raxml.pbs

#!/bin/bash

## Introductory Example for running RAxML
## Copyright (c) 2015 The Center for Advanced Research Computing
##                            at The University of New Mexico
#PBS -lnodes=1:ppn=8
#PBS -lwalltime=24:00:00

# Load the environment modules system
source /etc/profile.d/modules.sh

# Load the RaxML software to access the executable "raxmlHPC-HYBRID"
module load raxml/8.1.17/openmpi/1.8.4/intel/15.0.1

# Determine the total number of processors allocated to this job
export PROCS=$(cat $PBS_NODEFILE | wc -l)

# Determine Core/ node
export CORES=$(grep "processor" /proc/cpuinfo | wc -l)

# Now run it! 
# Modify the following line for your particular job:
mpirun -np $PROCS -machinefile $PBS_NODEFILE raxmlHPC-HYBRID -T $CORES -f a -x 12345 -p 12345 -# 50 -m GTRGAMMA -s ASIP_phasedOG.fas -n outputfile.out