Thanks Barry!! I tried and it worked nice, but it will be improved if I could manage the off-diagonal elements block by block. I have a stencil with 5 points (in 1D) and the coupling with the i+1 is different with respect to the i+2 elements. I found on PetsC site a reference to DMDASetGetMatrix function, but there are no examples. Can you give me an example with a simple matrix? Or there is a simpler way to treat the different off-diagonal blocks separately?
Thank you again Francesco > Il giorno 02/nov/2015, alle ore 17:54, Barry Smith <[email protected]> ha > scritto: > > > Don't do any of that stuff you tried below. Just use DMDASetFillBlocks() > before DMCreateMatrix() > > Barry > > >> On Nov 2, 2015, at 9:58 AM, Francesco Magaletti >> <[email protected]> wrote: >> >> Hi everyone, >> >> I’m trying to solve a system of PDE’s with a full implicit time integration >> and a DMDA context to manage the cartesian structured grid. >> I don’t know the actual jacobian matrix (actually it is too cumbersome to be >> easily evaluated analytically) so I used SNESComputeJacobianDefaultColor to >> approximate it: >> >> DMSetMatType(da,MATAIJ); >> DMCreateMatrix(da,&J); >> TSGetSNES(ts, &snes); >> SNESSetJacobian(snes, J, J, SNESComputeJacobianDefaultColor,0); >> >> All it works perfectly but it happens that, when I increase the number of >> grid points, I go out of memory since the matrix becomes too big to be >> stored despite my estimate of memory consumption which is much lower than >> the actual one. Indeed a more careful analysis (with -mat_view) shows that >> there are a lot of zeros in the nonzero structure of the jacobian. I read in >> the manual that DMCreateMatrix preallocates the matrix by somewhat using the >> stencil width of the DMDA context, but in my case I don’t really need all >> those elements for every equation. >> I then tried with a poor preallocation, hoping petsC could manage it with >> some malloc on the fly: >> >> MatCreateAIJ(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,size,size,3,0,0,0,&J); >> MatSetOption(J,MAT_NEW_NONZERO_LOCATIONS,PETSC_TRUE); >> MatSetOption(J,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE); >> MatSetOption(J,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE); >> TSGetSNES(ts, &snes); >> SNESSetJacobian(snes, J, J, SNESComputeJacobianDefaultColor,0); >> >> but now it gives me runtime errors: >> >> [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> [0]PETSC ERROR: Object is in wrong state >> [0]PETSC ERROR: Matrix must be assembled by calls to MatAssemblyBegin/End(); >> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for >> trouble shooting. >> [0]PETSC ERROR: Petsc Release Version 3.6.0, Jun, 09, 2015 >> [0]PETSC ERROR: ./bubble_petsc on a arch-linux2-c-debug named ... Mon Nov 2 >> 16:24:12 2015 >> [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ >> --with-fc=gfortran --download-fblaslapack --download-mpich >> [0]PETSC ERROR: #1 MatFDColoringCreate() line 448 in >> /home/magaletto/Scaricati/petsc-3.6.0/src/mat/matfd/fdmatrix.c >> [0]PETSC ERROR: #2 SNESComputeJacobianDefaultColor() line 67 in >> /home/magaletto/Scaricati/petsc-3.6.0/src/snes/interface/snesj2.c >> [0]PETSC ERROR: #3 SNESComputeJacobian() line 2223 in >> /home/magaletto/Scaricati/petsc-3.6.0/src/snes/interface/snes.c >> [0]PETSC ERROR: #4 SNESSolve_NEWTONLS() line 231 in >> /home/magaletto/Scaricati/petsc-3.6.0/src/snes/impls/ls/ls.c >> [0]PETSC ERROR: #5 SNESSolve() line 3894 in >> /home/magaletto/Scaricati/petsc-3.6.0/src/snes/interface/snes.c >> [0]PETSC ERROR: #6 TSStep_Theta() line 197 in >> /home/magaletto/Scaricati/petsc-3.6.0/src/ts/impls/implicit/theta/theta.c >> [0]PETSC ERROR: #7 TSStep() line 3098 in >> /home/magaletto/Scaricati/petsc-3.6.0/src/ts/interface/ts.c >> [0]PETSC ERROR: #8 TSSolve() line 3282 in >> /home/magaletto/Scaricati/petsc-3.6.0/src/ts/interface/ts.c >> >> If I use instead the same preallocation but with the FD calculation without >> coloring it runs without problems (it is only extremely slow) and it uses >> the correct number of nonzero values: >> >> MatCreateAIJ(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,size,size,3,0,0,0,&J); >> MatSetOption(J,MAT_NEW_NONZERO_LOCATIONS,PETSC_TRUE); >> MatSetOption(J,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE); >> MatSetOption(J,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE); >> TSGetSNES(ts, &snes); >> SNESSetJacobian(snes, J, J, SNESComputeJacobianDefault,&appctx); >> >> What do you suggest to solve this problem? >> I also tried to set up a first step with fd without coloring in order to >> allocate the correct amount of memory and nonzero structure and successively >> to switch to the colored version: >> >> TSSetIFunction(ts,NULL,FormIFunction,&appctx); >> >> MatCreateAIJ(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,size,size,3,0,0,0,&J); >> MatSetOption(J,MAT_NEW_NONZERO_LOCATIONS,PETSC_TRUE); >> MatSetOption(J,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE); >> MatSetOption(J,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE); >> TSGetSNES(ts, &snes); >> SNESSetJacobian(snes, J, J, SNESComputeJacobianDefault,&appctx); >> TSStep(ts); >> >> ISColoring iscoloring; >> MatColoring coloring; >> MatFDColoring matfdcoloring; >> MatColoringCreate(J,&coloring); >> MatColoringSetFromOptions(coloring); >> MatColoringApply(coloring,&iscoloring); >> MatFDColoringCreate(J,iscoloring,&matfdcoloring); >> MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode >> (*)(void))FormIFunction,&appctx); >> MatFDColoringSetFromOptions(matfdcoloring); >> MatFDColoringSetUp(J,iscoloring,matfdcoloring); >> SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,matfdcoloring); >> >> TSStep(ts); >> >> but again it gives me runtime errors: >> >> [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> [0]PETSC ERROR: Invalid argument >> [0]PETSC ERROR: Wrong type of object: Parameter # 1 >> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for >> trouble shooting. >> [0]PETSC ERROR: Petsc Release Version 3.6.0, Jun, 09, 2015 >> [0]PETSC ERROR: ./bubble_petsc on a arch-linux2-c-debug named ... Mon Nov 2 >> 16:37:24 2015 >> [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ >> --with-fc=gfortran --download-fblaslapack --download-mpich >> [0]PETSC ERROR: #1 TSGetDM() line 4093 in >> /home/magaletto/Scaricati/petsc-3.6.0/src/ts/interface/ts.c >> [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> [0]PETSC ERROR: Corrupt argument: >> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >> [0]PETSC ERROR: Invalid Pointer to Object: Parameter # 1 >> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for >> trouble shooting. >> [0]PETSC ERROR: Petsc Release Version 3.6.0, Jun, 09, 2015 >> [0]PETSC ERROR: ./bubble_petsc on a arch-linux2-c-debug named ... Mon Nov 2 >> 16:37:24 2015 >> [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ >> --with-fc=gfortran --download-fblaslapack --download-mpich >> [0]PETSC ERROR: #2 DMGetLocalVector() line 44 in >> /home/magaletto/Scaricati/petsc-3.6.0/src/dm/interface/dmget.c >> >> ===================================================================================== >> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES >> = EXIT CODE: 11 >> = CLEANING UP REMAINING PROCESSES >> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES >> ===================================================================================== >> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) >> >> where is my mistake? >> >> Your sincerely, >> Francesco >
