Hello, I have uploaded files (in the patches section of http://sourceforge.net/projects/mpiblast/) that implement the following changes to mpiformatdb and mpiblast: mpiformatdb: * Fixed fragment size calculation to increase the size of the "runt" (i.e. last) fragment. By giving each worker process approximately the same amount of work to do, load balancing is improved. * Changed the definition of the command line argument "-N X" so that, when possible, X fragments are created and numbered from [0, ..., X - 1]. This addresses a common complaint on the bioclusters list. * Added a command line argument "--decomp" that will display all possible fragment decompositions and suggest decompositions that maximize the relative size of the runt fragment (to improve load balancing). Due to the blast requirement restricting fragment sizes to whole integer multiples of a megabyte, not all fragment decompositions are (a) allowed and (b) equally efficient. * Changed the return value to be the actual number of fragments created (useful for automation). mpiblast: * Improved memory management. * Added a new function, sendResults(), that returns the blast results from a worker to the master using less memory than sendFile(). This allows the use of larger queries (i.e. querying the entire y. pestis genome against the nr database can now be completed on a master node with 2 GB of ram memory. Before this change, it could not be completed without exhausting all available memory). Rewrote the receiveResults() function to work with the new sendResults() function. Comments and feedback are welcome. Regards, Jason Gans Biosciences Division, B-1 Los Alamos National Laboratory