$Name: fa35_03_06 $ - $Id: readme.pvm_3.3,v 1.15 2007/06/29 20:23:58 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 /^>>> 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.
