[petsc-users] Building MatIS with dense local matrix ?
Franck Houssen
franck.houssen at inria.fr
Tue Jun 20 09:30:58 CDT 2017
OK. I moved from petsc-3.7.6 to development version (git clone bitbucket).
The very first version of the dummy example (= matISCSRDenseSquare/Rect.cpp) works with this fix: https://bitbucket.org/petsc/petsc/commits/4c8dd594d1988a0cbe282f8a37d9916f61e0c445 .
The second version of the dummy example works too with the fix if one moves to petsc bitbucket (master).
But, the code still breaks in "my" initial "real" case (using now master from petsc bitbucket)... With another error "SEGV under MatISSetMPIXAIJPreallocation_Private" (note: this is not a "new non zero" message, this seems to be another problem).
Here is a third version of the dummy example that breaks with "SEGV under MatISSetMPIXAIJPreallocation_Private" (using master from petsc bitbucket) : the idea is the same but with N procs (not only 2) and a rectangular matrix of size N*(N+1).
With 2 procs, it works (all cases).
With 4 procs, new problems occur:
>> mpirun -n 4 ./matISCSRDenseSquare.exe csr; mpirun -n 4 ./matISCSRDenseSquare.exe dense => OK
>> mpirun -n 4 ./matISCSRDenseRect.exe csr => OK
but
>> mpirun -n 4 ./matISCSRDenseRect.exe dense;
dense
dense
dense
dense
[3]PETSC ERROR: ------------------------------------------------------------------------
[3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[3]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[3]PETSC ERROR: likely location of problem given in stack below
[3]PETSC ERROR: --------------------- Stack Frames ------------------------------------
[3]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[3]PETSC ERROR: INSTEAD the line number of the start of the function
[3]PETSC ERROR: is given.
[3]PETSC ERROR: [3] MatISSetMPIXAIJPreallocation_Private line 1055 /home/fghoussen/Documents/INRIA/petsc/src/mat/impls/is/matis.c
[3]PETSC ERROR: [3] MatISGetMPIXAIJ_IS line 1230 /home/fghoussen/Documents/INRIA/petsc/src/mat/impls/is/matis.c
[3]PETSC ERROR: [3] MatISGetMPIXAIJ line 1384 /home/fghoussen/Documents/INRIA/petsc/src/mat/impls/is/matis.c
[3]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
I tried to go through this with caution... But I have to say I feel messy. Can you reproduce this problem at your side ?
Franck
>> git diff .
--- a/matISCSRDenseRect.cpp
+++ b/matISCSRDenseRect.cpp
@@ -14,19 +14,17 @@ int main(int argc,char **argv) {
if (matType != "csr" && matType != "dense") {cout << "error: need arg = csr or dense" << endl; return 1;}
PetscInitialize(&argc, &argv, NULL, NULL);
- int size = 0; MPI_Comm_size(MPI_COMM_WORLD, &size); if (size != 2) {cout << "error: mpi != 2" << endl; return 1;}
+ int size = 0; MPI_Comm_size(MPI_COMM_WORLD, &size);
int rank = 0; MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- PetscInt localIdx[2] = {0, 0};
- if (rank == 0) {localIdx[0] = 0; localIdx[1] = 1;}
- else {localIdx[0] = 1; localIdx[1] = 2;}
+ PetscInt localIdx[2] = {rank, rank+1};
ISLocalToGlobalMapping rmap;
ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD, 1, 1, &rank, PETSC_COPY_VALUES, &rmap);
ISLocalToGlobalMapping cmap;
ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD, 1, 2, localIdx, PETSC_COPY_VALUES, &cmap);
Mat A;
- MatCreateIS(PETSC_COMM_WORLD, 1, PETSC_DECIDE, PETSC_DECIDE, 2, 3, rmap, cmap, &A);
+ MatCreateIS(PETSC_COMM_WORLD, 1, PETSC_DECIDE, PETSC_DECIDE, size, size+1, rmap, cmap, &A);
Mat Aloc;
if (matType == "csr") {cout << matType << endl; MatCreateSeqAIJ(PETSC_COMM_SELF, 1, 2, 2, NULL, &Aloc);}
--- a/matISCSRDenseSquare.cpp
+++ b/matISCSRDenseSquare.cpp
@@ -14,19 +14,17 @@ int main(int argc,char **argv) {
if (matType != "csr" && matType != "dense") {cout << "error: need arg = csr or dense" << endl; return 1;}
PetscInitialize(&argc, &argv, NULL, NULL);
- int size = 0; MPI_Comm_size(MPI_COMM_WORLD, &size); if (size != 2) {cout << "error: mpi != 2" << endl; return 1;}
+ int size = 0; MPI_Comm_size(MPI_COMM_WORLD, &size);
int rank = 0; MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- PetscInt localIdx[2] = {0, 0};
- if (rank == 0) {localIdx[0] = 0; localIdx[1] = 1;}
- else {localIdx[0] = 1; localIdx[1] = 2;}
+ PetscInt localIdx[2] = {rank, rank+1};
ISLocalToGlobalMapping rmap;
ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD, 1, 2, localIdx, PETSC_COPY_VALUES, &rmap);
ISLocalToGlobalMapping cmap;
ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD, 1, 2, localIdx, PETSC_COPY_VALUES, &cmap);
Mat A;
- MatCreateIS(PETSC_COMM_WORLD, 1, PETSC_DECIDE, PETSC_DECIDE, 3, 3, rmap, cmap, &A);
+ MatCreateIS(PETSC_COMM_WORLD, 1, PETSC_DECIDE, PETSC_DECIDE, size+1, size+1, rmap, cmap, &A);
Mat Aloc;
if (matType == "csr") {cout << matType << endl; MatCreateSeqAIJ(PETSC_COMM_SELF, 2, 2, 2, NULL, &Aloc);}
----- Mail original -----
> De: "Stefano Zampini" <stefano.zampini at gmail.com>
> À: "Franck Houssen" <franck.houssen at inria.fr>
> Cc: "PETSc users list" <petsc-users at mcs.anl.gov>
> Envoyé: Mardi 20 Juin 2017 13:23:27
> Objet: Re: [petsc-users] Building MatIS with dense local matrix ?
> Franck
> I tested your new example with master and it works. However, It doesn't work
> with maint. I fixed the rectangular case a while ago in master and forgot to
> add the change to maint too. Sorry for that.
> This should fix the problem with maint:
> https://bitbucket.org/petsc/petsc/commits/0ea065fb06d751599c4157d36bfe1a1b41348e0b
> Test your real case and let me know.
> If you could, it would be good to test against master too.
> Thanks,
> Stefano
> 2017-06-20 12:58 GMT+02:00 Franck Houssen < franck.houssen at inria.fr > :
> > As I said, it is often difficult to reduce the "real" problem: it turns out
> > that your fix solves the "matISCSRDenseSquare/Rect.cpp" dummy example I
> > sent, but, it's still not working in "my real" situation.
>
> > I changed a bit the "matISCSRDenseSquare/Rect.cpp" dummy example (see git
> > diff below - I just changed the point that overlaps) : the dummy example is
> > still failing
>
> > "mpirun -n 2 ./matISCSRDenseSquare.exe csr" and "mpirun -n 2
> > ./matISCSRDenseSquare.exe dense" : OK
>
> > but
>
> > "mpirun -n 2 ./matISCSRDenseRect.exe csr" and "mpirun -n 2
> > ./matISCSRDenseRect.exe dense": KO with error "Argument out of range - New
> > nonzero at (0,2) caused a malloc"
>
> > I would say, the problem (I am concerned with the "real" case) is around
> > lines 360-380 of /src/mat/impls/is/matis.c (not around 181 : this fixes a
> > valid problem, but, this problem is another one)
>
> > Franck
>
> > --- a/matISCSRDenseRect.cpp
>
> > +++ b/matISCSRDenseRect.cpp
>
> > @@ -18,7 +18,7 @@ int main(int argc,char **argv) {
>
> > int rank = 0; MPI_Comm_rank(MPI_COMM_WORLD, &rank);
>
> > PetscInt localIdx[2] = {0, 0};
>
> > - if (rank == 0) {localIdx[0] = 0; localIdx[1] = 1;}
>
> > + if (rank == 0) {localIdx[0] = 0; localIdx[1] = 2;}
>
> > else {localIdx[0] = 1; localIdx[1] = 2;}
>
> > ISLocalToGlobalMapping rmap;
>
> > ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD, 1, 1, &rank,
> > PETSC_COPY_VALUES, &rmap);
>
> > diff --git
> > a/Graphs/Franck/03.petscDDM/02.petscMailList/matISCSRDenseSquare.cpp
> > b/Graphs/Franck/03.petscDDM/02.petscMailList/matISCSRDenseSquare.cpp
>
> > index 4bc6190..4a6ea41 100644
>
> > --- a/matISCSRDenseSquare.cpp
>
> > +++ b/matISCSRDenseSquare.cpp
>
> > @@ -18,7 +18,7 @@ int main(int argc,char **argv) {
>
> > int rank = 0; MPI_Comm_rank(MPI_COMM_WORLD, &rank);
>
> > PetscInt localIdx[2] = {0, 0};
>
> > - if (rank == 0) {localIdx[0] = 0; localIdx[1] = 1;}
>
> > + if (rank == 0) {localIdx[0] = 0; localIdx[1] = 2;}
>
> > else {localIdx[0] = 1; localIdx[1] = 2;}
>
> > ISLocalToGlobalMapping rmap;
>
> > ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD, 1, 2, localIdx,
> > PETSC_COPY_VALUES, &rmap);
>
> > > De: "Stefano Zampini" < stefano.zampini at gmail.com >
> >
>
> > > À: "Franck Houssen" < franck.houssen at inria.fr >
> >
>
> > > Cc: "PETSc users list" < petsc-users at mcs.anl.gov >
> >
>
> > > Envoyé: Mardi 20 Juin 2017 00:23:24
> >
>
> > > Objet: Re: [petsc-users] Building MatIS with dense local matrix ?
> >
>
> > > It should be fixed now in maint and master
> >
>
> > > https://bitbucket.org/petsc/petsc/commits/4c8dd594d1988a0cbe282f8a37d9916f61e0c445
> >
>
> > > Thanks for reporting the problem,
> >
>
> > > Stefano
> >
>
> > > > On Jun 19, 2017, at 10:46 PM, Stefano Zampini <
> > > > stefano.zampini at gmail.com
> > > > >
> > > > wrote:
> > >
> >
>
> > > > Franck,
> > >
> >
>
> > > > Thanks. I'll get back soon with a fix.
> > >
> >
>
> > > > Stefano
> > >
> >
>
> > > > Il 19 Giu 2017 18:17, "Franck Houssen" < franck.houssen at inria.fr > ha
> > > > scritto:
> > >
> >
>
> > > > > The problem was difficult to reduce as reducing make things
> > > > > disappear...
> > > > > Luckily, I believe I got it (or at least, it looks "like" the one I
> > > > > "really"
> > > > > have...).
> > > >
> > >
> >
>
> > > > > Seems that for square matrix, it works fine for csr and dense matrix.
> > > > > But,
> > > > > If
> > > > > I am not mistaken, it does not for dense rectangular matrix (still OK
> > > > > for
> > > > > csr).
> > > >
> > >
> >
>
> > > > > matISCSRDenseSquare.cpp: 2 procs, global 3x3 matrix, each proc adds a
> > > > > 2x2
> > > > > local matrix in the global matrix.
> > > >
> > >
> >
>
> > > > > matISCSRDenseRect.cpp: 2 procs, global 2 x3 matrix, each proc adds a
> > > > > 1
> > > > > x2
> > > > > local vector in the global matrix.
> > > >
> > >
> >
>
> > > > > reminder: running debian/testing with gcc-6.3 + petsc-3.7.6
> > > >
> > >
> >
>
> > > > > Franck
> > > >
> > >
> >
>
> > > > > >> mpirun -n 2 ./matISCSRDenseSquare.exe csr; mpirun -n 2
> > > > > >> ./matISCSRDenseSquare.exe dense
> > > >
> > >
> >
>
> > > > > csr
> > > >
> > >
> >
>
> > > > > csr
> > > >
> > >
> >
>
> > > > > Mat Object: 2 MPI processes
> > > >
> > >
> >
>
> > > > > type: is
> > > >
> > >
> >
>
> > > > > Mat Object: 1 MPI processes
> > > >
> > >
> >
>
> > > > > type: seqaij
> > > >
> > >
> >
>
> > > > > row 0: (0, 1.) (1, 0.)
> > > >
> > >
> >
>
> > > > > row 1: (0, 0.) (1, 1.)
> > > >
> > >
> >
>
> > > > > Mat Object: 1 MPI processes
> > > >
> > >
> >
>
> > > > > type: seqaij
> > > >
> > >
> >
>
> > > > > row 0: (0, 1.) (1, 0.)
> > > >
> > >
> >
>
> > > > > row 1: (0, 0.) (1, 1.)
> > > >
> > >
> >
>
> > > > > dense
> > > >
> > >
> >
>
> > > > > dense
> > > >
> > >
> >
>
> > > > > Mat Object: 2 MPI processes
> > > >
> > >
> >
>
> > > > > type: is
> > > >
> > >
> >
>
> > > > > Mat Object: 1 MPI processes
> > > >
> > >
> >
>
> > > > > type: seqdense
> > > >
> > >
> >
>
> > > > > 1.0000000000000000e+00 0.0000000000000000e+00
> > > >
> > >
> >
>
> > > > > 0.0000000000000000e+00 1.0000000000000000e+00
> > > >
> > >
> >
>
> > > > > Mat Object: 1 MPI processes
> > > >
> > >
> >
>
> > > > > type: seqdense
> > > >
> > >
> >
>
> > > > > 1.0000000000000000e+00 0.0000000000000000e+00
> > > >
> > >
> >
>
> > > > > 0.0000000000000000e+00 1.0000000000000000e+00
> > > >
> > >
> >
>
> > > > > >> mpirun -n 2 ./matISCSRDenseRect.exe csr; mpirun -n 2
> > > > > >> ./matISCSRDenseRect.exe dense
> > > >
> > >
> >
>
> > > > > csr
> > > >
> > >
> >
>
> > > > > csr
> > > >
> > >
> >
>
> > > > > Mat Object: 2 MPI processes
> > > >
> > >
> >
>
> > > > > type: is
> > > >
> > >
> >
>
> > > > > Mat Object: 1 MPI processes
> > > >
> > >
> >
>
> > > > > type: seqaij
> > > >
> > >
> >
>
> > > > > row 0: (0, 1.) (1, 0.)
> > > >
> > >
> >
>
> > > > > Mat Object: 1 MPI processes
> > > >
> > >
> >
>
> > > > > type: seqaij
> > > >
> > >
> >
>
> > > > > row 0: (0, 1.) (1, 0.)
> > > >
> > >
> >
>
> > > > > dense
> > > >
> > >
> >
>
> > > > > dense
> > > >
> > >
> >
>
> > > > > [0]PETSC ERROR: --------------------- Error Message
> > > > > --------------------------------------------------------------
> > > >
> > >
> >
>
> > > > > [0]PETSC ERROR: Argument out of range
> > > >
> > >
> >
>
> > > > > [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message
> > > > > --------------------------------------------------------------
> > > >
> > >
> >
>
> > > > > [1]PETSC ERROR: Argument out of range
> > > >
> > >
> >
>
> > > > > [1]PETSC ERROR: New nonzero at (0,1) caused a malloc
> > > >
> > >
> >
>
> > > > > Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to
> > > > > turn
> > > > > off
> > > > > this check
> > > >
> > >
> >
>
> > > > > [1]PETSC ERROR: See
> > > > > http://www.mcs.anl.gov/petsc/documentation/faq.html
> > > > > for
> > > > > trouble shooting.
> > > >
> > >
> >
>
> > > > > [1]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
> > > >
> > >
> >
>
> > > > > [1]PETSC ERROR: ./matISCSRDenseRect.exe on a arch-linux2-c-debug
> > > > > named
> > > > > yoda
> > > > > by fghoussen Mon Jun 19 18:08:58 2017
> > > >
> > >
> >
>
> > > > > New nonzero at (0,1) caused a malloc
> > > >
> > >
> >
>
> > > > > Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to
> > > > > turn
> > > > > off
> > > > > this check
> > > >
> > >
> >
>
> > > > > [0]PETSC ERROR: See
> > > > > http://www.mcs.anl.gov/petsc/documentation/faq.html
> > > > > for
> > > > > trouble shooting.
> > > >
> > >
> >
>
> > > > > [0]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
> > > >
> > >
> >
>
> > > > > [1]PETSC ERROR: Configure options
> > > > > --prefix=/home/fghoussen/Documents/INRIA/petsc-3.7.6/local
> > > > > --with-mpi=1
> > > > > --with-pthread=1 --download-f2cblaslapack=yes --download-mumps=yes
> > > > > --download-scalapack=yes --download-superlu=yes
> > > > > --download-suitesparse=yes
> > > >
> > >
> >
>
> > > > > [1]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 616 in
> > > > > /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/impls/aij/mpi/mpiaij.c
> > > >
> > >
> >
>
> > > > > [1]PETSC ERROR: #2 MatSetValues() line 1190 in
> > > > > /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/interface/matrix.c
> > > >
> > >
> >
>
> > > > > [1]PETSC ERROR: #3 MatSetValuesLocal() line 2053 in
> > > > > /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/interface/matrix.c
> > > >
> > >
> >
>
> > > > > [1]PETSC ERROR: #4 MatISGetMPIXAIJ_IS() line 365 in
> > > > > /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/impls/is/matis.c
> > > >
> > >
> >
>
> > > > > [1]PETSC ERROR: #5 MatISGetMPIXAIJ() line 437 in
> > > > > /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/impls/is/matis.c
> > > >
> > >
> >
>
> > > > > [0]PETSC ERROR: ./matISCSRDenseRect.exe on a arch-linux2-c-debug
> > > > > named
> > > > > yoda
> > > > > by fghoussen Mon Jun 19 18:08:58 2017
> > > >
> > >
> >
>
> > > > > [0]PETSC ERROR: Configure options
> > > > > --prefix=/home/fghoussen/Documents/INRIA/petsc-3.7.6/local
> > > > > --with-mpi=1
> > > > > --with-pthread=1 --download-f2cblaslapack=yes --download-mumps=yes
> > > > > --download-scalapack=yes --download-superlu=yes
> > > > > --download-suitesparse=yes
> > > >
> > >
> >
>
> > > > > [0]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 582 in
> > > > > /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/impls/aij/mpi/mpiaij.c
> > > >
> > >
> >
>
> > > > > [0]PETSC ERROR: #2 MatSetValues() line 1190 in
> > > > > /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/interface/matrix.c
> > > >
> > >
> >
>
> > > > > [0]PETSC ERROR: #3 MatSetValuesLocal() line 2053 in
> > > > > /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/interface/matrix.c
> > > >
> > >
> >
>
> > > > > [0]PETSC ERROR: #4 MatISGetMPIXAIJ_IS() line 365 in
> > > > > /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/impls/is/matis.c
> > > >
> > >
> >
>
> > > > > [0]PETSC ERROR: #5 MatISGetMPIXAIJ() line 437 in
> > > > > /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/impls/is/matis.c
> > > >
> > >
> >
>
> > > > > Mat Object: 2 MPI processes
> > > >
> > >
> >
>
> > > > > type: is
> > > >
> > >
> >
>
> > > > > Mat Object: 1 MPI processes
> > > >
> > >
> >
>
> > > > > type: seqdense
> > > >
> > >
> >
>
> > > > > 1.0000000000000000e+00 0.0000000000000000e+00
> > > >
> > >
> >
>
> > > > > Mat Object: 1 MPI processes
> > > >
> > >
> >
>
> > > > > type: seqdense
> > > >
> > >
> >
>
> > > > > 1.0000000000000000e+00 0.0000000000000000e+00
> > > >
> > >
> >
>
> > > > > >> diff matISCSRDenseSquare.cpp matISCSRDenseRect.cpp
> > > >
> > >
> >
>
> > > > > 3c3
> > > >
> > >
> >
>
> > > > > < // ~> g++ -o matISCSRDenseSquare.exe matISCSRDenseSquare.cpp
> > > > > -lpetsc
> > > > > -lm;
> > > > > mpirun -n 2 matISCSRDenseSquare.exe
> > > >
> > >
> >
>
> > > > > ---
> > > >
> > >
> >
>
> > > > > > // ~> g++ -o matISCSRDenseRect.exe matISCSRDenseRect.cpp -lpetsc
> > > > > > -lm;
> > > > > > mpirun -n 2 matISCSRDenseRect.exe
> > > >
> > >
> >
>
> > > > > 24c24
> > > >
> > >
> >
>
> > > > > < ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD, 1, 2, localIdx,
> > > > > PETSC_COPY_VALUES, &rmap);
> > > >
> > >
> >
>
> > > > > ---
> > > >
> > >
> >
>
> > > > > > ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD, 1, 1, &rank,
> > > > > > PETSC_COPY_VALUES, &rmap);
> > > >
> > >
> >
>
> > > > > 29c29
> > > >
> > >
> >
>
> > > > > < MatCreateIS(PETSC_COMM_WORLD, 1, PETSC_DECIDE, PETSC_DECIDE, 3, 3,
> > > > > rmap,
> > > > > cmap, &A);
> > > >
> > >
> >
>
> > > > > ---
> > > >
> > >
> >
>
> > > > > > MatCreateIS(PETSC_COMM_WORLD, 1, PETSC_DECIDE, PETSC_DECIDE, 2, 3,
> > > > > > rmap,
> > > > > > cmap, &A);
> > > >
> > >
> >
>
> > > > > 32,33c32,33
> > > >
> > >
> >
>
> > > > > < if (matType == "csr") {cout << matType << endl;
> > > > > MatCreateSeqAIJ(PETSC_COMM_SELF, 2, 2, 2, NULL, &Aloc);}
> > > >
> > >
> >
>
> > > > > < else {cout << matType << endl; MatCreateSeqDense(PETSC_COMM_SELF,
> > > > > 2,
> > > > > 2,
> > > > > NULL, &Aloc);}
> > > >
> > >
> >
>
> > > > > ---
> > > >
> > >
> >
>
> > > > > > if (matType == "csr") {cout << matType << endl;
> > > > > > MatCreateSeqAIJ(PETSC_COMM_SELF, 1, 2, 2, NULL, &Aloc);}
> > > >
> > >
> >
>
> > > > > > else {cout << matType << endl; MatCreateSeqDense(PETSC_COMM_SELF,
> > > > > > 1,
> > > > > > 2,
> > > > > > NULL, &Aloc);}
> > > >
> > >
> >
>
> > > > > 35,36c35,36
> > > >
> > >
> >
>
> > > > > < PetscScalar localVal[4] = {1., 0., 0., 1.};
> > > >
> > >
> >
>
> > > > > < MatSetValues(Aloc, 2, localIdx, 2, localIdx, localVal, ADD_VALUES);
> > > > > //
> > > > > Add
> > > > > local 2x2 matrix
> > > >
> > >
> >
>
> > > > > ---
> > > >
> > >
> >
>
> > > > > > PetscScalar localVal[2] = {1., 0.}; PetscInt oneLocalRow = 0;
> > > >
> > >
> >
>
> > > > > > MatSetValues(Aloc, 1, &oneLocalRow, 2, localIdx, localVal,
> > > > > > ADD_VALUES);
> > > > > > //
> > > > > > Add local row
> > > >
> > >
> >
>
> > > > > > De: "Stefano Zampini" < stefano.zampini at gmail.com >
> > > > >
> > > >
> > >
> >
>
> > > > > > À: "Franck Houssen" < franck.houssen at inria.fr >
> > > > >
> > > >
> > >
> >
>
> > > > > > Cc: "PETSc users list" < petsc-users at mcs.anl.gov >
> > > > >
> > > >
> > >
> >
>
> > > > > > Envoyé: Lundi 19 Juin 2017 15:25:35
> > > > >
> > > >
> > >
> >
>
> > > > > > Objet: Re: [petsc-users] Building MatIS with dense local matrix ?
> > > > >
> > > >
> > >
> >
>
> > > > > > Can you send a minimal working example so that I can fix the code?
> > > > >
> > > >
> > >
> >
>
> > > > > > Thanks
> > > > >
> > > >
> > >
> >
>
> > > > > > Stefano
> > > > >
> > > >
> > >
> >
>
> > > > > > Il 19 Giu 2017 15:20, "Franck Houssen" < franck.houssen at inria.fr >
> > > > > > ha
> > > > > > scritto:
> > > > >
> > > >
> > >
> >
>
> > > > > > > Hi,
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > I try to call MatISGetMPIXAIJ on a MatIS (A) that has been feed
> > > > > > > locally
> > > > > > > by
> > > > > > > sequential (Aloc) dense matrix.
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > Seems this ends up with this error: [0]PETSC ERROR: New nonzero
> > > > > > > at
> > > > > > > (0,1)
> > > > > > > caused a malloc. Is this a known error / limitation ? (not
> > > > > > > supposed
> > > > > > > to
> > > > > > > work
> > > > > > > with dense matrix ?)
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > This (pseudo code) works fine:
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > MatCreateIS(..., A)
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > MatCreateSeqAIJ(..., Aloc)
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > MatISSetLocalMat(pcA, pcALoc)
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > MatISGetMPIXAIJ(A, ...) // OK !
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > When I try to replace MatCreateSeqAIJ(..., Aloc) with
> > > > > > > MatCreateSeqDense(...,
> > > > > > > Aloc), it does no more work.
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > Franck
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > PS: running debian/testing with gcc-6.3 + petsc-3.7.6
> > > > > >
> > > > >
> > > >
> > >
> >
>
> --
> Stefano
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20170620/6f3598c2/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: matISCSRDenseRect.cpp
Type: text/x-c++src
Size: 1730 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20170620/6f3598c2/attachment-0002.cpp>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: matISCSRDenseSquare.cpp
Type: text/x-c++src
Size: 1726 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20170620/6f3598c2/attachment-0003.cpp>
More information about the petsc-users
mailing list