Metabolomics 2008 4th Annual Conference, Sept. 2-6, 2008
new Team members: Saeed Khazaie
Blast Benchmarks
Document Actions
The
Applications
Program distribution:
blastn (Nucleotide-nucleotide BLAST) 50%
megablast (Large numbers of query sequences) 10%
blastp (Protein-protein BLAST) 20%
blastx (
nucleotide query sequence against a protein sequence database)
10%
tblastn (
protein query against the six-frame translations of a nucleotide sequence database)
5%
tblastx (nucleotide query against the six-frame translations of a nucleotide sequence database) 5%
Results {Version 2.2.13}
Dual Xeon 3.6 GHz - 885 sec. or 14:45 min
Dual Opteron 2.8 GHz - 930 sec. or 15:30 min (Win32, Dual Opteron 254 2.8 Ghz - ARECA 1120 RAID5)
Download
The benchmark files (just extract to a folder)
ftp://ftp.ncbi.nih.gov/blast/demo/benchmark [PPT] [ZIP]
The blast files for WIN32, LINUX, Solaris, IRIX, Sparc, PPC, MacOSX
ftp://ftp.ncbi.nih.gov/blast/executables/LATEST
Windows Timethis
TimeThis.exe
Make.exe for running the benchmark from MingW - with all UNIX tools for Windows
MingW or [EXE]
Adjust the path folders in the makefile so they point to the right benchmark files and executables (put them in one root folder)
Run the benchmark with the make command: timethis "make -j 4 >> bresult.txt"
This will run the benchmark with four threads provided by make (it will split the workload).
Applications
- Evaluate the relative performance of BLAST running on different hardware
- Evaluate the relative performance of different BLAST implementations
blastn (Nucleotide-nucleotide BLAST) 50%
megablast (Large numbers of query sequences) 10%
blastp (Protein-protein BLAST) 20%
blastx (
tblastn (
tblastx (nucleotide query against the six-frame translations of a nucleotide sequence database) 5%
Results {Version 2.2.13}
Dual Xeon 3.6 GHz - 885 sec. or 14:45 min
Dual Opteron 2.8 GHz - 930 sec. or 15:30 min (Win32, Dual Opteron 254 2.8 Ghz - ARECA 1120 RAID5)
Download
The benchmark files (just extract to a folder)
ftp://ftp.ncbi.nih.gov/blast/demo/benchmark [PPT] [ZIP]
The blast files for WIN32, LINUX, Solaris, IRIX, Sparc, PPC, MacOSX
ftp://ftp.ncbi.nih.gov/blast/executables/LATEST
Windows Timethis
TimeThis.exe
Make.exe for running the benchmark from MingW - with all UNIX tools for Windows
MingW or [EXE]
Adjust the path folders in the makefile so they point to the right benchmark files and executables (put them in one root folder)
Run the benchmark with the make command: timethis "make -j 4 >> bresult.txt"
This will run the benchmark with four threads provided by make (it will split the workload).
Created by
kind
Last modified 2006-05-23 03:03 PM
Last modified 2006-05-23 03:03 PM
