[petsc-users] I am wondering if there is a way to implement SPMM
Hong
hzhang at mcs.anl.gov
Wed Aug 5 22:23:58 CDT 2015
Cong,
Can you write out math equations for mpk_monomial (),
list input and output parameters.
Note:
1. MatDuplicate() does not need to be followed by MatAssemblyBegin/End
2. MatMatMult(A,Km(stepIdx-1),MAT_REUSE_MATRIX,..) must be called after
MatMatMult(A,Km(stepIdx-1),MAT_INITIAL_MATRIX,..)
Hong
On Wed, Aug 5, 2015 at 8:56 PM, Cong Li <solvercorleone at gmail.com> wrote:
> The entire source code files are attached.
>
> Also I copy and paste the here in this email
>
> thanks
>
> program test
>
> implicit none
>
> #include <finclude/petscsys.h>
> #include <finclude/petscvec.h>
> #include <finclude/petscmat.h>
> #include <finclude/petscviewer.h>
>
>
> PetscViewer :: view
> ! sparse matrix
> Mat :: A
> ! distributed dense matrix of size n x m
> Mat :: B, X, R, QDlt, AQDlt
> ! distributed dense matrix of size n x (m x k)
> Mat :: Q, K, AQ_p, AQ
> ! local dense matrix (every process keep the identical copies), (m x k)
> x (m x k)
> Mat :: AConjPara, QtAQ, QtAQ_p, Dlt
>
> PetscInt :: nDim, mDim, rhsNDim,rhsMDim,ierr, maxIter, iter,
> step_k,bsize
> PetscInt :: ownRowS,ownRowE
> PetscScalar, allocatable :: XInit(:,:)
> PetscInt :: XInitI, XInitJ
> PetscScalar :: v=1.0
> PetscBool :: flg
> PetscMPIInt :: size, rank
>
> character(128) :: fin, rhsfin
>
>
> call PetscInitialize(PETSC_NULL_CHARACTER,ierr)
> call MPI_Comm_size(PETSC_COMM_WORLD,size,ierr)
> call MPI_Comm_rank(PETSC_COMM_WORLD,rank,ierr)
>
> ! read binary matrix file
> call PetscOptionsGetString(PETSC_NULL_CHARACTER,'-f',fin,flg,ierr)
> call PetscOptionsGetString(PETSC_NULL_CHARACTER,'-r',rhsfin,flg,ierr)
>
> call PetscOptionsGetInt(PETSC_NULL_CHARACTER,'-i',maxIter,flg,ierr)
> call PetscOptionsGetInt(PETSC_NULL_CHARACTER,'-k',step_k,flg,ierr)
> call PetscOptionsGetInt(PETSC_NULL_CHARACTER,'-w',bsize,flg,ierr)
>
>
> call PetscViewerBinaryOpen(PETSC_COMM_WORLD,fin,FILE_MODE_READ,view,ierr)
> call MatCreate(PETSC_COMM_WORLD,A,ierr)
> call MatSetType(A,MATAIJ,ierr)
> call MatLoad(A,view,ierr)
> call PetscViewerDestroy(view,ierr)
> ! for the time being, assume mDim == nDim is true
> call MatGetSize(A, nDim, mDim, ierr)
>
> if (rank == 0) then
> print*,'Mat Size = ', nDim, mDim
> end if
>
> call MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY, ierr)
> call MatGetOwnershipRange(A,ownRowS,ownRowE, ierr)
>
> ! create right-and-side matrix
> ! for the time being, choose row-wise decomposition
> ! for the time being, assume nDim%size = 0
> call MatCreateDense(PETSC_COMM_WORLD, (ownRowE - ownRowS), &
> bsize, nDim, bsize,PETSC_NULL_SCALAR, B, ierr)
> call PetscViewerBinaryOpen(PETSC_COMM_WORLD,rhsfin,FILE_MODE_READ,view,
> ierr)
> call MatLoad(B,view,ierr)
> call PetscViewerDestroy(view,ierr)
> call MatGetSize(B, rhsMDim, rhsNDim, ierr)
> if (rank == 0) then
> print*,'MRHS Size actually are:', rhsMDim, rhsNDim
> print*,'MRHS Size should be:', nDim, bsize
> end if
> call MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY, ierr)
>
> ! inintial value guses X
> allocate(XInit(nDim,bsize))
> do XInitI=1, nDim
> do XInitJ=1, bsize
> XInit(XInitI,XInitJ) = 1.0
> end do
> end do
>
> call MatCreateDense(PETSC_COMM_WORLD, (ownRowE - ownRowS), &
> bsize, nDim, bsize,XInit, X, ierr)
>
> call MatAssemblyBegin(X, MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd (X, MAT_FINAL_ASSEMBLY, ierr)
>
>
> ! B, X, R, QDlt, AQDlt
> call MatDuplicate(B, MAT_DO_NOT_COPY_VALUES, R, ierr)
> call MatAssemblyBegin(R, MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd (R, MAT_FINAL_ASSEMBLY, ierr)
>
> call MatDuplicate(B, MAT_DO_NOT_COPY_VALUES, QDlt, ierr)
> call MatAssemblyBegin(QDlt, MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd (QDlt, MAT_FINAL_ASSEMBLY, ierr)
>
> call MatDuplicate(B, MAT_DO_NOT_COPY_VALUES, AQDlt, ierr)
> call MatAssemblyBegin(AQDlt, MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd (AQDlt, MAT_FINAL_ASSEMBLY, ierr)
>
> ! Q, K, AQ_p, AQ of size n x (m x k)
> call MatCreateDense(PETSC_COMM_WORLD, (ownRowE - ownRowS), &
> (bsize*step_k), nDim,
> (bsize*step_k),PETSC_NULL_SCALAR, Q, ierr)
> call MatAssemblyBegin(Q, MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd(Q, MAT_FINAL_ASSEMBLY, ierr)
>
> call MatDuplicate(Q, MAT_DO_NOT_COPY_VALUES, K, ierr)
> call MatAssemblyBegin(K, MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd(K, MAT_FINAL_ASSEMBLY, ierr)
>
> call MatDuplicate(Q, MAT_DO_NOT_COPY_VALUES, AQ_p, ierr)
> call MatAssemblyBegin(AQ_p, MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd(AQ_p, MAT_FINAL_ASSEMBLY, ierr)
>
> call MatDuplicate(Q, MAT_DO_NOT_COPY_VALUES, AQ, ierr)
> call MatAssemblyBegin(AQ, MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd(AQ, MAT_FINAL_ASSEMBLY, ierr)
>
> ! QtAQ, QtAQ_p, Dlt of size (m x k) x (m x k)
> call MatCreateSeqDense(PETSC_COMM_SELF,(bsize*step_k),(bsize*step_k),&
> PETSC_NULL_SCALAR, QtAQ, ierr)
> call MatAssemblyBegin(QtAQ, MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd (QtAQ, MAT_FINAL_ASSEMBLY, ierr)
>
> call MatDuplicate(QtAQ, MAT_DO_NOT_COPY_VALUES, QtAQ_p , ierr)
> call MatAssemblyBegin(QtAQ_p, MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd (QtAQ_p, MAT_FINAL_ASSEMBLY, ierr)
>
> call MatDuplicate(QtAQ, MAT_DO_NOT_COPY_VALUES, Dlt , ierr)
> call MatAssemblyBegin(Dlt, MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd (Dlt, MAT_FINAL_ASSEMBLY, ierr)
>
> call MatDuplicate(QtAQ, MAT_DO_NOT_COPY_VALUES, AConjPara , ierr)
> call MatAssemblyBegin(AConjPara, MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd (AConjPara, MAT_FINAL_ASSEMBLY, ierr)
>
> ! calculation for R
>
> ! call matrix powers kernel
> call mpk_monomial (K, A, R, step_k, rank,size)
>
> ! destory matrices
> deallocate(XInit)
>
> call MatDestroy(B, ierr)
> call MatDestroy(X, ierr)
> call MatDestroy(R, ierr)
> call MatDestroy(QDlt, ierr)
> call MatDestroy(AQDlt, ierr)
> call MatDestroy(Q, ierr)
> call MatDestroy(K, ierr)
> call MatDestroy(AQ_p, ierr)
> call MatDestroy(AQ, ierr)
> call MatDestroy(QtAQ, ierr)
> call MatDestroy(QtAQ_p, ierr)
> call MatDestroy(Dlt, ierr)
>
>
> call PetscFinalize(ierr)
>
> stop
>
> end program test
>
>
> subroutine mpk_monomial (K, A, R, step_k, rank, sizeMPI)
> implicit none
>
> #include <finclude/petscsys.h>
> #include <finclude/petscvec.h>
> #include <finclude/petscmat.h>
> #include <finclude/petscviewer.h>
>
> Mat :: K, Km(step_k)
> Mat :: A, R
> PetscMPIInt :: sizeMPI, rank
> PetscInt :: nDim, bsize, step_k, local_RRow, local_RCol, genIdx
> PetscInt :: ierr
> PetscInt :: stepIdx, blockShift, localRsize
> PetscScalar :: KArray(1), RArray(1), PetscScalarSize
> PetscOffset :: KArrayOffset, RArrayOffset
>
> call MatGetSize(R, nDim, bsize, ierr)
> if (rank == 0) then
> print*,'Mat Size = ', nDim, bsize
> end if
>
> call MatGetArray(K,KArray,KArrayOffset,ierr)
>
> call MatGetLocalSize(R,local_RRow,local_RCol)
> ! print *, "local_RRow,local_RCol", local_RRow,local_RCol
>
> ! get arry from R to add values to K(1)
> call MatGetArray(R,RArray,RArrayOffset,ierr)
>
> call MatCreateDense(PETSC_COMM_WORLD, PETSC_DECIDE, &
> PETSC_DECIDE , nDim, bsize,KArray(KArrayOffset +
> 1), Km(1), ierr)
>
>
> ! call PetscMemmove(KArray(KArrayOffset + 1),RArray(RArrayOffset + 1) &
> ! ,local_RRow * local_RCol *
> STORAGE_SIZE(PetscScalarSize), ierr)
>
> localRsize = local_RRow * local_RCol
> do genIdx= 1, localRsize
> KArray(KArrayOffset + genIdx) = RArray(RArrayOffset + genIdx)
> end do
>
>
> call MatRestoreArray(R,RArray,RArrayOffset,ierr)
>
> call MatAssemblyBegin(Km(1), MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd (Km(1), MAT_FINAL_ASSEMBLY, ierr)
>
> do stepIdx= 2, step_k
>
> blockShift = KArrayOffset + (stepIdx-1) * (local_RRow * local_RCol)
>
> call MatCreateDense(PETSC_COMM_WORLD, PETSC_DECIDE, &
> PETSC_DECIDE , nDim, bsize,KArray(blockShift+1),
> Km(stepIdx), ierr)
> call MatAssemblyBegin(Km(stepIdx), MAT_FINAL_ASSEMBLY, ierr)
> call MatAssemblyEnd (Km(stepIdx), MAT_FINAL_ASSEMBLY, ierr)
>
> end do
>
> call MatRestoreArray(K,KArray,KArrayOffset,ierr)
>
> ! do stepIdx= 2, step_k
> do stepIdx= 2,2
>
> call
> MatMatMult(A,Km(stepIdx-1),MAT_REUSE_MATRIX,PETSC_DEFAULT_INTEGER,Km(stepIdx),
> ierr)
> ! call
> MatMatMult(A,Km(stepIdx-1),MAT_INITIAL_MATRIX,PETSC_DEFAULT_INTEGER,Km(stepIdx),
> ierr)
> end do
>
> ! call MatView(K,PETSC_VIEWER_STDOUT_WORLD,ierr)
>
> end subroutine mpk_monomial
>
>
>
> Cong Li
>
> On Thu, Aug 6, 2015 at 3:30 AM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
>>
>> Send the entire code so that we can compile it and run it ourselves to
>> see what is going wrong.
>>
>> Barry
>>
>> > On Aug 5, 2015, at 4:42 AM, Cong Li <solvercorleone at gmail.com> wrote:
>> >
>> > Hi
>> >
>> > I tried the method you suggested. However, I got the error message.
>> > My code and message are below.
>> >
>> > K is the big matrix containing column matrices.
>> >
>> > code:
>> >
>> > call MatGetArray(K,KArray,KArrayOffset,ierr)
>> >
>> > call MatGetLocalSize(R,local_RRow,local_RCol)
>> >
>> > call MatGetArray(R,RArray,RArrayOffset,ierr)
>> >
>> > call MatCreateDense(PETSC_COMM_WORLD, PETSC_DECIDE, &
>> > PETSC_DECIDE , nDim, bsize,KArray(KArrayOffset
>> + 1), Km(1), ierr)
>> >
>> > localRsize = local_RRow * local_RCol
>> > do genIdx= 1, localRsize
>> > KArray(KArrayOffset + genIdx) = RArray(RArrayOffset + genIdx)
>> > end do
>> >
>> > call MatRestoreArray(R,RArray,RArrayOffset,ierr)
>> >
>> > call MatAssemblyBegin(Km(1), MAT_FINAL_ASSEMBLY, ierr)
>> > call MatAssemblyEnd (Km(1), MAT_FINAL_ASSEMBLY, ierr)
>> >
>> > do stepIdx= 2, step_k
>> >
>> > blockShift = KArrayOffset + (stepIdx-1) * (local_RRow * local_RCol)
>> >
>> > call MatCreateDense(PETSC_COMM_WORLD, PETSC_DECIDE, &
>> > PETSC_DECIDE , nDim,
>> bsize,KArray(blockShift+1), Km(stepIdx), ierr)
>> > call MatAssemblyBegin(Km(stepIdx), MAT_FINAL_ASSEMBLY, ierr)
>> > call MatAssemblyEnd (Km(stepIdx), MAT_FINAL_ASSEMBLY, ierr)
>> > end do
>> >
>> > call MatRestoreArray(K,KArray,KArrayOffset,ierr)
>> >
>> > do stepIdx= 2, step_k
>> >
>> > call
>> MatMatMult(A,Km(stepIdx-1),MAT_REUSE_MATRIX,PETSC_DEFAULT_INTEGER,Km(stepIdx),
>> ierr)
>> > end do
>> >
>> >
>> > And I got the error message as below:
>> >
>> >
>> > [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>> > [0]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> > [0]PETSC ERROR: or see
>> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC
>> ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to
>> find memory corruption errors
>> > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> > [0]PETSC ERROR: to get more information on the crash.
>> > [0]PETSC ERROR: --------------------- Error Message
>> ------------------------------------
>> > [0]PETSC ERROR: Signal received!
>> > [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11
>> 22:15:24 CDT 2013
>> > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> > [0]PETSC ERROR: See docs/index.html for manual pages.
>> > [0]PETSC ERROR: --------------------[1]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>> > ----------------------------------------------------
>> > [0]PETSC ERROR: ./kmath.bcbcg on a arch-fuji named p01-024 by a03293
>> Wed Aug 5 18:24:40 2015
>> > [0]PETSC ERROR: Libraries linked from
>> /volume1/home/ra000005/a03293/kmathlibbuild/petsc-3.3-p7/arch-fujitsu-sparc64fx-opt/lib
>> > [0]PETSC ERROR: Configure run at Tue Jul 28 19:23:51 2015
>> > [0]PETSC ERROR: Configure options --known-level1-dcache-size=32768
>> --known-level1-dcache-linesize=32 --known-level1-dcache-assoc=0
>> --known-memcmp-ok=1 --known-sizeof-char=1 --known-sizeof-void-p=8
>> --known-sizeof-short=2 --known-sizeof-int=4 --known-sizeof-long=8
>> --known-sizeof-long-long=8 --known-sizeof-float=4 --known-sizeof-double=8
>> --known-sizeof-size_t=8 --known-bits-per-byte=8 --known-sizeof-MPI_Comm=8
>> --known-sizeof-MPI_Fint=4 --known-mpi-long-double=1
>> --known-mpi-c-double-complex=1 --with-cc=mpifccpx --CFLAGS="-mt -Xg"
>> --COPTFLAGS=-Kfast,openmp --with-cxx=mpiFCCpx --CXXFLAGS=-mt
>> --CXXOPTFLAGS=-Kfast,openmp --with-fc=mpifrtpx --FFLAGS=-Kthreadsafe
>> --FOPTFLAGS=-Kfast,openmp --with-blas-lapack-lib="-SCALAPACK -SSL2"
>> --with-x=0 --with-c++-support --with-batch=1 --with-info=1
>> --with-debugging=0 --known-mpi-shared-libraries=0 --with-valgrind=0
>> > [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: User provided function() line 0 in unknown directory
>> unknown file
>> >
>> --------------------------------------------------------------------------
>> > [mpi::mpi-api::mpi-abort]
>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>> > with errorcode 59.
>> >
>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> > You may or may not see output from other processes, depending on
>> > exactly when Open MPI kills them.
>> >
>> --------------------------------------------------------------------------
>> > [p01-024:26516]
>> /opt/FJSVtclang/GM-1.2.0-18/lib64/libmpi.so.0(orte_errmgr_base_error_abort+0x84)
>> [0xffffffff0091f684]
>> > [p01-024:26516]
>> /opt/FJSVtclang/GM-1.2.0-18/lib64/libmpi.so.0(ompi_mpi_abort+0x51c)
>> [0xffffffff006c389c]
>> > [p01-024:26516]
>> /opt/FJSVtclang/GM-1.2.0-18/lib64/libmpi.so.0(MPI_Abort+0x6c)
>> [0xffffffff006db3ac]
>> > [p01-024:26516]
>> /opt/FJSVtclang/GM-1.2.0-18/lib64/libtrtmet_c.so.1(MPI_Abort+0x2c)
>> [0xffffffff00281bf0]
>> > [p01-024:26516] ./kmath.bcbcg [0x1bf620]
>> > [p01-024:26516] ./kmath.bcbcg [0x1bf20c]
>> > [p01-024:26516] /lib64/libc.so.6(killpg+0x48) [0xffffffff02d52600]
>> > [p01-024:26516] [(nil)]
>> > [p01-024:26516] ./kmath.bcbcg [0x1a2054]
>> > [p01-024:26516] ./kmath.bcbcg [0x1064f8]
>> > [p01-024:26516] ./kmath.bcbcg(MAIN__+0x9dc) [0x105d1c]
>> > [p01-024:26516] ./kmath.bcbcg(main+0xec) [0x8a329c]
>> > [p01-024:26516] /lib64/libc.so.6(__libc_start_main+0x194)
>> [0xffffffff02d3b81c]
>> > [p01-024:26516] ./kmath.bcbcg [0x1051ec]
>> > [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or
>> the batch system) has told this process to end
>> > [0]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> > [0]PETSC ERROR: or see
>> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC
>> ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to
>> find memory corruption errors
>> > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> > [0]PETSC ERROR: to get more information on the crash.
>> > [0]PETSC ERROR: --------------------- Error Message
>> ------------------------------------
>> > [0]PETSC ERROR: Signal received!
>> > [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11
>> 22:15:24 CDT 2013
>> > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> > [0]PETSC ERROR: See docs/index.html for manual pages.
>> > [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: ./kmath.bcbcg on a arch-fuji named p01-024 by a03293
>> Wed Aug 5 18:24:40 2015
>> > [0]PETSC ERROR: Libraries linked from
>> /volume1/home/ra000005/a03293/kmathlibbuild/petsc-3.3-p7/arch-fujitsu-sparc64fx-opt/lib
>> > [0]PETSC ERROR: Configure run at Tue Jul 28 19:23:51 2015
>> > [0]PETSC ERROR: Configure options --known-level1-dcache-size=32768
>> --known-level1-dcache-linesize=32 --known-level1-dcache-assoc=0
>> --known-memcmp-ok=1 --known-sizeof-char=1 --known-sizeof-void-p=8
>> --known-sizeof-short=2 --known-sizeof-int=4 --known-sizeof-long=8
>> --known-sizeof-long-long=8 --known-sizeof-float=4 --known-sizeof-double=8
>> --known-sizeof-size_t=8 --known-bits-per-byte=8 --known-sizeof-MPI_Comm=8
>> --known-sizeof-MPI_Fint=4 --known-mpi-long-double=1
>> --known-mpi-c-double-complex=1 --with-cc=mpifccpx --CFLAGS="-mt -Xg"
>> --COPTFLAGS=-Kfast,openmp --with-cxx=mpiFCCpx --CXXFLAGS=-mt
>> --CXXOPTFLAGS=-Kfast,openmp --with-fc=mpifrtpx --FFLAGS=-Kthreadsafe
>> --FOPTFLAGS=-Kfast,openmp --with-blas-lapack-lib="-SCALAPACK -SSL2"
>> --with-x=0 --with-c++-support --with-batch=1 --with-info=1
>> --with-debugging=0 --known-mpi-shared-libraries=0 --with-valgrind=0
>> > [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: User provided function() line 0 in unknown directory
>> unknown file
>> > [ERR.] PLE 0019 plexec One of MPI processes was
>> aborted.(rank=0)(nid=0x020a0028)(CODE=1938,793745140674134016,15104)
>> >
>> > However, if I change from
>> > call
>> MatMatMult(A,Km(stepIdx-1),MAT_REUSE_MATRIX,PETSC_DEFAULT_INTEGER,Km(stepIdx),
>> ierr)
>> > to
>> > call MatMatMult(A,Km(stepIdx-1),
>> MAT_INITIAL_MATRIX,PETSC_DEFAULT_INTEGER,Km(stepIdx), ierr)
>> >
>> > everything is fine.
>> >
>> > could you please suggest some way to solve this?
>> >
>> > Thanks
>> >
>> > Cong Li
>> >
>> > On Wed, Aug 5, 2015 at 10:53 AM, Cong Li <solvercorleone at gmail.com>
>> wrote:
>> > Thank you very much for your help and suggestions.
>> > With your help, finally I could continue my project.
>> >
>> > Regards
>> >
>> > Cong Li
>> >
>> >
>> >
>> > On Wed, Aug 5, 2015 at 3:09 AM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>> >
>> > From the manual page: Unless scall is MAT_REUSE_MATRIX C will be
>> created.
>> >
>> > Since you want to use the C that is passed in you should use
>> MAT_REUSE_MATRIX.
>> >
>> > Note that since your B and C matrices are dense the issue of sparsity
>> pattern of C is not relevant.
>> >
>> > Barry
>> >
>> > > On Aug 4, 2015, at 11:59 AM, Cong Li <solvercorleone at gmail.com>
>> wrote:
>> > >
>> > > Thanks very much. This answer is very helpful.
>> > > And I have a following question.
>> > > If I create B1, B2, .. by the way you suggested and then use
>> MatMatMult to do SPMM.
>> > > PetscErrorCode MatMatMult(Mat A,Mat B,MatReuse scall,PetscReal
>> fill,Mat *C)
>> > > should I use MAT_REUSE_MATRIX for MatReuse part of the arguement.
>> > >
>> > > Thanks
>> > >
>> > > Cong Li
>> > >
>> > > On Wed, Aug 5, 2015 at 1:27 AM, Barry Smith <bsmith at mcs.anl.gov>
>> wrote:
>> > >
>> > > > On Aug 4, 2015, at 4:09 AM, Cong Li <solvercorleone at gmail.com>
>> wrote:
>> > > >
>> > > > I am sorry that I should have explained it more clearly.
>> > > > Actually I want to compute a recurrence.
>> > > >
>> > > > Like, I want to firstly compute A*X1=B1, and then calculate
>> A*B1=B2, A*B2=B3 and so on.
>> > > > Finally I want to combine all these results into a bigger matrix
>> C=[B1,B2 ...]
>> > >
>> > > First create C with MatCreateDense(,&C). Then call
>> MatDenseGetArray(C,&array); then create B1 with
>> MatCreateDense(....,array,&B1); then create
>> > > B2 with MatCreateDense(...,array+shift,&B2) etc where shift equals
>> the number of __local__ rows in B1 times the number of columns in B1, then
>> create B3 with a larger shift etc.
>> > >
>> > > Note that you are "sharing" the array space of C with B1, B2, B3,
>> ..., each Bi contains its columns of the C matrix.
>> > >
>> > > Barry
>> > >
>> > >
>> > >
>> > > >
>> > > > Is there any way to do this efficiently.
>> > > >
>> > > >
>> > > >
>> > > > On Tue, Aug 4, 2015 at 5:45 PM, Patrick Sanan <
>> patrick.sanan at gmail.com> wrote:
>> > > > On Tue, Aug 04, 2015 at 03:42:14PM +0900, Cong Li wrote:
>> > > > > Thanks for your reply.
>> > > > >
>> > > > > I have an other question.
>> > > > > I want to do SPMM several times and combine result matrices into
>> one bigger
>> > > > > matrix.
>> > > > > for example
>> > > > > I firstly calculate AX1=B1, AX2=B2 ...
>> > > > > then I want to combine B1, B2.. to get a C, where C=[B1,B2...]
>> > > > >
>> > > > > Could you please suggest a way of how to do this.
>> > > > This is just linear algebra, nothing to do with PETSc specifically.
>> > > > A * [X1, X2, ... ] = [AX1, AX2, ...]
>> > > > >
>> > > > > Thanks
>> > > > >
>> > > > > Cong Li
>> > > > >
>> > > > > On Tue, Aug 4, 2015 at 3:27 PM, Jed Brown <jed at jedbrown.org>
>> wrote:
>> > > > >
>> > > > > > Cong Li <solvercorleone at gmail.com> writes:
>> > > > > >
>> > > > > > > Hello,
>> > > > > > >
>> > > > > > > I am a PhD student using PETsc for my research.
>> > > > > > > I am wondering if there is a way to implement SPMM (Sparse
>> matrix-matrix
>> > > > > > > multiplication) by using PETSc.
>> > > > > >
>> > > > > >
>> > > > > >
>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatMatMult.html
>> > > > > >
>> > > >
>> > >
>> > >
>> >
>> >
>> >
>>
>>
>
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