1#!/usr/local/bin/bash 2 3# These are example SCRIPTs to run PFAM with MPI ON PBS. Minor changes would be needed for LSF etc 4# executable for mpirun, e.g. from OpenMPI 5MPIRUN_EXEC=`which mpirun` 6# these arguments are valid for OpenMPI, change them for Intel's 7MPIRUN_ARGS="-gmca mpi_warn_on_fork 0 -cpus-per-proc 1 -np $2 -machinefile workers.$PBS_JOBID.mpi" 8 9#executable of hhmscan 10HMMSCAN_EXEC=`which hmmscan` 11 12#your PFAM database 13PFAMDB=/home/pap056/30day/databases/pfam/Pfam-AB.hmm.bin 14 15# no need to change the following 16 17export OMP_NUM_THREADS=1 18# the PBS_O_WORKDIR is where you launched the script from. Feel free to change this if you need 19# to launch it from a difference directory 20cd $PBS_O_WORKDIR 21cat ${PBS_NODEFILE} > workers.$PBS_JOBID.mpi 22$MPIRUN_EXEC $MPIRUN_ARGS ffindex_apply_mpi \ 23 -d "$1"_out2.db \ 24 -i "$1"_out2.db.idx \ 25 $1 \ 26 $1.idx \ 27 -- $HMMSCAN_EXEC -o /dev/null --cpu 1 --noali --cut_nc --acc --notextw --domtblout /dev/stdout $PFAMDB - 28