X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Ffasta34%2Freadme.pvm_3.3;fp=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Ffasta34%2Freadme.pvm_3.3;h=6e916a869f37189bde911bec386a2f431a3ac46e;hb=dbde3fb6f00b9bb770343631a517c0e599db8528;hp=0000000000000000000000000000000000000000;hpb=85f830bbd51a7277994bd4233141016304e210c9;p=jabaws.git diff --git a/website/archive/binaries/mac/src/fasta34/readme.pvm_3.3 b/website/archive/binaries/mac/src/fasta34/readme.pvm_3.3 new file mode 100644 index 0000000..6e916a8 --- /dev/null +++ b/website/archive/binaries/mac/src/fasta34/readme.pvm_3.3 @@ -0,0 +1,210 @@ + + $Name: fa_34_26_5 $ - $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 /^>>><< 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. +