On 14-Nov-03, Malay Kumar Basu wrote: > Hello Gurus: > > Here is my cluster config: > > Master - cpu 2 Xeon with hyperthreading 2 GB RAM > 4 x nodes each - cpu 1 P4 hyperthreading 1 GB RAM > > SGE recognizes total 12 cpus. > > When hyperthreading on the whole setup can have 12 cpus, otherwise 6. > What should be the optimal BLAST database fragments for mpiBLAST? As I understand it, you won't get superlinear speedup until the fragments are small enough to fit in L2 cache, and that's only practical if you have a very large number of nodes, and a very large set of queries to run through it. Otherwise, I'd set the size so that the chunk sits nicely in RAM and there's still room for the dynamic expansion that BLAST will need - something like 512MB chunks (or total_db_size/6 if that's smaller). But then we don't use mpiBLAST much here at all, so you might get a much better answer from someone more experienced than me. Tim -- Dr Tim Cutts Informatics Systems Group Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK