[petsc-users] I am wondering if there is a way to implement SPMM
Cong Li
solvercorleone at gmail.com
Wed Aug 5 20:56:24 CDT 2015
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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