Difference between revisions of "GARLI"
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|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules --> | |{{#vardefine:mod|1}} <!--Present instructions for running the software with modules --> | ||
| − | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | + | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> |
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | ||
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<!--Location--> | <!--Location--> | ||
{{App_Location|app={{#var:app}}|{{#var:ver}}}} | {{App_Location|app={{#var:app}}|{{#var:ver}}}} | ||
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Garli 2.0 is installed in /apps/garli/2.0 | Garli 2.0 is installed in /apps/garli/2.0 | ||
| + | ==Available versions== | ||
| + | * 2.0 | ||
<!-- --> | <!-- --> | ||
{{#if: {{#var: mod}}|==Running the application using modules== | {{#if: {{#var: mod}}|==Running the application using modules== | ||
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | ||
| + | Available modules: | ||
| + | * garli/2.0 - the serial version of Garli (default). | ||
| + | * garli/2.0-mp - the OpenMP and the OpenMPI versions of Garli. | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
| − | + | See [https://www.nescent.org/wg_garli/FAQ 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 [http://www.google.com/url?sa=t&source=web&cd=2&sqi=2&ved=0CBkQFjAB&url=http%3A%2F%2Fhelix.nih.gov%2FApplications%2Fvelvet_manual.pdf&rct=j&q=velvet%20assembler%20manual&ei=Lr1WToqdIsGG0QGJyamyDA&usg=AFQjCNH2VB2-la3kWazMqdl3ms-xkCocVw user manual] for more information). To decide whether the performance gain with the multithreaded version is worth it for your particular job see the [https://www.nescent.org/wg_garli/FAQ#Should_I_use_a_multi-threaded_.28openMP.29_version_of_GARLI_if_I.E2.80.99m_using_a_computer_with_multiple_processors.2Fcores.3F Garli FAQ on using the OpenMP version]. | ||
| + | |||
| + | The MPI version of Garli is discussed in the [https://www.nescent.org/wg_garli/FAQ#What_is_the_parallel_MPI_version_of_GARLI.3F_Should_I_use_it.3F 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 <code>mpirun</code> MPI wrapper to run it. For example, | ||
| + | mpirun -np 12 Garli-mpi 12 | ||
| + | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
Revision as of 18:19, 14 June 2012
Description
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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.
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).
- garli/2.0-mp - the OpenMP and the OpenMPI versions of 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