mpiblast
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mpiblast [2010/01/18 12:11] – 172.26.0.166 | mpiblast [2010/01/19 11:10] – 172.26.0.166 | ||
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http:// | http:// | ||
+ | OpenMPI FAQ: http:// | ||
< | < | ||
- | * **--nfrags=10** Specifies | + | * **nfrags** |
- | http:// | ||
- | ===== Updating BLAST Databases ===== | ||
- | http:// | ||
===== Notes on .ncbirc ==== | ===== Notes on .ncbirc ==== | ||
Notes on setting up the '' | Notes on setting up the '' | ||
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< | < | ||
+ | ==== SGE Support ==== | ||
+ | See this FAQ entry: http:// | ||
+ | < | ||
+ | MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.3.2)</ | ||
===== Benchmarks ===== | ===== Benchmarks ===== | ||
- | < | + | < |
| | ||
real 7m48.052s | real 7m48.052s | ||
user 7m40.775s | user 7m40.775s | ||
- | sys | + | sys |
- | < | + | < |
+ | Total Execution Time: 395.754 | ||
+ | |||
+ | real 6m36.841s | ||
+ | user 12m13.891s | ||
+ | sys | ||
+ | |||
+ | With 12 jobs, sge, mpiblast, 6 nodes did it in: | ||
+ | < | ||
+ | Total Execution Time: 98.3068</ | ||
+ | |||
+ | 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. | ||
+ | |||
+ | ===== Links ===== | ||
+ | * Submitting MPI jobs using SGE: http:// | ||
+ | * mpiBLAST Guide: http:// | ||
+ | * Updating the BLAST databases: http:// |