Difference between revisions of "GARLI"

Revision as of 01:53, 10 August 2012

Description

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

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 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.
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