The need for (vector) speed.

A commenter asked yesterday about support for Sun SPARC VIS instructions in HMMER3, and I accidentally deleted the comment in an enthusiastic burst of spam-purging. Have now upgraded WordPress and turned on the akismet spam filter; will see if that helps.

Anyway, in penance for my poor comment moderation: a description of HMMER3’s use of SIMD vector instructions, and a bit of a road map for going forward with support for vector instruction sets beyond Intel/AMD SSE instructions.

Continue reading →