Matrix input file format

[Evrim Dizemen]

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
>>
>