[petsc-users] How to have a local copy (sequential) of a parallel matrix
ehsan sadrfaridpour
it.sadr at gmail.com
Tue Jul 5 17:58:48 CDT 2016
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.
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
>
>
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