[petsc-users] How to have a local copy (sequential) of a parallel matrix
Matthew Knepley
knepley at gmail.com
Tue Jul 5 20:02:45 CDT 2016
On Tue, Jul 5, 2016 at 5:58 PM, ehsan sadrfaridpour <it.sadr at gmail.com>
wrote:
> Sorry, I think your suggestion needs something, since it doesn't compile.
>
> error: expected initializer before ‘*’ token
>> Mat m_WA_nt_local *m_WA_nt_local;
>>
>
>
> Yes, this is the same problem that compiled and worked but it has a bug.
> I faced this problem and I tried to define the array of Matrices to fix
> this 4 days ago.
>
> However, my first email today is the problem that array of matrices caused
> me.
> I get a little confused in the logic.
>
> Let me review what is happening:
> As this method is collective, all the processes needs to run it.
> Therefore, I need to define a local matrix and create it for all of the
> processes.
>
No no no. Each process extracts a SET of SEQUENTIAL matrices. Each proc
choose how many
it will extract (could be 0).
Thanks,
Matt
> Only for the process I want to have the local matrix, I request a matrix
> (matrices) and for the rest of them I pass 0 in the MatGetSubMatrices.
> I am suspicious about creating only 1 matrix for any process, while I
> expect an array of matrices in the MatGetSubMatrices.
>
>
>
>
>
> On Tue, Jul 5, 2016 at 6:43 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
>>
>> > On Jul 5, 2016, at 5:36 PM, Matthew Knepley <knepley at gmail.com> wrote:
>> >
>> > On Tue, Jul 5, 2016 at 5:26 PM, ehsan sadrfaridpour <it.sadr at gmail.com>
>> wrote:
>> > Thanks for your prompt reply. Using & solve this problem, but then I
>> have another problem.
>> >
>> > Rest of the Code:
>> > Mat m_WA_nt_local;
>> > MatCreateSeqAIJ(PETSC_COMM_SELF,num_points,num_points,
>> pre_init_size, NULL, &m_WA_nt_local);
>> > PetscPrintf(PETSC_COMM_SELF, "[CS][pCalc_P] rank:%d, num_points:%d,
>> p_init:%d\n", rank, num_points, pre_init_size);
>> >
>> > IS set;
>> > if(rank ==0){
>> > // - - - - - create local matrix - - - - -
>> > PetscPrintf(PETSC_COMM_SELF, "[CS][pCalc_P] rank:%d,
>> num_points:%d\n", rank, num_points);
>> > ISCreateStride(PETSC_COMM_SELF, num_points, 0, 1, &set);
>> > ISView(set, PETSC_VIEWER_STDOUT_SELF);
>> > MatGetSubMatrices(m_WA_norm_T, 1, &set, &set,
>> MAT_INITIAL_MATRIX, &m_WA_nt_local);
>> > }else{
>> > MatGetSubMatrices(m_WA_norm_T, 0, &set, &set,
>> MAT_INITIAL_MATRIX, &m_WA_nt_local);
>> > }
>> >
>> > This returns an ARRAY of Mat objects, not just one.
>>
>> Didn't we just do this email a couple of days ago?
>>
>> You need
>>
>> Mat m_WA_nt_local *m_WA_nt_local;
>> > MatGetSubMatrices(m_WA_norm_T, 0, &set, &set, MAT_INITIAL_MATRIX,
>> &m_WA_nt_local);
>>
>>
>>
>>
>>
>> >
>> > Matt
>> >
>> >
>> > Error in compile:
>> > /home/esfp/dev/ws_qt/mlsvm/coarsening.cc: In member function ‘_p_Mat*
>> Coarsening::pCalc_P(_p_Mat*&, _p_Vec*&, std::vector<long unsigned int>&,
>> cs_info&)’:
>> > /home/esfp/dev/ws_qt/mlsvm/coarsening.cc:113:89: error: cannot convert
>> ‘_p_Mat**’ to ‘_p_Mat***’ for argument ‘6’ to ‘PetscErrorCode
>> MatGetSubMatrices(Mat, PetscInt, _p_IS* const*, _p_IS* const*, MatReuse,
>> _p_Mat***)’
>> > MatGetSubMatrices(m_WA_norm_T, 1, &set, &set,
>> MAT_INITIAL_MATRIX, &m_WA_nt_local);
>> >
>> ^
>> > /home/esfp/dev/ws_qt/mlsvm/coarsening.cc:115:89: error: cannot convert
>> ‘_p_Mat**’ to ‘_p_Mat***’ for argument ‘6’ to ‘PetscErrorCode
>> MatGetSubMatrices(Mat, PetscInt, _p_IS* const*, _p_IS* const*, MatReuse,
>> _p_Mat***)’
>> > MatGetSubMatrices(m_WA_norm_T, 0, &set, &set,
>> MAT_INITIAL_MATRIX, &m_WA_nt_local);
>> >
>> ^
>> >
>> >
>> > On Tue, Jul 5, 2016 at 6:21 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>> >
>> > It should be
>> >
>> > Mat m_WA_nt_local;
>> >
>> > > MatCreateSeqAIJ(PETSC_COMM_SELF,num_points,num_points, pre_init_size,
>> NULL, &m_WA_nt_local);
>> >
>> ^^^^^^^^^^^^
>> note the &
>> >
>> >
>> >
>> > > On Jul 5, 2016, at 5:13 PM, ehsan sadrfaridpour <it.sadr at gmail.com>
>> wrote:
>> > >
>> > > I faced a problem with my code. The problem is related to
>> MatCreateSeqAIJ().
>> > > I comment the rest of my code and just keeping the below lines cause
>> me the error.
>> > > Code:
>> > > Mat * m_WA_nt_local;
>> > > MatCreateSeqAIJ(PETSC_COMM_SELF,num_points,num_points,
>> pre_init_size, NULL, m_WA_nt_local);
>> > > PetscPrintf(PETSC_COMM_SELF, "[CS][pCalc_P] rank:%d,
>> num_points:%d, p_init:%d\n", rank, num_points, pre_init_size);
>> > >
>> > > exit(1);
>> > >
>> > > Error:
>> > > [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> > > [0]PETSC ERROR: Null argument, when expecting valid pointer
>> > > [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> > > [1]PETSC ERROR: Null argument, when expecting valid pointer
>> > > [1]PETSC ERROR: Null Pointer: Parameter # 2
>> > > [1]PETSC ERROR: See
>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>> > > [2]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> > > [2]PETSC ERROR: Null argument, when expecting valid pointer
>> > > [2]PETSC ERROR: Null Pointer: Parameter # 2
>> > > [2]PETSC ERROR: See
>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>> > > [2]PETSC ERROR: Petsc Release Version 3.6.3, unknown
>> > > [2]PETSC ERROR: ut_main on a linux-cxx-debug named grappelli by esfp
>> Tue Jul 5 18:05:15 2016
>> > > [2]PETSC ERROR: Configure options PETSC_ARCH=linux-cxx-debug
>> --with-cc=gcc --with-cxx=g++ --with-clanguage=c++ --with-gnu-compilers=1
>> --with-mpi-compilers=1 --with-debugging=1 --with-shared-libraries=1
>> --download-openmpi=1 --download-f2cblaslapack --download-superlu_dist=1
>> --download-superlu=1 --download-metis=1 --download-parmetis=1
>> --download-blacs=1 --with-hdf5 --with-hdf5-dir=/usr/local/hdf5/
>> > > [2]PETSC ERROR: #1 MatCreate() line 79 in
>> /home/esfp/tools/libraries/petsc/src/mat/utils/gcreate.c
>> > > [2]PETSC ERROR: #2 MatCreateSeqAIJ() line 3471 in
>> /home/esfp/tools/libraries/petsc/src/mat/impls/aij/seq/aij.c
>> > > Null Pointer: Parameter # 2
>> > > [0]PETSC ERROR: See
>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>> > > [0]PETSC ERROR: Petsc Release Version 3.6.3, unknown
>> > > [0]PETSC ERROR: ut_main on a linux-cxx-debug named grappelli by esfp
>> Tue Jul 5 18:05:15 2016
>> > > [0]PETSC ERROR: Configure options PETSC_ARCH=linux-cxx-debug
>> --with-cc=gcc --with-cxx=g++ --with-clanguage=c++ --with-gnu-compilers=1
>> --with-mpi-compilers=1 --with-debugging=1 --with-shared-libraries=1
>> --download-openmpi=1 --download-f2cblaslapack --download-superlu_dist=1
>> --download-superlu=1 --download-metis=1 --download-parmetis=1
>> --download-blacs=1 --with-hdf5 --with-hdf5-dir=/usr/local/hdf5/
>> > > [0]PETSC ERROR: #1 MatCreate() line 79 in
>> /home/esfp/tools/libraries/petsc/src/mat/utils/gcreate.c
>> > > [0]PETSC ERROR: #2 MatCreateSeqAIJ() line 3471 in
>> /home/esfp/tools/libraries/petsc/src/mat/impls/aij/seq/aij.c
>> > > [1]PETSC ERROR: Petsc Release Version 3.6.3, unknown
>> > > [1]PETSC ERROR: ut_main on a linux-cxx-debug named grappelli by esfp
>> Tue Jul 5 18:05:15 2016
>> > > [1]PETSC ERROR: Configure options PETSC_ARCH=linux-cxx-debug
>> --with-cc=gcc --with-cxx=g++ --with-clanguage=c++ --with-gnu-compilers=1
>> --with-mpi-compilers=1 --with-debugging=1 --with-shared-libraries=1
>> --download-openmpi=1 --download-f2cblaslapack --download-superlu_dist=1
>> --download-superlu=1 --download-metis=1 --download-parmetis=1
>> --download-blacs=1 --with-hdf5 --with-hdf5-dir=/usr/local/hdf5/
>> > > [1]PETSC ERROR: #1 MatCreate() line 79 in
>> /home/esfp/tools/libraries/petsc/src/mat/utils/gcreate.c
>> > > [1]PETSC ERROR: #2 MatCreateSeqAIJ() line 3471 in
>> /home/esfp/tools/libraries/petsc/src/mat/impls/aij/seq/aij.c
>> > > [CS][pCalc_P] rank:1, num_points:10, p_init:300
>> > > [CS][pCalc_P] rank:2, num_points:10, p_init:300
>> > > [CS][pCalc_P] rank:0, num_points:10, p_init:300
>> > >
>> > > As you can see nothing is NULL in my call to the MatCreateSeqAIJ.
>> > >
>> > > I tried to debug it with -start_in_debugger, but I got another error.
>> > > $ make ut_main && mpirun -n 3 ut_main -start_in_debugger
>> > > /home/esfp/tools/libraries/petsc/linux-cxx-debug/bin/mpicxx -o
>> ut_main.o -c -Wall -Wwrite-strings -Wno-strict-aliasing
>> -Wno-unknown-pragmas -g -O0 -fPIC
>> -I/home/esfp/tools/libraries/petsc/include
>> -I/home/esfp/tools/libraries/petsc/linux-cxx-debug/include
>> -I/usr/local/hdf5/include -std=c++11 -g -O3 `pwd`/ut_main.cc
>> > > /home/esfp/tools/libraries/petsc/linux-cxx-debug/bin/mpicxx -Wall
>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -O0 -I.
>> svm.o solver.o model_selection.o ut_ms.o ut_common.o ut_kf.o
>> ut_partitioning.o ds_node.o ds_graph.o coarsening.o ut_coarsening.o
>> partitioning.o ut_mr.o pugixml.o config_params.o etimer.o common_funcs.o
>> OptionParser.o loader.o ut_loader.o k_fold.o ut_main.o
>> -Wl,-rpath,/home/esfp/tools/libraries/petsc/linux-cxx-debug/lib
>> -L/home/esfp/tools/libraries/petsc/linux-cxx-debug/lib -lpetsc
>> -Wl,-rpath,/home/esfp/tools/libraries/petsc/linux-cxx-debug/lib
>> -lsuperlu_4.3 -lsuperlu_dist_4.1 -lf2clapack -lf2cblas -lm -lparmetis
>> -lmetis -lX11 -Wl,-rpath,/usr/local/hdf5/lib -L/usr/local/hdf5/lib
>> -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lhwloc -lm
>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.8
>> -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -Wl,-rpath,/usr/lib/x86_64-linux-gnu
>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu
>> -L/lib/x86_64-linux-gnu -lmpi_usempi -lmpi_mpifh -lgfortran -lm -lgfortran
>> -lm -lquadmath -lm -lmpi_cxx -lstdc++
>> -Wl,-rpath,/home/esfp/tools/libraries/petsc/linux-cxx-debug/lib
>> -L/home/esfp/tools/libraries/petsc/linux-cxx-debug/lib
>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.8
>> -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -Wl,-rpath,/usr/lib/x86_64-linux-gnu
>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu
>> -L/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu
>> -L/usr/lib/x86_64-linux-gnu -ldl
>> -Wl,-rpath,/home/esfp/tools/libraries/petsc/linux-cxx-debug/lib -lmpi
>> -lgcc_s -lpthread -ldl -o ut_main
>> > > /bin/rm -f ut_main.o
>> > > [0]PETSC ERROR: PETSC: Attaching gdb to ut_main of pid 2818 on
>> display :0 on machine grappelli
>> > > [1]PETSC ERROR: PETSC: Attaching gdb to ut_main of pid 2819 on
>> display :0 on machine grappelli
>> > > [2]PETSC ERROR: PETSC: Attaching gdb to ut_main of pid 2820 on
>> display :0 on machine grappelli
>> > >
>> > >
>> > > And I got below error in gdb GUI:
>> > > <image.png>
>> > >
>> > > I appreciate your support.
>> > >
>> > > Best regards,
>> > > Ehsan
>> > >
>> > > On Wed, Jun 29, 2016 at 4:31 PM, Barry Smith <bsmith at mcs.anl.gov>
>> wrote:
>> > >
>> > > On all other processes don't pass in 1 pass in 0 since all other
>> processes want 0 sub matrices
>> > >
>> > >
>> > > > On Jun 29, 2016, at 3:24 PM, ehsan sadrfaridpour <it.sadr at gmail.com>
>> wrote:
>> > > >
>> > > > Thanks, the IS problem is solved.
>> > > > But now I have another problem to compile the code.
>> > > >
>> > > > I use below code:
>> > > > Mat m_WA_nt_local;
>> > > > MatCreateSeqAIJ(PETSC_COMM_SELF,num_points,num_points,
>> Config_params::getInstance()->get_pre_init_loader_matrix(), NULL,
>> &m_WA_nt_local);
>> > > > IS set;
>> > > > if(rank ==0){
>> > > > ISCreateStride(PETSC_COMM_SELF, num_points, 0, 1, &set);
>> > > > ISView(set, PETSC_VIEWER_STDOUT_SELF);
>> > > > }
>> > > > MatGetSubMatrices(m_WA_norm_T, 1, &set, &set,
>> MAT_INITIAL_MATRIX, &m_WA_nt_local);
>> > > >
>> > > > The error I get is :
>> > > > error: cannot convert ‘_p_Mat**’ to ‘_p_Mat***’ for argument ‘6’ to
>> ‘PetscErrorCode MatGetSubMatrices(Mat, PetscInt, _p_IS* const*, _p_IS*
>> const*, MatReuse, _p_Mat***)’
>> > > > MatGetSubMatrices(m_WA_norm_T, 1, &set, &set,
>> MAT_INITIAL_MATRIX, &m_WA_nt_local);
>> > > >
>> > > >
>> > > > I tried to go around it by define a array of Matrices using "Mat *
>> m_WA_nt_local"
>> > > > So, the first 2 lines changed to below and I can compile the code.
>> > > > Mat * m_WA_nt_local;
>> > > > MatCreateSeqAIJ(PETSC_COMM_SELF,num_points,num_points,
>> Config_params::getInstance()->get_pre_init_loader_matrix(), NULL,
>> m_WA_nt_local);
>> > > >
>> > > >
>> > > >
>> > > > However, I get errors like below when I run the code with 2 mpi
>> process.
>> > > > --------------------- Error Message
>> --------------------------------------------------------------
>> > > > [1]PETSC ERROR: Invalid argument
>> > > > [1]PETSC ERROR: Wrong type of object: Parameter # 3
>> > > > [1]PETSC ERROR: See
>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>> > > > [1]PETSC ERROR: Petsc Release Version 3.6.3, unknown
>> > > > [1]PETSC ERROR: ut_main on a linux-cxx-debug named grappelli by
>> esfp Wed Jun 29 16:21:04 2016
>> > > > [1]PETSC ERROR: Configure options PETSC_ARCH=linux-cxx-debug
>> --with-cc=gcc --with-cxx=g++ --with-clanguage=c++ --with-gnu-compilers=1
>> --with-mpi-compilers=1 --with-debugging=1 --with-shared-libraries=1
>> --download-openmpi=1 --download-f2cblaslapack --download-superlu_dist=1
>> --download-superlu=1 --download-metis=1 --download-parmetis=1
>> --download-blacs=1 --with-hdf5 --with-hdf5-dir=/usr/local/hdf5/
>> > > > [1]PETSC ERROR: #1 MatGetSubMatrices() line 6605 in
>> /home/esfp/tools/libraries/petsc/src/mat/interface/matrix.c
>> > > >
>> > > >
>> > > > I think I need to do something for other processes, but I don't
>> know what I need to do.
>> > > >
>> > > > Best,
>> > > > Ehsan
>> > > >
>> > > >
>> > > >
>> > > > On Wed, Jun 29, 2016 at 4:03 PM, Dave May <dave.mayhem23 at gmail.com>
>> wrote:
>> > > >
>> > > >
>> > > > On Wednesday, 29 June 2016, ehsan sadrfaridpour <it.sadr at gmail.com>
>> wrote:
>> > > > I faced the below error during compiling my code for using
>> MatGetSubMatrices.
>> > > >
>> > > > error: cannot convert ‘IS {aka _p_IS*}’ to ‘_p_IS* const*’ for
>> argument ‘3’ to ‘PetscErrorCode MatGetSubMatrices(Mat, PetscInt, _p_IS*
>> const*, _p_IS* const*, MatReuse, _p_Mat***)’
>> > > > MatGetSubMatrices(m_WA_norm_T, 1, set, set,
>> MAT_INITIAL_MATRIX, &m_local_W);
>> > > >
>> > > > My code :
>> > > > PetscMPIInt rank;
>> > > > MPI_Comm_rank(PETSC_COMM_WORLD, &rank);
>> > > >
>> > > > if(rank ==0){
>> > > > Mat m_local_W;
>> > > > MatCreateSeqAIJ(PETSC_COMM_SELF,num_points,num_points,
>> num_nz, NULL,&m_local_W);// try to reserve space for only number of final
>> non zero entries for each fine node (e.g. 4)
>> > > > IS set;
>> > > > ISCreateStride(PETSC_COMM_SELF, num_points, 0, 1, &set_row);
>> > > > MatGetSubMatrices(m_WA_norm_T, 1, set_row, set_col,
>> MAT_INITIAL_MATRIX, &m_local_W);
>> > > >
>> > > > }
>> > > >
>> > > > I followed below example:
>> > > >
>> http://www.mcs.anl.gov/petsc/petsc-current/src/vec/is/is/examples/tutorials/ex2.c.html
>> > > >
>> > > > This code won't work in parallel.
>> > > > The man page says this function is collective on Mat. You need to
>> move the call to MatGetSubMatrices outside of the if(rank==0) loop.
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > > On Wed, Jun 29, 2016 at 3:19 PM, ehsan sadrfaridpour <
>> it.sadr at gmail.com> wrote:
>> > > > Thanks a lot for great support.
>> > > >
>> > > > On Wed, Jun 29, 2016 at 3:11 PM, Barry Smith <bsmith at mcs.anl.gov>
>> wrote:
>> > > >
>> > > > MatGetSubmatrices() just have the first process request all the
>> rows and columns and the others request none. You can use ISCreateStride()
>> to create the ISs without having to make an array of all the indices.
>> > > >
>> > > >
>> > > > > On Jun 29, 2016, at 1:43 PM, ehsan sadrfaridpour <
>> it.sadr at gmail.com> wrote:
>> > > > >
>> > > > > Hi,
>> > > > >
>> > > > > I need to have access to most of elements of a parallel MPIAIJ
>> matrix only from 1 process (rank 0).
>> > > > > I tried to copy or duplicate it to SEQAIJ, but I faced problems.
>> > > > >
>> > > > > How can I have a local copy of a matrix which is distributed on
>> multiple process? I don't want to update the matrix, and the read-only
>> version of it would be enough.
>> > > > >
>> > > > > Best,
>> > > > > Ehsan
>> > > > >
>> > > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > >
>> > >
>> >
>> >
>> >
>> >
>> >
>> > --
>> > What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> > -- Norbert Wiener
>>
>>
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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