[petsc-users] I am wondering if there is a way to implement SPMM
Cong Li
solvercorleone at gmail.com
Wed Aug 5 04:42:16 CDT 2015
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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