mpiblast
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mpiblast [2010/01/18 12:11] – 172.26.0.166 | mpiblast [2010/01/29 09:34] – 172.26.0.166 | ||
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Parallel implementation of NCBI's BLAST algorithm. | Parallel implementation of NCBI's BLAST algorithm. | ||
- | 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 '' | ||
Line 41: | Line 39: | ||
< | < | ||
+ | ==== 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</ | ||
+ | |||
+ | < | ||
+ | |||
+ | real 3m6.163s | ||
+ | user 0m0.046s | ||
+ | sys | ||
+ | |||
+ | |||
+ | 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 ===== | ||
+ | |||
+ | ==== Number of Jobs ==== | ||
+ | |||
+ | https:// | ||
+ | |||
+ | %%With formatdb, the number of nodes refers to compute node number. | ||
+ | With mpiBLAST, np refers to number of processes, which isn' | ||
+ | necessarily linked to compute node or processor number. You can run | ||
+ | 10 processes on 4 processors. But it's recommended to run a single | ||
+ | process per processor. But the minimum number of processes for | ||
+ | mpiBLAST is 3, no matter what your compute node number is.%% | ||
+ | ==== Number of Fragments ==== | ||
+ | Rule of thumb for large databases, one segment for every gigabyte (144 GB, 144 segments). | ||
+ | |||
+ | * http:// | ||
+ | * https:// | ||
+ | |||
+ | ==== Incorrect mpiBLAST Version ==== | ||
+ | You're not crazy, it's a known issue: http:// | ||
+ | < | ||
+ | mpiblast-1.5.0-pio | ||
+ | $ mpiblast --version | ||
+ | mpiblast version 1.4.0 | ||
+ | </ | ||
+ | |||
+ | ===== Links ===== | ||
+ | * Submitting MPI jobs using SGE: http:// | ||
+ | * mpiBLAST Guide: http:// | ||
+ | * Updating the BLAST databases: http:// | ||
+ | * Rocks documentation on mpiBLAST: http:// |