petsc-master 2014-12-24
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MatSeqAIJSetPreallocation

For good matrix assembly performance the user should preallocate the matrix storage by setting the parameter nz (or the array nnz). By setting these parameters accurately, performance during matrix assembly can be increased by more than a factor of 50.

Synopsis

#include "petscmat.h" 
PetscErrorCode  MatSeqAIJSetPreallocation(Mat B,PetscInt nz,const PetscInt nnz[])
Collective on MPI_Comm

Input Parameters

B - The matrix
nz - number of nonzeros per row (same for all rows)
nnz - array containing the number of nonzeros in the various rows (possibly different for each row) or NULL

Notes

If nnz is given then nz is ignored

The AIJ format (also called the Yale sparse matrix format or compressed row storage), is fully compatible with standard Fortran 77 storage. That is, the stored row and column indices can begin at either one (as in Fortran) or zero. See the users' manual for details.

Specify the preallocated storage with either nz or nnz (not both). Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory allocation. For large problems you MUST preallocate memory or you will get TERRIBLE performance, see the users' manual chapter on matrices.

You can call MatGetInfo() to get information on how effective the preallocation was; for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; You can also run with the option -info and look for messages with the string malloc in them to see if additional memory allocation was needed.

Developers: Use nz of MAT_SKIP_ALLOCATION to not allocate any space for the matrix entries or columns indices

By default, this format uses inodes (identical nodes) when possible, to improve numerical efficiency of matrix-vector products and solves. We search for consecutive rows with the same nonzero structure, thereby reusing matrix information to achieve increased efficiency.

Options Database Keys

-mat_no_inode - Do not use inodes
-mat_inode_limit <limit> - Sets inode limit (max limit=5)
-mat_aij_oneindex - Internally use indexing starting at 1 rather than 0. Note that when calling MatSetValues(), the user still MUST index entries starting at 0!

See Also

MatCreate(), MatCreateAIJ(), MatSetValues(), MatSeqAIJSetColumnIndices(), MatCreateSeqAIJWithArrays(), MatGetInfo()

Level:intermediate
Location:
src/mat/impls/aij/seq/aij.c
Index of all Mat routines
Table of Contents for all manual pages
Index of all manual pages

Examples

src/mat/examples/tutorials/ex15.c.html
src/mat/examples/tutorials/ex16.c.html
src/mat/examples/tutorials/ex17.c.html
src/ksp/ksp/examples/tutorials/ex2.c.html
src/ksp/ksp/examples/tutorials/ex3.c.html
src/ksp/ksp/examples/tutorials/ex4.c.html
src/ksp/ksp/examples/tutorials/ex7.c.html
src/ksp/ksp/examples/tutorials/ex18.c.html
src/ksp/ksp/examples/tutorials/ex52.c.html
src/ksp/ksp/examples/tutorials/ex55.c.html
src/ksp/ksp/examples/tutorials/ex56.c.html