mpiblast
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mpiblast [2010/01/19 09:17] – 172.26.0.166 | mpiblast [2010/01/19 11:10] – 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. | ||
- | 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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user 12m13.891s | user 12m13.891s | ||
sys | 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. | 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 ===== | ===== Links ===== | ||
* Submitting MPI jobs using SGE: http:// | * Submitting MPI jobs using SGE: http:// | ||
- | + | * mpiBLAST Guide: http://www.mpiblast.org/Docs/Guide | |
- | < | + | * Updating the BLAST databases: http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl |
- | $ sudo ln -s /scratch/ / | + | |
- | $ sudo chmod 777 /scratch/ | + | |
- | $ sudo chmod o+t /scratch/</code> | + |