The mpiBLAST module allows one to perform large, distributed BLAST database searches that could be prohibitively time-consuming on single-node computing systems.
You will learn from this exercise:
mpiBLAST
Shared=/work/01374/vaughn/mpiblast
Local=/tmp
NCBI
data=/work/01374/vaughn/mpiblast/data
#!/bin/bash
# You will learn from this exercise: ## The basics of configuring mpiBLAST ## Setting up a parallel environment (-pe) variable ## Launching MPI jobs using ibrun
#$ -V
#$ -cwd
#$ -N tut2-mpiblast
#$-A 20111206BIO
#$ -j y
#$ -pe 12way 48
#$ -q development
#$ -l h_rt=00:15:00
# Set up module module load mpiblast # ibrun is the MPI launcher at TACC # euc_assembly.fa contains 721 transcript assemblies from Eucalyptus that are 2kb or longer # plantrefseq.fa is the reference peptide set from NCBI refseq ## Corresponds to the database we built using mpiformatdb # We are asking blastx to emit tabular results ( -m 9 )
ibrun -n 24 -o 0 $TACC_MPIBLAST_BIN/mpiblast -p blastx \ -i euc_assembly.fa -d plantrefseq.fa -m 9 \ -o euc_assembly.blast9
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