mpiblast
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mpiblast [2010/01/20 13:03] – 172.26.0.166 | mpiblast [2010/01/29 09:35] – 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:// | + | |
< | < | ||
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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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process per processor. But the minimum number of processes for | process per processor. But the minimum number of processes for | ||
mpiBLAST is 3, no matter what your compute node number is.%% | mpiBLAST is 3, no matter what your compute node number is.%% | ||
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==== Number of Fragments ==== | ==== Number of Fragments ==== | ||
Rule of thumb for large databases, one segment for every gigabyte (144 GB, 144 segments). | Rule of thumb for large databases, one segment for every gigabyte (144 GB, 144 segments). | ||
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* http:// | * http:// | ||
* https:// | * https:// | ||
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+ | ==== 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 ===== | ===== Links ===== |