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

Barry Smith bsmith at mcs.anl.gov
Wed Aug 5 13:30:58 CDT 2015 

   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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