3.11. MPI-Blast

3.11.1. About

MPI-Blast is a program from LANL which parallelizes the NCBI Blast algorithms using Message Passing Interface library. The version of MPI-Blast included with Rocks is v1.4.0-May2006.

3.11.2. Usage

MPI-Blast is used in a similar manner to NCBI-Blast. MPI-Blast uses the same variables that are available for NCBI-Blast.

There are 3 steps to running MPI-Blast.

3.11.3. Running MPI Blast and SGE

This section gives a brief overview of running MPI Blast with SGE


Please note that an MPI blast job requires atleast 3 processors to run. The argument for mpirun specifying the number of processors should be factor of the number of pieces the blast database was divided into. If you're running on a cluster with 2 processors, SGE, by default, will not schedule a job which requires more than 2 slots to run.

3.11.4. Further Information

Further information about using mpiblast can be found at the MPI-Blast home page.

For support, please join the mpiblast mailing list