View source for RAxML

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[[Category:Software]][[Category:Bioinformatics]]
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Required variables:
app - lowercase name of the application e.g. "amber"
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
Optional variables:
INTEL - Version of the Intel Compiler e.g. "11.1"
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
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{|
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|{{#vardefine:app|raxml}}
|{{#vardefine:url|http://wwwkramer.in.tum.de/exelixis/software.html}}
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|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
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|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
|{{#vardefine:pbs|1}} <!--Enable PBS script wiki page link-->
|{{#vardefine:policy|}} <!--Enable policy section -->
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
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<!--Description-->
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

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. 
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{{App_Location|app={{#var:app}}|{{#var:ver}}}}
==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.
* 7.3.2.0705 - 2012-07-05 upstream code update (default).

==Variants of RAxML standard==
* OpenMP threaded version compiled with gcc- <code>/apps/RAxML/7.3.2-20120705/threaded/raxmlHPC-PTHREADS-SSE3</code>
* OpenMP threaded version compiled with Intel 11.1- <code>/apps/RAxML/7.3.2-20120705/intel/threaded/raxmlHPC-PTHREADS-SSE3</code>
* 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>
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{{#if: {{#var: mod}}|==Running the application using 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|}}
{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
{{#if: {{#var: pbs}}|==PBS Script Examples==

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

<source lang=bash>
#!/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
</source>

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{{#if: {{#var: policy}}|==Usage policy==
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
{{#if: {{#var: testing}}|==Performance==
WRITE PERFORMANCE TESTING RESULTS HERE|}}
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{{app}}} you have to cite it as follows:
WRITE CITATION HERE
|}}