$Name: fa35_03_06 $ - $Id: readme.mpi_3.3,v 1.6 2007/06/29 20:23:58 wrp Exp $ 20-August-2001 This file is obsolete - see readme.v34t0, readme.v33t0, and readme.pvm_3.4 for more up-to-date information. With version 3.4, the MPI programs are mp34comp*, mu34comp*, etc. ================ 20 January 2000 This distribution includes the first full-function MPI implementation of the libary-vs-library comparison programs. The following programs are available: Programs to produce conventional scores and alignments: mp3compfa protein vs protein, DNA vs DNA mp3compsw protein vs protein, DNA vs DNA mp3compfx/ DNA vs protein mp3comptfx/y protein vs DNA Programs to summarize the effectiveness of a search (require super-family-labeled databases): ms3compfa protein vs protein, DNA vs DNA ms3compsw protein vs protein, DNA vs DNA ms3compfx/ DNA vs protein ms3comptfx/y protein vs DNA Programs to report the scores and alignments of the highest scoring unrelated sequence (require super-family-labeled databases). These programs are used to evaluate the super-family labeling. mu3compfa protein vs protein, DNA vs DNA mu3compsw protein vs protein, DNA vs DNA mucompfx/ DNA vs protein mu3comptfx/y protein vs DNA Note that the current parallel implementations distribute the second database among 'N' parallel workers by approximately dividing the database into 'N' parts by seeking into the middle of the database and finding the next entry. This strategy fails when the database is a single long sequence (the first worker gets the entire database, the others get nothing). This version has been tested using the MPICH implementation of MPI, which is available from: ftp://ftp.mcs.anl.gov/mpi See readme.pvm_3.3 for other information about the development of these programs. Both the PVM (pv3compfa, etc.) and MPI (mp3compfa, etc.) sets of programs use the same sets of source files; differences in the two implementations are specified with #define PVM_SRC and #define MPI_SRC.
