|
|
| 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 |
|
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|
|
|
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|
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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