
  $Id: readme.mpi_3.3 5 2008-04-28 13:12:42Z pearson $

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This file is obsolete - see readme.v34t0, readme.v33t0, and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.

