Re: [petsc-users] Set matrix column to vector
On 02/09/14 09:41, Florian Lindner wrote: > Am 01.09.2014 16:11, schrieb Matthew Knepley: > >> I recommend running using the debugger so you can get a stack trace, and >> perhaps see >> exactly what the problem is. You can also run under valgrind as the error >> says. > > This of course I tried, but had no real success. It crashes in > ISLocalToGlobalMappingApply, on the first line: PetscInt i,bs = > mapping->bs,Nmax = bs*mapping->n; > > It crashes only when using MatSetValuesLocal, not when using MatSetValues. > > I've created an example that compiles just fine: > http://pastebin.com/iEkLK9DZ You never create a local to global mapping and set it on the matrix, so that mapping is NULL inside ISLocalToGlobalMappingApply. You need to do something like: ISLocalToGlobalMappingCreate(..., &rmapping); ISLocalToGlobalMappingCreate(..., &cmapping); MatSetLocalToGlobalMapping(mat, rmapping, cmapping); Then you can use MatSetValuesLocal. Cheers, Lawrence
Re: [petsc-users] Set matrix column to vector
Am 01.09.2014 16:11, schrieb Matthew Knepley:
I recommend running using the debugger so you can get a stack trace,
and
perhaps see
exactly what the problem is. You can also run under valgrind as the
error
says.
This of course I tried, but had no real success. It crashes in
ISLocalToGlobalMappingApply, on the first line: PetscInt i,bs =
mapping->bs,Nmax = bs*mapping->n;
It crashes only when using MatSetValuesLocal, not when using
MatSetValues.
I've created an example that compiles just fine:
http://pastebin.com/iEkLK9DZ
Sorry, I really got no idea what could be the problem her.
Thx,
Florian
#include
#include "petscmat.h"
#include "petscviewer.h"
// Compiling with: mpic++ -g3 -Wall -I ~/software/petsc/include -I
~/software/petsc/arch-linux2-c-debug/include -L
~/software/petsc/arch-linux2-c-debug/lib -lpetsc test.cpp
// Running without mpirun.
int main(int argc, char **args)
{
PetscInitialize(&argc, &args, "", NULL);
PetscErrorCode ierr = 0;
int num_rows = 10;
Mat matrix;
Vec vector;
// Create dense matrix, but code should work for sparse, too (I hope).
ierr = MatCreateDense(PETSC_COMM_WORLD, PETSC_DECIDE, PETSC_DECIDE,
num_rows, 4, NULL, &matrix); CHKERRQ(ierr);
ierr = MatAssemblyBegin(matrix, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = MatAssemblyEnd(matrix, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD, &vector); CHKERRQ(ierr);
ierr = VecSetSizes(vector, PETSC_DECIDE, num_rows); CHKERRQ(ierr);
ierr = VecSetFromOptions(vector); CHKERRQ(ierr);
// Init vector with 0, 1, ... , num_rows-1
PetscScalar *a;
PetscInt range_start, range_end, pos = 0;
VecGetOwnershipRange(vector, &range_start, &range_end);
ierr = VecGetArray(vector, &a); CHKERRQ(ierr);
for (PetscInt i = range_start; i < range_end; i++) {
a[pos] = pos + range_start;
pos++;
}
VecRestoreArray(vector, &a);
// VecAssemblyBegin(vector); VecAssemblyEnd(vector); I don't think
it's needed here, changes nothing.
ierr = VecView(vector, PETSC_VIEWER_STDOUT_WORLD); CHKERRQ(ierr);
PetscInt irow[num_rows];
const PetscInt col = 2;
const PetscScalar *vec;
for (int i = 0; i < num_rows; i++) {
irow[i] = i;
}
ierr = VecGetArrayRead(vector, &vec); CHKERRQ(ierr);
// MatSetValuesLocal(Mat mat,PetscInt nrow,const PetscInt
irow[],PetscInt ncol,const PetscInt icol[],const PetscScalar
y[],InsertMode addv)
ierr = MatSetValuesLocal(matrix, num_rows, irow, 1, &col, vec,
INSERT_VALUES); CHKERRQ(ierr);
// Works fine with MatSetValues
ierr = VecRestoreArrayRead(vector, &vec); CHKERRQ(ierr);
ierr = MatAssemblyBegin(matrix, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = MatAssemblyEnd(matrix, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = MatView(matrix, PETSC_VIEWER_STDOUT_WORLD); CHKERRQ(ierr);
PetscFinalize();
return 0;
}
Re: [petsc-users] Set matrix column to vector
On Mon, Sep 1, 2014 at 8:44 AM, Florian Lindner wrote:
> Am 01.09.2014 12:45, schrieb Matthew Knepley:
>
>> On Mon, Sep 1, 2014 at 4:10 AM, Florian Lindner
>> wrote:
>>
>> Hello,
>>>
>>> I want to set the entire column of a N x M matrix to a N vector. What is
>>> the best way to do that?
>>>
>>> My first guess would be to VecGetArray and use that array for
>>> MatSetValuesLocal with nrow = VecGetLocalSize. What is the best to say
>>> MatSetValuesLocal that I want to set all rows continuesly (same like
>>> passing irow = [0, 1, ..., VecGetLocalSize-1]?
>>>
>>> Any better way?
>>>
>>>
>> You are assuming dense storage above, so you can use
>>
>>
>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/
>> MatDenseGetArray.html+
>>
>
> How can you tell that I'm assuming dense storage. My matrix is actually
> dense, but I try to write my code as generic as possible (being a very
> petsc newbie). I have that code which crashes at the moment:
>
I recommend running using the debugger so you can get a stack trace, and
perhaps see
exactly what the problem is. You can also run under valgrind as the error
says.
Matt
> void set_column_vector(Vector v, int col)
> {
> PetscErrorCode ierr = 0;
> const PetscScalar *vec;
> PetscInt size, mat_rows, mat_cols;
> VecGetLocalSize(v.vector, &size);
> cout << "Vector Size = " << size << endl;
>
> MatGetSize(matrix, &mat_rows, &mat_cols);
> cout << "Matrix Rows = " << mat_rows << " Columns = " << mat_cols
> << endl;
> PetscInt irow[size];
> for (int i = 0; i < size; i++) {
> irow[i] = i;
> }
>
> ierr = VecGetArrayRead(v.vector, &vec); CHKERRV(ierr);
> ierr = MatSetValuesLocal(matrix, size-1, irow, 1, &col, vec,
> INSERT_VALUES); CHKERRV(ierr);
> ierr = VecRestoreArrayRead(v.vector, &vec); CHKERRV(ierr);
> ierr = MatAssemblyBegin(matrix, MAT_FINAL_ASSEMBLY); CHKERRV(ierr);
> ierr = MatAssemblyEnd(matrix, MAT_FINAL_ASSEMBLY); CHKERRV(ierr);
> }
>
> v.vector is a Vec, matrix is a Mat. col = 1. It's compiled with mpic++,
> but started without, just ./a.out. Output is:
>
> Vector Size = 20
> Matrix Rows = 20 Columns = 5
> [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: likely location of problem given in stack below
> [0]PETSC ERROR: - Stack Frames
>
> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> [0]PETSC ERROR: INSTEAD the line number of the start of the function
> [0]PETSC ERROR: is given.
> [0]PETSC ERROR: [0] MatSetValuesLocal line 1950
> /home/florian/software/petsc/src/mat/interface/matrix.c
> [0]PETSC ERROR: - Error Message
> --
> [0]PETSC ERROR: Signal received
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.5.1, unknown
> [0]PETSC ERROR: ./a.out on a arch-linux2-c-debug named asaru by florian
> Mon Sep 1 15:37:32 2014
> [0]PETSC ERROR: Configure options --with-c2html=0
> [0]PETSC ERROR: #1 User provided function() line 0 in unknown file
> --
> 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.
> --
>
>
> Any idea what the problem is?
>
> Thanks!
> Florian
>
--
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
Re: [petsc-users] Set matrix column to vector
Am 01.09.2014 15:44, schrieb Florian Lindner:
Am 01.09.2014 12:45, schrieb Matthew Knepley:
On Mon, Sep 1, 2014 at 4:10 AM, Florian Lindner
wrote:
Hello,
I want to set the entire column of a N x M matrix to a N vector. What
is
the best way to do that?
My first guess would be to VecGetArray and use that array for
MatSetValuesLocal with nrow = VecGetLocalSize. What is the best to
say
MatSetValuesLocal that I want to set all rows continuesly (same like
passing irow = [0, 1, ..., VecGetLocalSize-1]?
Any better way?
You are assuming dense storage above, so you can use
http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatDenseGetArray.html+
How can you tell that I'm assuming dense storage. My matrix is
actually dense, but I try to write my code as generic as possible
(being a very petsc newbie). I have that code which crashes at the
moment:
void set_column_vector(Vector v, int col)
{
PetscErrorCode ierr = 0;
const PetscScalar *vec;
PetscInt size, mat_rows, mat_cols;
VecGetLocalSize(v.vector, &size);
cout << "Vector Size = " << size << endl;
MatGetSize(matrix, &mat_rows, &mat_cols);
cout << "Matrix Rows = " << mat_rows << " Columns = " <<
mat_cols << endl;
PetscInt irow[size];
for (int i = 0; i < size; i++) {
irow[i] = i;
}
ierr = VecGetArrayRead(v.vector, &vec); CHKERRV(ierr);
ierr = MatSetValuesLocal(matrix, size-1, irow, 1, &col, vec,
INSERT_VALUES); CHKERRV(ierr);
Correction:
ierr = MatSetValuesLocal(matrix, size, irow, 1, &col, vec,
INSERT_VALUES);
size-1 was just one of my debugging experiments.
ierr = VecRestoreArrayRead(v.vector, &vec); CHKERRV(ierr);
ierr = MatAssemblyBegin(matrix, MAT_FINAL_ASSEMBLY);
CHKERRV(ierr);
ierr = MatAssemblyEnd(matrix, MAT_FINAL_ASSEMBLY); CHKERRV(ierr);
}
v.vector is a Vec, matrix is a Mat. col = 1. It's compiled with
mpic++, but started without, just ./a.out. Output is:
Vector Size = 20
Matrix Rows = 20 Columns = 5
[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: likely location of problem given in stack below
[0]PETSC ERROR: - Stack Frames
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
available,
[0]PETSC ERROR: INSTEAD the line number of the start of the
function
[0]PETSC ERROR: is given.
[0]PETSC ERROR: [0] MatSetValuesLocal line 1950
/home/florian/software/petsc/src/mat/interface/matrix.c
[0]PETSC ERROR: - Error Message
--
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See
http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
shooting.
[0]PETSC ERROR: Petsc Release Version 3.5.1, unknown
[0]PETSC ERROR: ./a.out on a arch-linux2-c-debug named asaru by
florian Mon Sep 1 15:37:32 2014
[0]PETSC ERROR: Configure options --with-c2html=0
[0]PETSC ERROR: #1 User provided function() line 0 in unknown file
--
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.
--
Any idea what the problem is?
Thanks!
Florian
Re: [petsc-users] Set matrix column to vector
Am 01.09.2014 12:45, schrieb Matthew Knepley:
On Mon, Sep 1, 2014 at 4:10 AM, Florian Lindner
wrote:
Hello,
I want to set the entire column of a N x M matrix to a N vector. What
is
the best way to do that?
My first guess would be to VecGetArray and use that array for
MatSetValuesLocal with nrow = VecGetLocalSize. What is the best to say
MatSetValuesLocal that I want to set all rows continuesly (same like
passing irow = [0, 1, ..., VecGetLocalSize-1]?
Any better way?
You are assuming dense storage above, so you can use
http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatDenseGetArray.html+
How can you tell that I'm assuming dense storage. My matrix is actually
dense, but I try to write my code as generic as possible (being a very
petsc newbie). I have that code which crashes at the moment:
void set_column_vector(Vector v, int col)
{
PetscErrorCode ierr = 0;
const PetscScalar *vec;
PetscInt size, mat_rows, mat_cols;
VecGetLocalSize(v.vector, &size);
cout << "Vector Size = " << size << endl;
MatGetSize(matrix, &mat_rows, &mat_cols);
cout << "Matrix Rows = " << mat_rows << " Columns = " << mat_cols
<< endl;
PetscInt irow[size];
for (int i = 0; i < size; i++) {
irow[i] = i;
}
ierr = VecGetArrayRead(v.vector, &vec); CHKERRV(ierr);
ierr = MatSetValuesLocal(matrix, size-1, irow, 1, &col, vec,
INSERT_VALUES); CHKERRV(ierr);
ierr = VecRestoreArrayRead(v.vector, &vec); CHKERRV(ierr);
ierr = MatAssemblyBegin(matrix, MAT_FINAL_ASSEMBLY);
CHKERRV(ierr);
ierr = MatAssemblyEnd(matrix, MAT_FINAL_ASSEMBLY); CHKERRV(ierr);
}
v.vector is a Vec, matrix is a Mat. col = 1. It's compiled with mpic++,
but started without, just ./a.out. Output is:
Vector Size = 20
Matrix Rows = 20 Columns = 5
[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: likely location of problem given in stack below
[0]PETSC ERROR: - Stack Frames
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
available,
[0]PETSC ERROR: INSTEAD the line number of the start of the
function
[0]PETSC ERROR: is given.
[0]PETSC ERROR: [0] MatSetValuesLocal line 1950
/home/florian/software/petsc/src/mat/interface/matrix.c
[0]PETSC ERROR: - Error Message
--
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.5.1, unknown
[0]PETSC ERROR: ./a.out on a arch-linux2-c-debug named asaru by florian
Mon Sep 1 15:37:32 2014
[0]PETSC ERROR: Configure options --with-c2html=0
[0]PETSC ERROR: #1 User provided function() line 0 in unknown file
--
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.
--
Any idea what the problem is?
Thanks!
Florian
Re: [petsc-users] Set matrix column to vector
On Mon, Sep 1, 2014 at 4:10 AM, Florian Lindner wrote: > Hello, > > I want to set the entire column of a N x M matrix to a N vector. What is > the best way to do that? > > My first guess would be to VecGetArray and use that array for > MatSetValuesLocal with nrow = VecGetLocalSize. What is the best to say > MatSetValuesLocal that I want to set all rows continuesly (same like > passing irow = [0, 1, ..., VecGetLocalSize-1]? > > Any better way? > You are assuming dense storage above, so you can use http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatDenseGetArray.html Matt > Thanks, > Florian > -- 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
[petsc-users] Set matrix column to vector
Hello, I want to set the entire column of a N x M matrix to a N vector. What is the best way to do that? My first guess would be to VecGetArray and use that array for MatSetValuesLocal with nrow = VecGetLocalSize. What is the best to say MatSetValuesLocal that I want to set all rows continuesly (same like passing irow = [0, 1, ..., VecGetLocalSize-1]? Any better way? Thanks, Florian
