Please reply to the list as well.
Instead of creating a new matrix, you should cast system.matrix to a
PetscMatrix and then call MatSetOption on that.
David
On Tue, Oct 6, 2015 at 10:06 AM, Вася Бубликов <gream...@gmail.com> wrote:
> David
>
> Thank you for your answer. Here is a short program to try out your first
> suggestion:
>
> #include <iostream>
> #include <vector>
> #include <set>
> #include <algorithm>
> #include <fstream>
> #include <string>
> #include <ctime>
> // libmesh includes
> #include "libmesh/libmesh.h"
> #include "libmesh/mesh.h"
> #include "libmesh/linear_implicit_system.h"
> #include "libmesh/equation_systems.h"
> #include "libmesh/fe.h"
> #include "libmesh/quadrature_trap.h"
> #include "libmesh/dof_map.h"
> #include "libmesh/sparse_matrix.h"
> #include "libmesh/petsc_matrix.h"
> #include "libmesh/numeric_vector.h"
> #include "libmesh/dense_matrix.h"
> #include "libmesh/dense_submatrix.h"
> #include "libmesh/dense_vector.h"
> #include "libmesh/dense_subvector.h"
> #include "libmesh/perf_log.h"
> #include "libmesh/elem.h"
> #include "libmesh/boundary_info.h"
> #include "libmesh/string_to_enum.h"
> #include "libmesh/getpot.h"
> #include "libmesh/vtk_io.h"
> #include "libmesh/mesh_data.h"
> #include "libmesh/mesh_base.h"
>
> using namespace libMesh;
>
> int main (int argc, char** argv)
> {
> LibMeshInit init (argc, argv);
> SerialMesh mesh(init.comm());
> mesh.read("SquareWithCircle.unv");
> mesh.print_info();
> EquationSystems equation_systems (mesh);
> LinearImplicitSystem& system =
> equation_systems.add_system<LinearImplicitSystem> ("Elasticity");
> PetscMatrix<Number> Matrix(init.comm());
> std::cout << "Enable non neighbours interactions" << std::endl;
> MatSetOption( Matrix.mat(), MAT_NEW_NONZERO_ALLOCATION_ERR,
> PETSC_FALSE);
> unsigned int u_var = system.add_variable("u", FIRST, LAGRANGE); //
> displacement X
> unsigned int v_var = system.add_variable("v", FIRST, LAGRANGE); //
> displacement Y
> equation_systems.init();
> equation_systems.print_info();
> Matrix.attach_dof_map(system.get_dof_map());
> std::cout << "Initialize matrix" << std::endl;
> Matrix.init();
> std::cout << "Make my matrix the system matrix" << std::endl;
> system.matrix = &Matrix;
> return 0;
> }
>
>
> it compiles fine but then I run it MatSetOption command causes an error:
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Corrupt argument:
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> [0]PETSC ERROR: Invalid Pointer to Object: Parameter # 1
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.6.1, Jul, 22, 2015
> [0]PETSC ERROR: ./error.o on a arch-linux-c-opt named izmailovo by gream
> Tue Oct 6 17:01:25 2015
> [0]PETSC ERROR: Configure options --prefix=/opt/petsc/linux-c-opt
> --PETSC_ARCH=arch-linux-c-opt --with-shared-libraries=1 --COPTFLAGS=-O3
> --CXXOPTFLAGS=-O3 --with-mumps=1 --with-hdf5=1 --with-scalapack=1
> --with-suitesparse=1 --with-metis=1 --with-parmetis=1 --with-ptscotch=1
> --with-ptscotch-lib="[libesmumps.so,libptscotch.so,libptscotcherr.so,libscotch.so,libscotcherr.so,libbz2.so]"
> --with-ptscotch-include=/usr/include/scotch --with-superlu=1
> --with-superlu-lib=-lsuperlu --with-superlu-include=/usr/include/superlu
> --with-ml=1
> [0]PETSC ERROR: #1 MatSetOption() line 5261 in
> /tmp/yaourt-tmp-gream/aur-petsc/src/petsc-3.6.1/src/mat/interface/matrix.c
>
> Roman
>
> 2015-10-06 13:20 GMT+03:00 David Knezevic <david.kneze...@akselos.com>:
>
>> This is a PETSc error that you're hitting because you're adding new
>> non-zeros in the matrix. PETSc tries to help you by throwing an error if
>> you do this, because allocating new non-zeros (outside the specified
>> sparsity pattern) can slow down your program a lot.
>>
>> The easy fix is indicated in the PETSc error message:
>> "Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to turn
>> off this check"
>> To do this, you need to cast your matrix to a PetscMatrix, then do
>> petsc_matrix->mat() to get the PETSc Mat that you can pass to MatSetOption.
>>
>> The more involved fix is to augment your sparsity pattern (e.g. see
>> miscellaneous_ex9).
>>
>> David
>>
>>
>>
>> On Tue, Oct 6, 2015 at 6:13 AM, Вася Бубликов <gream...@gmail.com> wrote:
>>
>>> Dear Sirs,
>>>
>>> I'm trying to make Libmesh work with a simple linear elasticity problem
>>> using linear systems example 4 as an example. I need to force the top
>>> boundary remain flat, i.e. all normal displacements are of the same value
>>> to be computed.
>>> To obtain this, for example to make the displacements for DOFs
>>> i1,i2,i3..in
>>> the same as for the DOF j, I add penalty (1e10) to K(in,in) and subtract
>>> it
>>> from K(in,j) meaning to add 1e10*(U_in - U_j) = 0 to the in'th equation
>>> in the assembly function. But as soon as in and j are on different finite
>>> elements I get the same error no matter which particular c++ function I
>>> use
>>> (system.matrix->add(i,j,value) system.matrix->add_matrix(DenseMatrix)
>>> or system.matrix->add(SparseMatrix) ). I would be very mush obliged if
>>> you
>>> helped me.
>>>
>>> Kind regards,
>>> Roman Khudobin
>>> Research Assistant ICHPH RAS
>>>
>>> [0]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> [0]PETSC ERROR: Argument out of range
>>> [0]PETSC ERROR: New nonzero at (17,47) 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 3.6.1, Jul, 22, 2015
>>> [0]PETSC ERROR: ./constrain.o on a arch-linux-c-opt named izmailovo by
>>> gream Tue Oct 6 12:55:21 2015
>>> [0]PETSC ERROR: Configure options --prefix=/opt/petsc/linux-c-opt
>>> --PETSC_ARCH=arch-linux-c-opt --with-shared-libraries=1 --COPTFLAGS=-O3
>>> --CXXOPTFLAGS=-O3 --with-mumps=1 --with-hdf5=1 --with-scalapack=1
>>> --with-suitesparse=1 --with-metis=1 --with-parmetis=1 --with-ptscotch=1
>>>
>>> --with-ptscotch-lib="[libesmumps.so,libptscotch.so,libptscotcherr.so,libscotch.so,libscotcherr.so,libbz2.so]"
>>> --with-ptscotch-include=/usr/include/scotch --with-superlu=1
>>> --with-superlu-lib=-lsuperlu --with-superlu-include=/usr/include/superlu
>>> --with-ml=1
>>> [0]PETSC ERROR: #1 MatSetValues_SeqAIJ() line 485 in
>>>
>>> /tmp/yaourt-tmp-gream/aur-petsc/src/petsc-3.6.1/src/mat/impls/aij/seq/aij.c
>>> [0]PETSC ERROR: #2 MatSetValues() line 1173 in
>>>
>>> /tmp/yaourt-tmp-gream/aur-petsc/src/petsc-3.6.1/src/mat/interface/matrix.c
>>>
>>> --------------------------------------------------------------------------
>>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>>> with errorcode 1.
>>>
>>> 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.
>>>
>>> --------------------------------------------------------------------------
>>>
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Libmesh-users mailing list
>>> Libmesh-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>
>>>
>>
>
------------------------------------------------------------------------------
_______________________________________________
Libmesh-users mailing list
Libmesh-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/libmesh-users
