mpiblast
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionLast revisionBoth sides next revision | ||
mpiblast [2010/01/29 09:37] – 172.26.0.166 | mpiblast [2010/01/29 09:42] – 172.26.0.166 | ||
---|---|---|---|
Line 3: | Line 3: | ||
* http:// | * http:// | ||
- | * OpenMPI FAQ: http:// | ||
< | < | ||
Line 42: | Line 41: | ||
MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.3.2)</ | MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.3.2)</ | ||
===== Benchmarks ===== | ===== Benchmarks ===== | ||
+ | |||
+ | ==== Standard BLAST ==== | ||
< | < | ||
| | ||
Line 47: | Line 48: | ||
user 7m40.775s | user 7m40.775s | ||
sys | sys | ||
+ | ==== MPI Blast with 4 jobs, 1 node ==== | ||
< | < | ||
Total Execution Time: 395.754 | Total Execution Time: 395.754 | ||
Line 55: | Line 56: | ||
sys | sys | ||
- | With 12 jobs, sge, mpiblast, 6 nodes did it in: | + | ==== MPI Blast with 12 jobs, 6 nodes ==== |
< | < | ||
Total Execution Time: 98.3068</ | Total Execution Time: 98.3068</ | ||
+ | ==== Paracel Blast ==== | ||
< | < | ||
Line 67: | Line 69: | ||
The number of processes for an MPI job should be +1 of the number of CPUs because one process is used as the master to control the other jobs. | The number of processes for an MPI job should be +1 of the number of CPUs because one process is used as the master to control the other jobs. | ||
+ | |||
===== Random Notes ===== | ===== Random Notes ===== | ||
Line 91: | Line 94: | ||
</ | </ | ||
You're not crazy, it's a known issue. 1.5.0 reports as 1.4.0: http:// | You're not crazy, it's a known issue. 1.5.0 reports as 1.4.0: http:// | ||
- | |||
===== Links ===== | ===== Links ===== | ||
* Submitting MPI jobs using SGE: http:// | * Submitting MPI jobs using SGE: http:// | ||
Line 98: | Line 100: | ||
* Rocks documentation on mpiBLAST: http:// | * Rocks documentation on mpiBLAST: http:// | ||
* wwwblast: http:// | * wwwblast: http:// | ||
+ | * OpenMPI FAQ: http:// |