Difference between revisions of "RAxML"

Revision as of 15:26, 22 October 2012

Description

RAxML (Randomized Axelerated Maximum Likelihood) written by Alexandros Stamatakis and others is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.

Required Modules

modules documentation

Serial

raxml

Parallel (MPI)

intel
openmpi
raxml

System Variables

HPC_{{#uppercase:raxml}}_DIR - installation directory

PBS Script Examples

{{#fileAnchor: raxml.threaded.pbs}} Download raw source of the [{{#fileLink: raxml.threaded.pbs}} raxml.threaded.pbs]

#!/bin/sh
#PBS -N RAxML
#PBS -m bea
#PBS -M <YOUR E-MAIL HERE>
#PBS -o raxml.$PBS_JOBID.out
#PBS -e raxml.$PBS_JOBID.err
#PBS -l nodes=1:ppn=4
#PBS -l pmem=450mb
#PBS -l walltime=24:00:00
#
# Change to the directory where you type qsub. Should be in /scratch, not your $HOME
cd $PBS_O_WORKDIR

# Load the raxml environment
module load raxml

# The raxml command, modify as needed. Read the manual or use raxmlHPC-PTHREADS-SSE3 -help to see options
# Note the use of the variable $PBS_NP defined by the scheduler based on your resource request
raxmlHPC-PTHREADS-SSE3 -f d -m GTRCAT -s your_data.phy -n output_name -p 3112 -b 758 -N 500  -T $PBS_NP

@@ Line 52: / Line 52: @@
 # Change to the directory where you type qsub. Should be in /scratch, not your $HOME
 cd $PBS_O_WORKDIR
-# Get number of cores--set number of cores above in nodes=1:ppn=number of cores wanted
-# raxmlHPC-PTHREADS-SSE3 can only use cores on a single node, so do not change nodes=1
-# By using this, you don't need to change the value for -T in the raxml command, though
-#  if you change to a single core, raxml will fail saying you need to use 2 or more.
-#  For single processor jobs use raxmlHPC-SSE3 and nodes=1:ppn=1.
-NPROCS=`wc -l < $PBS_NODEFILE`
 # Load the raxml environment
-module load intel/11.1 raxml
+module load raxml
 # The raxml command, modify as needed. Read the manual or use raxmlHPC-PTHREADS-SSE3 -help to see options
-# Note the use of the variable $NPROCS defined above with the -T option, no need to change this
+# Note the use of the variable $PBS_NP defined by the scheduler based on your resource request
-raxmlHPC-PTHREADS-SSE3 -f d -m GTRCAT -s your_data.phy -n output_name -p 3112 -b 758 -N 500  -T $NPROCS
+raxmlHPC-PTHREADS-SSE3 -f d -m GTRCAT -s your_data.phy -n output_name -p 3112 -b 758 -N 500  -T $PBS_NP
 </source>