:32 PM, Matthew Knepley wrote: > >> On Fri, Jan 20, 2012 at 6:28 PM, Xuefei (Rebecca) Yuan <xyuan at lbl.gov> >> wrote: >> Hello Matt, >> >> I have changed the code as >> >> ierr = MatSetOption(jacobian, MAT_IGNORE_ZERO_ENTRIES, >> PETSC_TRUE);CHKERRQ(ierr); >> ierr = MatAssemblyBegin(jacobian, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); >> ierr = MatAssemblyEnd(jacobian, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); >> >> You have to set it before you start setting values, so we know to ignore >> them. >> >> Matt >> >> but still get the same result as before, the matrix still has 5776 nonzeros: >> >> % Size = 100 100 >> 2 % Nonzeros = 5776 >> 3 zzz = zeros(5776,3); >> >> Then I switch the order as >> >> ierr = MatAssemblyBegin(jacobian, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); >> ierr = MatAssemblyEnd(jacobian, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); >> ierr = MatSetOption(jacobian, MAT_IGNORE_ZERO_ENTRIES, >> PETSC_TRUE);CHKERRQ(ierr); >> >> nothing changed. >> >> The version is 3.1-p8. >> >> Thanks very much! >> >> Best regards, >> >> Rebecca >> >> >> >> >> On Jan 20, 2012, at 4:09 PM, Matthew Knepley wrote: >> >>> On Fri, Jan 20, 2012 at 6:02 PM, Xuefei (Rebecca) Yuan <xyuan at lbl.gov> >>> wrote: >>> Hello all, >>> >>> This is a test for np=1 case of the nonzero structure of the jacobian >>> matrix. The jacobian matrix is created via >>> >>> ierr = >>> DMDACreate2d(comm,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX, >>> parameters.mxfield, parameters.myfield, PETSC_DECIDE, PETSC_DECIDE, 4, 2, >>> 0, 0, &da);CHKERRQ(ierr); >>> >>> ierr = DMCreateMatrix(DMMGGetDM(dmmg), MATAIJ, &jacobian);CHKERRQ(ierr); >>> >>> After creation of the jacobian matrix, >>> >>> ierr = MatAssemblyBegin(jacobian, >>> MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); >>> ierr = MatAssemblyEnd(jacobian, >>> MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); >>> >>> PetscViewer viewer; >>> char fileName[120]; >>> sprintf(fileName, "jacobian_after_creation.m");CHKERRQ(ierr); >>> >>> FILE * fp; >>> >>> ierr = >>> PetscViewerASCIIOpen(PETSC_COMM_WORLD,fileName,&viewer);CHKERRQ(ierr); >>> ierr = >>> PetscViewerSetFormat(viewer,PETSC_VIEWER_ASCII_MATLAB);CHKERRQ(ierr); >>> ierr = MatView (jacobian, viewer); CHKERRQ (ierr); >>> ierr = PetscFOpen(PETSC_COMM_WORLD,fileName,"a",&fp); >>> CHKERRQ(ierr); >>> ierr = >>> PetscViewerASCIIPrintf(viewer,"spy((spconvert(zzz)));\n");CHKERRQ(ierr); >>> ierr = PetscFClose(PETSC_COMM_WORLD,fp);CHKERRQ(ierr); >>> PetscViewerDestroy(&viewer); >>> >>> I took a look at the structure of the jacobian by storing it in the matlab >>> format, the matrix has 5776 nonzeros entries, however, those values are all >>> zeros at the moment as I have not insert or add any values into it yet, the >>> structure shows: (the following figure shows a global replacement of 0.0 by >>> 1.0 for those 5776 numbers) >>> >>> >>> >>> >>> Inside the FormJacobianLocal() function, I have selected the index to pass >>> to the nonzero values to jacobian, for example, >>> >>> ierr = MatSetValuesStencil(jacobian, 1, &row, 6, col, v, >>> INSERT_VALUES);CHKERRQ(ierr); >>> >>> where >>> >>> col[0].i = column[4].i; >>> col[1].i = column[5].i; >>> col[2].i = column[6].i; >>> col[3].i = column[9].i; >>> col[4].i = column[10].i; >>> col[5].i = column[12].i; >>> >>> >>> col[0].j = column[4].j; >>> col[1].j = column[5].j; >>> col[2].j = column[6].j; >>> col[3].j = column[9].j; >>> col[4].j = column[10].j; >>> col[5].j = column[12].j; >>> >>> col[0].c = column[4].c; >>> col[1].c = column[5].c; >>> col[2].c = column[6].c; >>> col[3].c = column[9].c; >>> col[4].c = column[10].c; >>> col[5].c = column[12].c; >>> >>> v[0] = value[4]; >>> v[1] = value[5]; >>> v[2] = value[6]; >>> v[3] = value[9]; >>> v[4] = value[10]; >>> v[5] = value[12]; >>> >>> and did not pass the zero entries into the jacobian matrix. However, after >>> inserting or adding all values to the matrix, by the same routine above to >>> take a look at the jacobian matrix in matlab format, the matrix still has >>> 5776 nonzeros, in which 1075 numbers are nonzeros, and the other 4701 >>> numbers are all zeros. The spy() gives >>> >>> >>> >>> >>> for the true nonzero structures. >>> >>> But the ksp_view will give the nonzeros number as 5776, instead of 1075: >>> >>> linear system matrix = precond matrix: >>> Matrix Object: Mat_0x84000000_1 1 MPI processes >>> type: seqaij >>> rows=100, cols=100 >>> total: nonzeros=5776, allocated nonzeros=5776 >>> >>> It is a waste of memory to have all those values of zeros been stored in >>> the jacobian. >>> >>> Is there anyway to get rid of those zero values in jacobian and has the >>> only nonzero numbers stored in jacobian? In such a case, the ksp_view will >>> tell that total: nonzeros=1075. >>> >>> MatSetOption(MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE); >>> >>> Matt >>> >>> Thanks very much! >>> >>> Have a nice weekend! >>> >>> Cheers, >>> >>> Rebecca >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> -- >>> 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 > > > > > -- > 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... 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