-rw-r--r-- | configure.ac | 62 | ||||
-rw-r--r-- | doc/build-cobalt.txt | 24 | ||||
-rw-r--r-- | src/Makefile.am | 6 | ||||
-rw-r--r-- | src/assign/assign_blast_scores.c | 27 | ||||
-rw-r--r-- | src/assign/assign_blast_scores.h | 12 | ||||
-rw-r--r-- | src/updator.c | 20 |
6 files changed, 127 insertions, 24 deletions
diff --git a/src/assign/assign_blast_scores.c b/src/assign/assign_blast_scores.c new file mode 100644 index 0000000..1cd491a --- a/dev/null +++ b/src/assign/assign_blast_scores.c @@ -0,0 +1,27 @@ +#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); + + MatDestroy (M); + + return; +} |