mpiblast
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mpiblast [2010/01/18 08:03] – 172.26.0.166 | mpiblast [2010/01/19 09:18] – 172.26.0.166 | ||
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http:// | http:// | ||
+ | OpenMPI FAQ: http:// | ||
- | * **--nfrags=10** Specifies | + | < |
+ | |||
+ | * **nfrags** specifies | ||
- | 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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===== wwwblast ===== | ===== wwwblast ===== | ||
http:// | http:// | ||
+ | |||
+ | |||
+ | ===== Frequently Asked Questions ===== | ||
+ | Collection of the more-helpful questions and answers from the [[http:// | ||
+ | ====How do I format a huge database? | ||
+ | |||
+ | Large databases like nt can consume several gigabytes of disk space and it is preferable to store them in compressed form. Starting with mpiBLAST 1.4.0 it is possible to pipe FastA formatted sequence data into mpiformatdb. This feature provides the ability to directly format a compressed (gzip/bzip etc.) database using command line syntax like: | ||
+ | < | ||
+ | |||
+ | ==== SGE Support ==== | ||
+ | See this FAQ entry: http:// | ||
+ | |||
+ | < | ||
+ | MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.3.2)</ | ||
+ | ===== Benchmarks ===== | ||
+ | < | ||
+ | | ||
+ | real 7m48.052s | ||
+ | user 7m40.775s | ||
+ | sys | ||
+ | |||
+ | < | ||
+ | Total Execution Time: 395.754 | ||
+ | |||
+ | real 6m36.841s | ||
+ | user 12m13.891s | ||
+ | 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. | ||
+ | ===== Links ===== | ||
+ | * Submitting MPI jobs using SGE: http:// | ||
+ | * Updating the BLAST databases: http:// | ||
+ | < | ||
+ | $ sudo ln -s /scratch/ / | ||
+ | $ sudo chmod 777 /scratch/ | ||
+ | $ sudo chmod o+t / |