Difference between revisions of "GARLI"

From UFRC
Jump to navigation Jump to search
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
__NOEDITSECTION__
[[Category:Software]]
+
[[Category:Software]][[Category:Phylogenetics]]
 
<!-- ########  Template Configuration ######## -->
 
<!-- ########  Template Configuration ######## -->
 
<!--Edit definitions of the variables used in template calls  
 
<!--Edit definitions of the variables used in template calls  
Line 43: Line 43:
 
Available modules:
 
Available modules:
 
* garli/2.0 - the serial version of Garli (default).
 
* garli/2.0 - the serial version of Garli (default).
* garli/2.0-mp - the OpenMP and the OpenMPI versions of Garli.
+
* load the intel module to enable the OpenMP (multi-threaded) version of Garli.
 +
* load both the intel and the openmpi modules to enable the MPI version of Garli
 +
 
 +
Examples:
 +
 
 +
Multi-threaded:
 +
module load intel/2012 garli
 +
MPI:
 +
module load intel/2012 openmpi/1.6 garli
 +
 
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
 
See [https://www.nescent.org/wg_garli/FAQ Garli FAQ]  
 
See [https://www.nescent.org/wg_garli/FAQ Garli FAQ]  

Revision as of 22:01, 2 August 2012

Description

{{{name}}} website  
GARLI is a program that performs phylogenetic inference using the maximum-likelihood criterion. Several sequence types are supported, including nucleotide, amino acid and codon. Version 2.0 adds support for partitioned models and morphology-like datatypes. Template:App Location Garli 2.0 is installed in /apps/garli/2.0

Available versions

  • 2.0

Running the application using modules

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

Get module information for garli:

$module spider garli

Load the default application module:

$module load garli

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

  • HPC_GARLI_DIR - directory where garli is located.

Available modules:

  • garli/2.0 - the serial version of Garli (default).
  • load the intel module to enable the OpenMP (multi-threaded) version of Garli.
  • load both the intel and the openmpi modules to enable the MPI version of Garli

Examples:

Multi-threaded:

module load intel/2012 garli

MPI:

module load intel/2012 openmpi/1.6 garli

How To Run

See Garli FAQ While the garli module provides the serial version of Garli there is a garli/2.0-mp module that provides both the multithreaded (OpenMP) and an MPI (OpenMPI) versions of Garli.

To use the OpenMP version of Garli, you must set the enviroment variables OMP_NUM_THREADS and OMP_THREAD_LIMIT to the appropriate values based on the core number request in your submission script. For example if you use #PBS -l nodes=1:ppn=8 in your script, also include export OMP_NUM_THREADS=7; export OMP_THREAD_LIMIT=8 (for a bash script) in the script itself (see the user manual for more information). To decide whether the performance gain with the multithreaded version is worth it for your particular job see the Garli FAQ on using the OpenMP version.

The MPI version of Garli is discussed in the Garli FAQ. See the FAQ entry help to decide whether it is appropriate to use the MPI version of Garli for your job. If you decide to use the MPI version of Garli, use the mpirun MPI wrapper to run it. For example,

mpirun -np 12 Garli-mpi 12