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#include "assign_blast_scores.h"
#include <petscmat.h>
#include <stdio.h>
void
assign_blast_scores (hid_t file_id)
{
/*
* Create a sparse matrix for the pairwise protein BLAST scores.
*
* 138,769 proteins x 138,769 proteins = 19,256,835,361 pairs. At 8
* bytes (double) per pair this will require 154.1 GB of memory to
* hold the full structure. This is available on the compute nodes
* of Cobalt however use of a sparse matrix should reduce this size
* dramatically.
*/
// http://www.netlib.org/blas/blast-forum/blas_sparse_proto.h
// blas_sparse_matrix M = BLAS_duscr_begin (138769, 138769);
Mat M;
MatCreateSeqAIJ (PETSC_COMM_SELF, 138769, 138769, 50, NULL, &M);
MatSetValue (M, 12, 8, 12.8, INSERT_VALUES);
MatAssemblyBegin (M, MAT_FINAL_ASSEMBLY);
MatAssemblyEnd (M, MAT_FINAL_ASSEMBLY);
/*
* Write the contents of the matrix to a HDF5 file.
*/
PetscViewer viewer;
// PetscErrorCode err =
// PetscViewerHDF5Open (PETSC_COMM_WORLD, "sparse.h5", FILE_MODE_WRITE, &viewer);
PetscErrorCode err =
PetscViewerBinaryOpen (PETSC_COMM_WORLD,
"sparse.petsc",
FILE_MODE_WRITE,
&viewer);
MatView (M, viewer);
PetscViewerDestroy (viewer);
MatDestroy (M);
return;
}
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