mpiBLAST 1.3.0 has (finally) been released. It incorporates several major design changes that improve reliablilty, performance, and accuracy.
Key enhancements are:
Utilizes latest NCBI Toolbox (Oct 20, 2004)
E-value scores are exact and identical to scores reported by NCBI BLAST by using both the effective query and effective database lengths. (It is necessary/required to patch the NCBI Toolbox before compilation)
Database pipelining speeds up database distribution by limiting access to shared filesystem. Number of concurrent accesses is a run-time option (--concurrent).
Results pipelining reduces memory requirements for large query sets.
Database distribution can occur through cp, scp, or rcp system calls, through MPI function calls (MPI_Send/MPI_Recv), or not at all if you choose to use the shared filesystem as local storage. It is a runtime option (--copy-via).
mpiBLAST version 1.3.0 was a long time in coming, but is the fastest, most exact, and most stable version of mpiBLAST yet.
Submitted by
Nobody
;
posted on
Wednesday, December 22, 2004
patch ncbi_Oct2004_evalue.patch mpiblast-1.3.0 fails
patching the ncbi toolbox (release 20041020) fails with
patch p0 < mpiblast-1.3.0/ncbi_Oct2004_evalue.patch
and outputs:
"Looks like a unified context diff
Hunk #3 failed at line 1148
Hunk #4 failed at line 1587
Hunk #5 failed at line 1613
Hunk #6 failed at line 5045
Hunk #7 failed at line 5055
5 out of 7 hunks failed: saving rejects to
~/ncbi/tools/blast.c.rej"
mpiblast-1.3.0 and ncbi.tar.gz were extracted on a Sun
V440 with OS Solaris 9. Apparently some changes were
made by the diff script but it appears not to be
complete. Do I have the proper blast.c ? Any comments welcome.
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