
 $Name: fa34t25d7 $ - $Id: readme.pvm_3.3,v 1.13 2000/08/04 18:45:15 wrp Exp $

================
pvcomp* - FAQ's, November, 1999

(The comments below apply to the pv3comp* programs.  This problem has
been addressed in the pv4comp* programs, by dramatically changing
the way databases are distributed.)

I believe that the number one reason why the pvcomp* programs do not
work properly is that the second library must be fully specified.
If you simply type:

	pv3compfa query.lib database.lib

The program will not be able to find database.lib on the worker machines.
You need to use:

	pv3compfa query.lib /home/user/lib/database.lib

and /home/user/lib/database.lib must be accessible to all of the worker
nodes.

To find error messages from the workers, look at /tmp/pvml.uid, where
uid is your unix uid.

================
Program summary:

Programs to produce conventional scores and alignments:

pv3compfa	protein vs protein, DNA vs DNA
pv3compsw	protein vs protein, DNA vs DNA
pv3compfx/	DNA vs protein
pv3comptfx/y	protein vs DNA

Programs to summarize the effectiveness of a search (require
super-family-labeled databases):

ps3compfa	protein vs protein, DNA vs DNA
ps3compsw	protein vs protein, DNA vs DNA
ps3compfx/	DNA vs protein
ps3comptfx/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.

pu3compfa	protein vs protein, DNA vs DNA
pu3compsw	protein vs protein, DNA vs DNA
pucompfx/	DNA vs protein
pu3comptfx/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).

================
Release notes:

--> July 18, 2000

Increase SQSZ in pxgetaa.c to 200000 for long Genbank entries.  This
may still not be long enough.  This increase may allow overlaps to
occur.

--> July 10, 2000

Corrections to the code for breaking up very long sequences.  The last
portion of a long sequence did not have the correct offset.

--> July 1, 2000

Modified pxgetaa.c to read Genbank flatfiles.

Additional pieces of a long sequence no longer have a '+' at the
beginning.

--> June 12, 2000

Restructured p_complib.c, p_workcomp.c to make the -m 9 display more
consistent with the fast33(_t) set of programs.  The alignment (%_id,
swscore, boundary) information is now calculated at the do_opt() stage
of the calculation.  This rearrangement uncovered a problem with the
do_opt() stage (s_func=1) that has been fixed.  This has not yet been
tested with the MPI implementation.

Many changes were made to allow k_H, k_comp information to be passed
back so that the -z 6 scaleswn.c (proc_hist_mle2) function could be
used.

--> February 6, 2000

Corrected some problems with proc_hist_ml() to correctly reinitialize
hist_db_size and num_db_entries.

--> January 20, 2000

   The structure of the p[vsu]comp* programs has not changed, but the
the code has been modified to accomodate both PVM and MPI versions of
the programs from the same source code.  Thus, all of the PVM-specific
code is now surrounded by #ifdef PVM_SRC/#endif.  The source files
pvcomplib.c and pvworkcomp.c have been replaced by p_complib.c and
p_workcomp.c, respectively.  Additional changes were made to ensure
that "FIRSTNODE" is used appropriately.  In general, FIRSTNODE=0 for
PVM programs (although with > 8 nodes, FIRSTNODE=1 may be more
effective), but FIRSTNODE=1 for MPI programs.

  Modest changes were made to reduce warning messages during
compilation.

--> January, 2000

   Modification to hxgetaa.c, pxgetaa.c to handle library sequences,
such as those from NCBI/NR, with very long comment lines.  Additional
modifications to correct problems with long comments, long DNA
sequences with pv3comptfx/tfy.

--> v3.33	December, 1999

Substantial updates to pvcomplib.c/pvworkcomp.c to improve efficiency
and to provide pv3compf[xy] and pv3comptf[xy].  Previous versions of
pvcomplib.c/pvworkcomp.c passed the entire struct mngmsg (structs.h)
each time a new query was initiated or alignments were required.  This
version sends struct mngmsg only once and sends struct qmng_str
(w_msg.h), which is much smaller, for the queries and alignments. In
addition, the buffer size for results is now variable (but can be as
large as 1200, vs 600 previously), which may improve performance when
large numbers of workers are available.  The maximum number of library
sequences per worker has been raised to 200,000 from 50,000.
Nevertheless, very large databases (est_human) may have too many
entries to be examined by 4 workers.

It is likely that pv3comptf[xy] may have problems with very long
sequences.  pv3compf[xy]/tf[xy] have not been tested extensively.

--> v3.32 December, 1999

Substantial corrections to showsum.c (showbest()) for the case of DNA
queries, where two scores are calculated for each query.  As a result
of the changes, bptr[] no longer mapped exactly to best[], which
caused a bug that was very difficult to track down.  To ensure that
bptr[]=best[], bptr[] is now re-initialized for each query.

The output format has changed significantly as well.  Lots of
redundant /** **/ comments have been removed.  An E() value has been
added to the "equ num:" line in showsum.c.

The organization of the inner while() loop in pvcomplib.c has been
modified so that new query sequences can be sent to workers
immediately as soon as a worker is available, rather than waiting for
all to finish and the statistical analysis.

--> v3.30	October, 1999

The p*comp*/c.work* programs have been renamed to pv3compfa,
ps3compfa, etc.  and c3.work* so that the older version 3.2 programs
can co-exist with this version.

Corrected problem with "-n" option that prevented it from functioning
properly.  Include "ACGTCN" in check for DNA query library.a

(from readme.pvm_3.2)

--> August, 1999

Corrected problem with opt_cut initialization that only appeared
with p?compfa programs.

--> v3.26	July, 1999

pvcomp* programs now use the same method for working with forward and
reverse strands as the standard fast*3(_t) programs.  Thus, statistics
for DNA sequences should be very similar for pvcompfa and fasta3 or
fasta3_t.

 		February, 1999

With release fasta32t02 of the FASTA package, the alignment
routines for pvcompfa, pvcompsw, etc now work properly
again.

The PVM versions of the FASTA and Smith-Waterman search programs
should now be functionally identical to the multithreaded (fasta3_t,
ssearch3_t) and non-threaded (fasta3, ssearch3) versions.

The programs have also been updated to provide similar -m 10
information to the non-pvm versions.  There are some slight
differences, because the pvcomp* versions are designed to work with
multiple sequences.  But, in general, a script that looks for /^>>>/
to start an alignment set and /^>>><<</ to end the set work
properly.

--> v3.23	March, 1999 

Modified Makefile.pvm, showsum.c so that showsum.c is used by
both the complib/_thr and pvcomplib (pvm parallel) versions.

Corrected bug in reading first query for DNA sequences.

--> v3.25	May, 1999

Fixed pvm_showalign.c so that FIRSTNODE (in msg.h) can be 1, rather
than 0.  #define FIRSTNODE 1 is recommended when the virtual machine
has 8 or more nodes.

