+++ /dev/null
-
- $Name: fa_34_26_5 $ - $Id: readme.pvm_3.4,v 1.3 2001/09/17 21:18:19 wrp Exp $
-
-
-20-August-2001
-
-The pvm/mpi complib programs have been substantially updated with
-release 3.4. See readme.v34t0 for more information. With version
-3.4, the MPI programs are mp34comp*, mu34comp*, etc.
-
-A major effect of this change is to disable automatic sequence type
-(protein/DNA) recognition with pv34compfa/mp34compfa. By default,
-protein libraries are assumed. Thus, pv34compfa/mp34compfa require
-the "-n" command line option when running pv34compfa/mp34compfa on DNA
-sequence libraries. This issue does not occur with the other
-programs, which will recognize the appropriate sequence type, because
-it is determined by the program (e.g. pv34compfx requires
-DNA:protein).
-
-================
-pv4comp* - July, August, 2000
-
-As noted in readme.pvm_3.3 - the major problem that users have had
-with the PVM/MPI version of the programs is in reading database files
-on the nodes. All previous versions of the program (pvcompfa,
-pv3compfa, etc) had the nodes read the databases in parallel. Thus,
-the database file had to be visible to the nodes, typically through
-NFS on modern clusters of workstations.
-
-This strategy caused some problems. It did not work on beowulf-type
-systems, where most of the nodes are in an isolated local network and
-do not have NFS access to the outside world. And it made it
-complicated to read more than one database file. Because specialized
-functions were used, the nodes could not read the full set of library
-file formats available to the other fasta programs.
-
-These problems have been addressed by significantly changing the the
-way the pv4comp*/mp4comp* programs read the second "reference"
-library. With these versions, both databases, but specifically the
-reference library, are read by a manager process. The manager process
-then sends the sequences to the workers. This solves problems with
-NFS reads from the workers (they don't do any), and uses exactly the
-same functions as the other fasta programs, so the full set of
-database formats can be read. In addition, the FASTLIBS database
-abbreviations are available. This also should also solve problems with
-searches of very long sequences (bacterial genomes); they can now be
-broken up into smaller pieces with the -N ##### option, as with
-fasta33/tfastx33.
-
-Thus, you are encouraged to use the pv4comp*/mp4comp* versions of the
-programs, which should run more like fasta33.
-
-================
-Program summary:
-
-Programs to produce conventional scores and alignments:
-
-pv4compfa protein vs protein, DNA vs DNA
-pv4compsw protein vs protein, DNA vs DNA
-pv4compfx/ DNA vs protein
-pv4comptfx/y protein vs DNA
-
-Programs to summarize the effectiveness of a search (require
-super-family-labeled databases):
-
-ps4compfa protein vs protein, DNA vs DNA
-ps4compsw protein vs protein, DNA vs DNA
-ps4compfx/ DNA vs protein
-ps4comptfx/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.
-
-pu4compfa protein vs protein, DNA vs DNA
-pu4compsw protein vs protein, DNA vs DNA
-pucompfx/ DNA vs protein
-pu4comptfx/y protein vs DNA
-
-================
-Release notes:
-
---> Aug. 4, 2000
-
-Compiled and tested mp4compfa/mp4compsw programs.
-
---> July 22, 2000
-
-First release of restructured p2_complib.c/p2_workcomp.c, which use
-the manager program to read both sequence databases and send the
-"reference database" to the workers.
-
git://source.jalview.org / jabaws.git / blobdiff