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;
+}