ncbi_Oct2004_evalue.patch - Bioinformatics.org

mpiBLAST 1.3.0 released
Submitted by Joe Landman; posted on Tuesday, December 14, 2004 (2 comments)

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.

Download it here:
http://mpiblast.lanl.gov

RPMs of 1.3.0 (source and binary) are available from Scalable Informatics download pages:
http://downloads.scalableinformatics.com/downloads/mpiblast/

Working mpich-1.2.6 RPMs (source and binaries) are also available:
http://downloads.scalableinformatics.com/downloads/mpich/

Discussion forums: mpiBLAST 1.3.0 released

Expanded view | Monitor forum | Save place

Message

ncbi_Oct2004_evalue.patch

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.

Post a followup to this message:

You have to be to post a reply.

Thread view

ncbi_Oct2004_evalue.patch

Submitted by Nobody; posted on Wednesday, December 22, 2004

ncbi_Oct2004_evalue.patch

Submitted by Nobody; posted on Thursday, February 17, 2005

i want cancer related genes in humo sapiens