Difference between revisions of "RAxML"

Revision as of 19:37, 10 August 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

# 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

@@ Line 19: / Line 19: @@
 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.
+<!--Modules-->
-==Installed Versions==
+==Required Modules==
-* 1.0.5-Light
+[[Modules|modules documentation]]
-* 7.3.0 (Standard)
+===Serial===
-* 7.3.0.0220 - 2012-02-20 upstream code update.
+*{{#var:app}}
-* 7.3.0.0307 - 2012-03-07 upstream code update.
+===Parallel (MPI)===
-* 7.3.2.0705 - 2012-07-05 upstream code update (default).
+*intel
+*openmpi
-==Variants of RAxML standard==
+*{{#var:app}}
-* OpenMP threaded version compiled with gcc- <code>/apps/RAxML/7.3.2-20120705/threaded/raxmlHPC-PTHREADS-SSE3</code>
+==System Variables==
-* OpenMP threaded version compiled with Intel 11.1- <code>/apps/RAxML/7.3.2-20120705/intel/threaded/raxmlHPC-PTHREADS-SSE3</code>
+* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
-* OpemMPI/OpenMP MPI and threaded hybrid version - <code>/apps/RAxML/7.3.2-20120705/intel/mpi/raxmlHPC-HYBRID-SSE3</code>
-* OpenMPI version - <code>/apps/RAxML/7.3.2-20120705/intel/mpi/raxmlHPC-MPI</code>
-<!-- -->
-{{#if: {{#var: mod}}|==Execution Environment and Modules==
-To use {{#var:app}} with the environment modules system at HPC the following commands are available:
-Get module information for {{lc: {{PAGENAME}}}}:
- $module spider {{#var:app}}
-{{#if: {{#var:intel}}|Load Intel compiler: {{#tag:pre|$module load intel/{{#var:intel}}}}|}}{{#if: {{#var:mpi}}|Load MPI implementation: {{#tag:pre|$module load {{#var:mpi}}}}|}}
-Load the application module:
- $module load {{#var:app}}
-The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
-* HPC_{{uc:{{#var:app}}}}_DIR - directory where {{#var:app}} is located.|}}
-To run the OpenMPI version load the following modules
- module load intel/11.1 openmpi/1.4.3 raxml/7.3.2.0705
 {{#if: {{#var: exe}}|==How To Run==
 WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}