GARLI

Description

garli 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.

This module provides access to the OpenMP version of Garli-2.0.

Environment Modules

Run module spider garli to find out what environment modules are available for this application.

Environment Variables

• HPC_GARLI_DIR - installation directory
• HPC_GARLI_BIN - executable directory

Additional Usage Information

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 environment 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 #SBATCH --cpus-per-task=8 in your script, also include export OMP_NUM_THREADS=7 and export OMP_THREAD_LIMIT=8 (for a bash script) in the script itself.

To decide whether the performance gain with the multithreaded version is worth it for your particular job see the Garli Website.

If you decide to use the MPI version of Garli, use the mpiexec MPI wrapper to run it. For example,

mpiexec Garli-mpi 12

Categories

biology, phylogenetics