Benchmark tests of NCBI Blast for Windows on Amazon Elastic Compute Cloud (EC2)
Amazon Elastic Compute Cloud (EC2) is a well-known cloud service.  If NCBI Blast works fast enough on EC2 instances, we can purchase EC2 instance when we need it and do not have to invest on expensive computers.
We performed the benchmark tests of NCBI Blast 2.2.25 and NCBI Blast+ 2.2.25 for Windows on several EC2 instances.
 
Test results for c3 instances are added.
 
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Up-to-date as of 11/21/2013
 
 
 
Blast and Blast+ Results
 
1. Test Conditions
EC2 instances tested
M3 Extra Large: 15 GB Memory, 13 EC2 Compute Units
M3 Double Extra Large: 30 GB Memory, 26 EC2 Compute Units
Cluster Compute Eight Extra Large: 60.5 GB Memory, 88 EC2 Compute Units
OS 64-bit Windows Server 2008 R2 (Same as Windows 7)
Query Sequences AF287139, 606 letters for blastn, ACL81455, 301 letters for blastp
Databases
nt 16,967,641 sequences; 43,737,939,670 total letters
nr 22,340,230 sequences; 7,678,059,998 total letters
64-bit NCBI Blast 2.2.25 and 64-bit NCBI Blast+ 2.2.25 are used.
Numbers in the table below are in seconds.
2. Results
Smaller number means faster instance
EC2 instance Price/hour1) blastn against nt blastp against nr
    NCBI Blast NCBI Blast+ NCBI Blast NCBI Blast+
M3 Extra Large $0.98 15.3 16.3 42.8 59.4
M3 Double Extra Large $1.96 8.3 8.8 22.1 31.2
Cluster Compute Eight Extra Large $2.97 6.6 7.2 18.4 26.9
NCBI Website2)     53)   163)
1) US East(Virginia) Region, Windows Instance, as of 1/3/2013
2) NCBI Blast+ 2.2.27
3) nt has16,967,778 sequences and 43,713,081,416 total letters. nr has 22,325,752 sequences and 7,673,265,207 total letters
3. Conclusions
  1. Both of NCBI Blast and NCBI Blast+ for Windows on M3 Extra Large are faster than NCBI Blast+ for linux on M3 Extra Large.
  2. Both of NCBI Blast and NCBI Blast+ for Windows on M3 Double Extra Large are faster than NCBI Blast+ for linux on M3 Double Extra Large.
  3. Both of NCBI Blast and NCBI Blast+ for Windows on Cluster Compute Eight Extra Large are fastest.
  4. NCBI Blast is faster than NCBI Blast+ on all instance types.
 
 
Blast+ Results
 
1. Test Conditions
EC2 instances tested
m3.xlarge(M3 Extra Large): 15 GB Memory, 13 EC2 Compute Units
m3.2xlarge(M3 Double Extra Large): 30 GB Memory, 26 EC2 Compute Units
c3.2xlarge: 15 GB Memory, 28 EC2 Compute Unit
c3.4xlarge: 30 GB Memory, 55 EC2 Compute Units
c3.8xlarge: 60 GB Memory, 108 EC2 Compute Units
OS 64-bit Windows Server 2008 R2 (Same as Windows 7)
Query Sequences AF287139, 606 letters for blastn, ACL81455, 301 letters for blastp
Databases
nt 20,472,768 sequences; 51,561,019,060total letters
nr 34,305,433  sequences; 12,011,942,272 total letters
BlastStation in the Cloud is used.  NCBI Blast+ version is 2.2.25.
Numbers in the table below are in seconds.
2. Results
Smaller number means faster instance
EC2 instance Price/hour1) blastn against nt blastp against nr
m3.xlarge $0.702 20.8 94.5
m3.2xlarge $1.404 12.3 51.3
c3.2xlarge $0.932 11.3 48.0
c3.4xlarge $1.864 7.5 27.5
c3.8xlarge $3.728 7.5 18.3

1) US East(Virginia) Region, Windows Instance, as of 11/21/2013

3. Conclusions
  1. c3.8xlarge is the fastest.
  2. c3.2xlarge is better than m3.2xlarge from a cost/performance viewpoint.