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NCBI Blast+ is a shared-memory program that runs on a single node with multiple threads. The Intel processors on the razor cluster will run blast about twice as fast as the AMD processors on trestles. The latest 2.3.0 version is considerably faster multi-threaded than earlier versions, but it still cannot effectively use all the cores in a node. 12-core nodes are sufficient since blast+ is not very scalable. It works better with a database on a local file system, so if doing a number of runs, it may be worthwhile to copy the database to your area of the local scratch disk, as shown. For a single run it is probably faster overall to read directly from the parallel filesystem database. If copying the database please remember to remove it at the end of the job. Please note the difference in paths between the clusters.


$ rsync -a /share/apps/bioinformatics/blast/db20150912/nt /local_scratch/$USER/
$ export BLASTDB=/local_scratch/$USER/nt
$ export PATH=$PATH:/share/apps/bioinformatics/blast/ncbi-blast-2.3.0+/bin
$ time  blastn -num_threads 32 -query queries/blastn/NM_001005648 -db $BLASTDB/nt >blast.output

real	0m11.438s
user	1m28.905s
sys	0m11.403s
$ rm -rf /local_scratch/$USER/nt


$ rsync -a /share/apps/blast/db20150912/nt /local_scratch/$USER/
$ export BLASTDB=/local_scratch/$USER/nt
$ export PATH=$PATH:/share/apps/blast/ncbi-blast-2.3.0+/bin
$ time  blastn -num_threads 16 -query queries/blastn/NM_001005648 -db $BLASTDB/nt >blast.output

real	0m5.917s
user	0m48.965s
sys	0m6.227s
$ rm -rf /local_scratch/$USER/nt
blast.1455638886.txt.gz · Last modified: 2016/02/16 16:08 by root