RAxML

Description

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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. Template:App Location

Installed Versions

• 1.0.5-Light
• 7.3.0 (Standard)
• 7.3.0.0220 - 2012-02-20 upstream code update.
• 7.3.0.0307 - 2012-03-07 upstream code update.
• 7.3.1.0705 - 2012-07-05 upstream code update (default).

Variants of RAxML standard

• OpenMP threaded version compiled with gcc- /apps/RAxML/7.3.1-20120705/threaded/raxmlHPC-PTHREADS-SSE3
• OpenMP threaded version compiled with Intel 11.1- /apps/RAxML/7.3.1-20120705/intel/threaded/raxmlHPC-PTHREADS-SSE3
• OpemMPI/OpenMP MPI and threaded hybrid version - /apps/RAxML/7.3.1-20120705/intel/mpi/raxmlHPC-HYBRID-SSE3
• OpenMPI version - /apps/RAxML/7.3.1-20120705/intel/mpi/raxmlHPC-MPI

Running the application using modules

To use raxml with the environment modules system at HPC the following commands are available:

Get module information for raxml:

$module spider raxml

Load the application module:

$module load raxml

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_RAXML_DIR - directory where raxml is located.

To run the OpenMPI version load the following modules

module load intel/11.1 openmpi/1.4.3 raxml/7.3.1.0705

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

# 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

# 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
raxmlHPC-PTHREADS-SSE3 -f d -m GTRCAT -s your_data.phy -n output_name -p 3112 -b 758 -N 500  -T $NPROCS