mpiblast
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mpiblast [2010/01/29 09:34] – 172.26.0.166 | mpiblast [2010/01/29 09:42] – 172.26.0.166 | ||
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* http:// | * http:// | ||
- | * OpenMPI FAQ: http:// | ||
< | < | ||
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The Data variable gives the location of the NCBI Data directory containing BLOSUM and PAM scoring matrices, among other things. The scoring matrix files are necessary for any type of protein BLAST search and should be accessible by all cluster nodes. The BLASTMAT variable also specifies the path to the scoring matrices, and will usually be identical to the Data variable. The BLASTDB variable tells standard NCBI blastall (not mpiBLAST) where to find BLAST databases. As previously mentioned, the Shared and Local variables give the shared and local database paths, respectively. By setting BLASTDB to the same path as Shared, it is possible for NCBI blastall to share the same databases that mpiBLAST uses. In such a configuration, | The Data variable gives the location of the NCBI Data directory containing BLOSUM and PAM scoring matrices, among other things. The scoring matrix files are necessary for any type of protein BLAST search and should be accessible by all cluster nodes. The BLASTMAT variable also specifies the path to the scoring matrices, and will usually be identical to the Data variable. The BLASTDB variable tells standard NCBI blastall (not mpiBLAST) where to find BLAST databases. As previously mentioned, the Shared and Local variables give the shared and local database paths, respectively. By setting BLASTDB to the same path as Shared, it is possible for NCBI blastall to share the same databases that mpiBLAST uses. In such a configuration, | ||
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- | ===== wwwblast ===== | ||
- | http:// | ||
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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 ==== | ||
< | < | ||
| | ||
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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 | ||
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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 ==== | ||
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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 ===== | ||
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* http:// | * http:// | ||
* https:// | * https:// | ||
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==== Incorrect mpiBLAST Version ==== | ==== Incorrect mpiBLAST Version ==== | ||
- | You're not crazy, it's a known issue: http:// | ||
< | < | ||
mpiblast-1.5.0-pio | mpiblast-1.5.0-pio | ||
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mpiblast version 1.4.0 | mpiblast version 1.4.0 | ||
</ | </ | ||
+ | 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:// | ||
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* Updating the BLAST databases: http:// | * Updating the BLAST databases: http:// | ||
* Rocks documentation on mpiBLAST: http:// | * Rocks documentation on mpiBLAST: http:// | ||
+ | * wwwblast: http:// | ||
+ | * OpenMPI FAQ: http:// |