mpiblast
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mpiblast [2010/01/19 09:17] – 172.26.0.166 | mpiblast [2010/01/20 12:19] – 172.26.0.166 | ||
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* **nfrags** specifies how many database fragments you want to split the original database into. This should be equal to how many different nodes you want to run mpiblast on. | * **nfrags** specifies how many database fragments you want to split the original database into. This should be equal to how many different nodes you want to run mpiblast on. | ||
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user 12m13.891s | user 12m13.891s | ||
sys | sys | ||
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+ | With 12 jobs, sge, mpiblast, 6 nodes did it in: | ||
+ | < | ||
+ | Total Execution Time: 98.3068</ | ||
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+ | < | ||
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+ | real 3m6.163s | ||
+ | user 0m0.046s | ||
+ | sys | ||
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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. | ||
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+ | https:// | ||
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+ | %%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.%% | ||
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===== Links ===== | ===== Links ===== | ||
* Submitting MPI jobs using SGE: http:// | * Submitting MPI jobs using SGE: http:// | ||
- | + | * mpiBLAST Guide: http://www.mpiblast.org/ | |
- | < | + | * Updating the BLAST databases: http://www.ncbi.nlm.nih.gov/blast/docs/ |
- | $ sudo ln -s /scratch/ /state/partition1 | + | * Rocks documentation on mpiBLAST: http://www.rocksclusters.org/ |
- | $ sudo chmod 777 /scratch/ | + | |
- | $ sudo chmod o+t /scratch/</code> | + |