MpiBlast

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Current Version

NCBI Blast: 6.1
mpiBlast: 1.5.0

mpiblast was compiled using the intel compilers and OpenMPI. This is the default setting for MPI based programs on the cluster, so as long as mpi-selector has not been used in your account, it should work just fine.

Location

NCBI Blast: /apps/blast/ncbi
mpiBlast: /apps/blast/bin/mpiblast

Instructions

Before running mpiBLAST, it is necessary to configure the shared and local storage paths that each node will use to access the database. A shared storage path is usually a path to a directory residing on a file server, such as NFS, AFS, or samba. The local storage path is typically a subdirectory within the /tmp directory, e.g. /tmp/mpiblast. As worker nodes search the database, they will copy fragments to the local storage directory. During subsequent searches of the same database, the fragments will already reside in local storage and thus will not need to be copied. Note that diskless nodes can be supported by setting the local storage path to be the same as the shared storage path. To configure mpiBLAST create a .ncbirc file in your home directory that looks like: 

[NCBI]
Data=/path/to/shared/storage/data

[BLAST]
BLASTDB=/path/to/shared/storage
BLASTMAT=/path/to/shared/storage/data

[mpiBLAST]
Shared=/path/to/shared/storage
Local=/path/to/local/storage

The Data variable gives the location of the NCBI Data directory containing BLOSUM and PAM scoring matrices, among other things. The scoring matrix files are necessary for any type of protein BLAST search and should be accessible by all cluster nodes. The BLASTMAT variable also specifies the path to the scoring matrices, and will usually be identical to the Data variable. The BLASTDB variable tells standard NCBI blastall (not mpiBLAST) where to find BLAST databases. As previously mentioned, the Shared and Local variables give the shared and local database paths, respectively. By setting BLASTDB to the same path as Shared, it is possible for NCBI blastall to share the same databases that mpiBLAST uses. In such a configuration, be sure to format all databases with mpiformatdb rather than formatdb.

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