|mpiFastA: parallel FastA services|
The FastA programs are implemented as parallel applications through Intel's MPICH libraries on HPC. The full suite of FastA programs are available and they continue to access the GCG libraries given proper library syntax.
Using mpiFastA on HPC
The following table lists the FastA single cpu progams that have corresponding mpi versions:
mpiFastA has been compiled on HPC using Intel's OpenMPI 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.