-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 @@ | |||
1 | #include "assign_blast_scores.h" | ||
2 | #include <petscmat.h> | ||
3 | #include <stdio.h> | ||
4 | |||
5 | void | ||
6 | assign_blast_scores (hid_t file_id) | ||
7 | { | ||
8 | /* | ||
9 | * Create a sparse matrix for the pairwise protein BLAST scores. | ||
10 | * | ||
11 | * 138,769 proteins x 138,769 proteins = 19,256,835,361 pairs. At 8 | ||
12 | * bytes (double) per pair this will require 154.1 GB of memory to | ||
13 | * hold the full structure. This is available on the compute nodes | ||
14 | * of Cobalt however use of a sparse matrix should reduce this size | ||
15 | * dramatically. | ||
16 | */ | ||
17 | |||
18 | // http://www.netlib.org/blas/blast-forum/blas_sparse_proto.h | ||
19 | // blas_sparse_matrix M = BLAS_duscr_begin (138769, 138769); | ||
20 | |||
21 | Mat M; | ||
22 | MatCreateSeqAIJ (PETSC_COMM_SELF, 138769, 138769, 50, NULL, &M); | ||
23 | |||
24 | MatDestroy (M); | ||
25 | |||
26 | return; | ||
27 | } | ||