[petsc-users] I am wondering if there is a way to implement SPMM
Cong Li
solvercorleone at gmail.com
Thu Aug 6 20:21:12 CDT 2015
Barry,
Thank you very much.
I will install and try the updated version.
Regards
Cong Li
On Fri, Aug 7, 2015 at 8:47 AM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
> Cong Li,
>
> I have updated PETSc to support the use of MatMatMult() per your
> needs. You will need to switch to the master development branch
> http://www.mcs.anl.gov/petsc/developers/index.html of PETSc so install
> that first.
>
> I found a number of bugs in your code that I needed to fix to get it to
> run successfully on 1 and 2 processes to correctly load the matrices and do
> everything else it was doing
> with the MatMatMult() (note I do not think it generates the right numbers
> but at least it doesn't crash and does successfully do the MatMatMult().
> I've attached the fixed files.
>
> Barry
>
>
> > On Aug 6, 2015, at 12:27 AM, Cong Li <solvercorleone at gmail.com> wrote:
> >
> > Barry,
> >
> > Exactly. And thanks for the explaination.
> >
> > Cong Li
> >
> > On Thu, Aug 6, 2015 at 1:29 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >
> > > On Aug 5, 2015, at 10:23 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, we want to reuse the space in the Km(stepIdx-1) from which it
> was created which means that MAT_INITIAL_MATRIX cannot be used. Since the
> result is always dense it is not the difficult case when a symbolic
> computation needs to be done initially so, at least in theory, he should
> not have to use MAT_INITIAL_MATRIX the first time through.
> >
> > Barry
> >
> > >
> > > 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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