RAxML

RAxML is available in both serial and parallel versions. To run the serial version load the hpc/RAxML-7.0.4 module. The executable is called raxmlHPC.

To run in parallel, load the following modules: hpc/openmpi-intel hpc/RAxML-7.0.4_MPI.

Here is a sample script to run on 8 cores in csh:

#!/bin/csh
#BSUB -q normal_parallel
#BSUB -o out
#BSUB -e err
#BSUB -n 8
#BSUB -a openmpi

mpirun.lsf raxmlHPC-MPI -s phyC_aa.phy -n phyC_aaboot.tre -m PROTGAMMAWAGF -f a -x 83257 -o Cleome_hassleriana_106_9_1.TX
T -P proteinModel -N 100