Using mpiFastA on HPC

The following table lists the FastA single cpu progams that have corresponding mpi versions:

Single CPU	MPI version
fasta34	mp34compfa
ssearch34	mp34compsw
fasts	mp34compfs
fastx	mp34compfx
fasty	mp34compfy
tfasts	mp34comptfs
tfastx	mp34comptfx
tfasty	mp34comptfy

mpiFastA has been compiled on HPC using Intel's MPICH libraries, and, therefore, that shell script must be sourced in your MOAB script.  A sample MOAB script to launch the MPI version of FastA to search the UniProt library follows:

#!/bin/bash
#MOAB -l nodes=16
#MOAB -j oe
#MOAB -m abe
#MOAB -N MP34COMPFA
source /usr/local/profile.d/openmpi-intel.sh
mpirun /opt/Bio/mpifasta/mp34compfa $HOME/test/test.fsa.pep \
@/panfs/storage.local/bio/gcgdata/fastadb/uniprot.fastadb

Note that the backslash continuation character does not work within MOAB scripts and is just used here to denote that the entire command needs to be on the same line.  See the FastA HPC page for further details.