[petsc-users] I am wondering if there is a way to implement SPMM
Cong Li
solvercorleone at gmail.com
Thu Aug 6 00:22:20 CDT 2015
Hong,
Sure.
I want to extend the Krylov subspace by step_k dimensions by using
monomial, which can be defined as
K={Km(1)m Km(2), ..., Km(step_k)}
={Km(1), AKm(1), AKm(2), ... , AKm(step_k-1)}
={R, AR, A^2R, ... A^(step_k-1)R}
, in one loop. So, my plan now is to firstly calculate the recurrence,
which is P_n(x)=xP_n-1(x), and then use the results to update the items in
K. And then, in the next loop of Krylov subspace method, the K will be
updated again.
Input of the the mpk_monomial subroutine, is a preallocated dense matrix K.
And, A and R are for updating K in the subroutine.
Thanks
Cong Li
On Thu, Aug 6, 2015 at 12:23 PM, Hong <hzhang at mcs.anl.gov> wrote:
> 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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