Dear Randall, I guess i began to understand the consepts but there is still a missing point that i do not know when and how we define Istart and Iend. I'll be glade if you can send me the pre_op3d routine so i can see the algorithm which is a black box for me now.
Thanks a lot EVRIM Randall Mackie wrote: > Hi Evrim, > > It's quite easy to modify your Fortran code to do what you want. I > thought > I had written it all out before, but I'll try again. There are many ways > to do this, but I'll start with the easiest, at least if you're going to > just modify your current sequential code. > > Let's say that your matrix has np global rows. Then > > call VecCreateMPI(PETSC_COMM_WORLD,PETSC_DECIDE,np,b,ierr) > call VecDuplicate(b,xsol,ierr) > call VecGetLocalSize(b,mloc,ierr) > call VecGetOwnershipRange(b,Istart,Iend,ierr) > > do i=Istart+1,Iend > loc(i)=i-1 > end do > > These statements create parallel vectors for the solution (xsol) and > the right hand side (b). The vector loc(i)is used to set values in the > vectors later. > > Then > > ! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > ! Create the linear solver context > ! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > > call KSPCreate(PETSC_COMM_WORLD,ksp,ierr) > > ! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > ! Create the scatter context for getting results back to > ! each node. > ! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > > call VecScatterCreateToAll(xsol,xToLocalAll,xseq,ierr) > > ! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > ! Create the matrix that defines the linear system, Ax = b, > ! for the EM problem. > ! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > > call pre_op3d(l,m,nzn,Istart,Iend,ijkhx,ijkhy,ijkhz,d_nnz,o_nnz) > > call MatCreateMPIAIJ(PETSC_COMM_WORLD,mloc,mloc,np,np, > . PETSC_NULL_INTEGER, d_nnz, PETSC_NULL_INTEGER, > . o_nnz,A,ierr) > > call set_op3d(A,l,m,nzn,period,resist,x,y,z,Istart,Iend, > . ijkhx,ijkhy,ijkhz) > > > The subroutine pre_op3d is an important routine and it figures out > how to pre-allocate space for your parallel matrix. This will be > the difference between near-instanteous assembly and 2.5 hours that > you experienced. Basically, it just computes the global column numbers, > and figures out if they are between Istart and Iend. I can send you > my subroutine if you'd like. > > The subroutine set_op3d.F actually assembles the parallel matrix and > goes like this: > > > jj=0 > > do i=1,l > do k=2,n > do j=2,m > > jj=jj+1 > row = jj-1 > > IF (jj >= Istart+1 .and. jj <= Iend) THEN > > compute elements... > > call MatSetValues(A,i1,row,ic,col,v,INSERT_VALUES, > . ierr) > > END IF > > end do > end do > end do > > At the end, > > call MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY,ierr) > call MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY,ierr) > > > Again, because you compute the pre-allocation, this is near-instanteous, > even for large models (larger than you're using). > > > Once you do that, you're golden: > > call KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN,ierr) > > etc. > > Randy M. > San Francisco > > > Evrim Dizemen wrote: >> Hi all, >> >> Again thanks for your comments. I guess i can not define the problem >> correctly. I have a sequantial fortran code giving me the global >> matrix of 200000x200000. The code writes the matrix in a binary file >> at little endian mode (i can write only the nonzero terms or the >> entire matrix). I tried to change the binary mode to big endian and >> read the global matrix by a c program as in the example >> /src/mat/example/tests/ex31.c. However the program reads binary file >> wrong and gives the following error message but the true value of >> no-nonzero in the binary file is 6 (for the test case 3x3 matrix) : >> >> reading matrix in binary from matrix.dat ... >> ------------------------------------------------------------------------ >> Petsc Release Version 2.3.1, Patch 13, Wed May 10 11:08:35 CDT 2006 >> BK revision: balay at asterix.mcs.anl.gov|ChangeSet|20060510160640|13832 >> See docs/changes/index.html for recent updates. >> See docs/faq.html for hints about trouble shooting. >> See docs/index.html for manual pages. >> ------------------------------------------------------------------------ >> ./ex31 on a linux named akbaba.ae.metu.edu.tr by evrim Thu Jun 15 >> 09:26:36 2006 >> Libraries linked from /home/evrim/petsc-2.3.1-p13/lib/linux >> Configure run at Tue May 30 10:26:48 2006 >> Configure options --with-scalar-type=complex --with-shared=0 >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: MatLoad_SeqAIJ() line 3055 in >> src/mat/impls/aij/seq/aij.c >> [0]PETSC ERROR: Read from file failed! >> [0]PETSC ERROR: Inconsistant matrix data in file. no-nonzeros = >> 100663296, sum-row-lengths = 234300 >> ! >> [0]PETSC ERROR: MatLoad() line 149 in src/mat/utils/matio.c >> [0]PETSC ERROR: main() line 37 in src/mat/examples/tests/ex31.c >> >> I want to send the global matrix at once to Petsc by a written input >> file (as i'm working on now) or by sending the matrix array from my >> fortran code and then partition it and solve iteratively. After the >> solution i also want to get the solution vector back to my fortran >> code. As i told in the previous mails i tried to send the matrix >> array to Petsc and used MatSetValues as reading one value at time in >> a do loop but it took about 2,5 hours to read the global matrix. >> Additionally i tried to read a row at a time but can not figure out >> a algorithm for this. Hence i do not prefer to create the matrix >> again in Petsc by MatSetValues. >> >> Aside i figured out that the binary files written in fortran and c >> are completely different from each other (fortran adds the size of >> the characters to the beginning and end of each character) so i wrote >> a c interface code to get the matrix array from the fortran code and >> write it to a binary file in c format. By this code i avoided from >> the additional information in the binary file but i still have the >> endianness problem. >> >> I know that i asked so much but since i'm a rookie in parallel >> programming, c language and library using i really need your comments >> on my problem. Sorry for this long mail and thanks a lot for your >> kind effort on guiding me. >> >> Thanks >> >> EVRIM >> >
