[petsc-users] I am wondering if there is a way to implement SPMM

Hong hzhang at mcs.anl.gov
Wed Aug 5 09:23:04 CDT 2015 

Cong:
You cannot use "MAT_REUSE_MATRIX" on arbitrary matrix product.
The correct process is

call MatMatMult(A,Km(stepIdx-1), MAT_INITIAL_MATRIX,PETSC_
DEFAULT_INTEGER,C, ierr)
call MatMatMult(A,Km(stepIdx-1), MAT_REUSE_MATRIX,PETSC_DEFAULT_INTEGER,C,
ierr)
i.e., C has data structure of A*Km(stepIdx-1) and is created in the first
call. C can be reused in the 2nd call when A or Km(stepIdx-1) changed
values, but not the structures.

In your case, Km(stepIdx) = A*Km(stepIdx-1). You should do
'call MatMatMult(A,Km(stepIdx-1), MAT_INITIAL_MATRIX
,PETSC_DEFAULT_INTEGER,Km(stepIdx), ierr)'
directly.

Hong

On Wed, 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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