# mpiblast

## Summary

+ **Module Name:** mpiblast
+ **Support Level:** Primary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://www.mpiblast.org/](http://www.mpiblast.org/)

## Software Description

mpiBLAST is a freely available, open-source, parallel implementation of
NCBI BLAST. mpiBLAST takes advantage of distributed computational
resources, i.e., a cluster, through explicit MPI communication and
thereby utilizes all available resources unlike standard NCBI BLAST
which can only take advantage of shared-memory multi-processor
computers. The primary advantage to using mpiBLAST versus traditional
NCBI BLAST is performance. mpiBLAST can increase performance by several
orders of magnitude while still retaining identical results as output
from NCBI BLAST.

## General Linux

To initialize this software in a Linux environment run the command:

    module load mpiblast

Before running mpiBLAST, a configuration file must be created.  Create
the file ~/.ncbirc (in your home directory) with the contents

    [mpiBLAST]
    Shared=/scratch.global/USERNAME/blastdb
    Local=/tmp

    [NCBI]
    Data=/common/software/install/migrated/mpiblast/VER/ncbi/data

    [BLAST]
    BLASTDB=/common/bioref/blast/current
    BLASTMAT=/common/software/install/migrated/mpiblast/VER/ncbi/data

where VER is the version of mpiBLAST you are using.

mpiBLAST cannot use serial ncbi BLAST databases (such as those in
/common/bioref/blast/current). You must create an mpiBLAST database using
mpiformatdb (uniref90.fasta db takes ~10 minutes to build, nr takes
~1hr).  Below is an example of using mpiformatdb:

    cd /scratch.global/USERNAME/blastdb
    wget url.to.dataset/dataset.fasta
    module load mpiblast
    mpiformatdb --nfrags=16 -i uniref90.fasta

It is highly recommended that
the number of fragments is the exact same number of cores performing the
search, or, when that is not possible, that the number of fragments is
an exact multiple of the number of cores, thus avoiding load unbalance,
which degrades performance.