$Name: fa35_03_06 $ - $Id: readme.pvm_3.4,v 1.5 2007/06/29 20:23:58 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.
