Benchmark tests of NCBI Blast+ on Mac OS X
We performed the benchmark tests of NCBI Blast+ 2.2.24 and compared it with NCBI Blast 2.2.24 results.
 
Up-to-date as of 10/4/2010
 
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1. Test Conditions
OS: Mac OS X 10.6.4 Snow Leopard
Hardware: 8-core Mac Pro, Xeon E5520 @ 2.27GHz, 32GB Memory, 640GB Hard Disk
NCBI Blast+: 2.2.24 downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.24/ncbi-blast-2.2.24+-universal-macosx.tar.gz
NCBI Blast: 2.2.24 downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.24/blast-2.2.24-universal-macosx.tar.gz
Numbers in the table below are real of /usr/bin/time in seconds.
2. Results
blastn
DB: nt.00 - nt.09 combined downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/ 
13,433,377 sequences; 33,261,831,042 total letters
Query Sequence: AF287139, 606 letters
# of Threads1) NCBI Blast+ NCBI Blast+ for x86_642) NCBI Blast NCBI Blast 2.2.20 for x86_64
1 29.3 19.7 84.5 46.9
2 20.0 11.8 59.3 28.7
4 14.4 8.2 mmap failed error 19.2
8 13.1 7.6 mmap failed error 14.6
12 13.0 7.2 mmap failed error 14.2
16 13.0 7.0 mmap failed error 13.8
blastp
DB: nr.00 - nr.04 combined downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/
11,921,515 sequences; 4,071,357,309 total letters
Query Sequence: ACL81455, 301 letters
# of Threads1) NCBI Blast+ NCBI Blast+ for x86_642) NCBI Blast NCBI Blast 2.2.20 for x86_64
1 241.0 126.1 202.9 124.8
2 156.4 69.5 145.7 78.9
4 114.6 38.3 116.7 56.6
8 93.3 20.6 102.6 45.9
12 90.0 17.1 100.6 43.7
16 87.7 15.1 100.7 42.1
         
3. Conclusions
3.1.blastn
      64 bit NCBI Blast+ is the fastest for all numbers of threads.
      Using more than 8 threads will not accelerate search speed any more.
      If enough memory is available, launching more instances with 8 threads is the best strategy.
3.2.blastp
      64 bit NCBI Blast+ is the fastest.
      NCBI Blast+ is the slowest for 1 and 2 threads.
      Using NCBI Blast+ on Core 2 Duo Macs is not a good idea.  Use 64 bit NCBI Blast+ instead.
1) Specified -num_threads n in the command arguments.
2) NCBI Blast+ was built with --with-64 configuration option.  Please refer to How to Build NCBI Blast+ for Mac OS X for details to build.  This 64 bit binary is available for download here .  It should work on Mac OS X 10.6 and 10.5 with 64 bit Intel processors, such as Core 2 Duo and Xeon.
 
 
 
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