[petsc-users] I am wondering if there is a way to implement SPMM
Cong Li
solvercorleone at gmail.com
Wed Aug 5 09:43:51 CDT 2015
Hong,
Thanks for your answer.
However, in my problem, I have a pre-allocated matrix K, and its columns
are associated with Km(1), .. Km(step_k) respectively. What I want to do is
to update Km(2) by using the result of A*Km(1), and then to update Km(3) by
using the product of A and updated Km(2) and so on.
So, I think I need to use MAT_REUSE_MATRIX from the beginning, since even
when it is the first time I call
MatMatMult(A,Km(stepIdx-1), MAT_REUSE_MATRIX,PETSC_
DEFAULT_INTEGER,Km(stepIdx), ierr)',
Km(stepIdx) have actually already been allocated (in K).
Do you think it is possible that I can do this, and could you please
suggest some possible ways.
Thanks
Cong Li
On Wed, Aug 5, 2015 at 11:23 PM, Hong <hzhang at mcs.anl.gov> wrote:
> 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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