Difference between revisions of "RAxML"
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| + | __NOTOC__ | ||
| + | __NOEDITSECTION__ | ||
| + | [[Category:Software]][[Category:Bioinformatics]] | ||
| + | <!-- ######## Template Configuration ######## --> | ||
| + | <!--Edit definitions of the variables used in template calls | ||
| + | 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" | ||
| + | --> | ||
| + | {| | ||
| + | <!--Main settings - REQUIRED--> | ||
| + | |{{#vardefine:app|raxml}} | ||
| + | |{{#vardefine:url|http://wwwkramer.in.tum.de/exelixis/software.html}} | ||
| + | <!--Compiler and MPI settings - OPTIONAL --> | ||
| + | |{{#vardefine:intel|}} <!-- E.g. "11.1" --> | ||
| + | |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" --> | ||
| + | <!--Choose sections to enable - OPTIONAL--> | ||
| + | |{{#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|}} <!--Enable PBS script wiki page link--> | ||
| + | |{{#vardefine:policy|}} <!--Enable policy section --> | ||
| + | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | ||
| + | |{{#vardefine:faq|}} <!--Enable FAQ section --> | ||
| + | |{{#vardefine:citation|}} <!--Enable Reference/Citation section --> | ||
| + | |} | ||
| + | <!-- ######## Template Body ######## --> | ||
| + | <!--Description--> | ||
| + | {{#if: {{#var: url}}| | ||
| + | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | ||
| + | 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. | ||
| + | <!--Location--> | ||
| + | {{App_Location|app={{#var:app}}|{{#var:ver}}}} | ||
| + | ==Installed Versions== | ||
| + | * 1.0.5-Light | ||
| + | * 7.3.0 (Standard) | ||
| + | ==Variants of RAxML standard== | ||
| + | * OpenMP threaded version - <code>/apps/RAxML/7.3.0/raxmlHPC-PTHREADS-SSE3</code> | ||
| + | * OpemMPI/OpenMP MPI and threaded hybrid version - <code>/apps/RAxML/7.3.0/raxmlHPC-HYBRID-SSE3</code> | ||
| + | * OpenMPI version - <code>/apps/RAxML/7.3.0/raxmlHPC-MPI</code> | ||
| + | <!-- --> | ||
| + | {{#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/10.1 openmpi/1.2.7 raxml/7.3.0 | ||
| + | {{#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== | ||
| + | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| + | {{#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 | ||
| + | |}} | ||
Revision as of 02:07, 1 February 2012
Description
{{{name}}} website
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)
Variants of RAxML standard
- OpenMP threaded version -
/apps/RAxML/7.3.0/raxmlHPC-PTHREADS-SSE3 - OpemMPI/OpenMP MPI and threaded hybrid version -
/apps/RAxML/7.3.0/raxmlHPC-HYBRID-SSE3 - OpenMPI version -
/apps/RAxML/7.3.0/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/10.1 openmpi/1.2.7 raxml/7.3.0