Difference between revisions of "GARLI"

Latest revision as of 16:53, 15 August 2022

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.

Required Modules

modules documentation

Serial

garli

Parallel (OpenMP)

intel
garli

Parallel (MPI)

intel
openmpi
garli

Additional Information

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 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; 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 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 mpiexec MPI wrapper to run it. For example,

mpiexec Garli-mpi 12

@@ Line 1: / Line 1: @@
 __NOTOC__
 __NOEDITSECTION__
-[[Category:Software]][[Category:Phylogenetics]]
+[[Category:Software]][[Category:Phylogenetics]][[Category:Biology]]
-<!-- ########  Template Configuration ######## -->
+{|<!--Main settings - REQUIRED-->
-<!--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|garli}}
 |{{#vardefine:url|https://www.nescent.org/wg_garli/Main_Page}}
-<!--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|1}} <!--Present manual instructions for running the software -->
 |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
@@ Line 31: / Line 16: @@
 <!--Description-->
 {{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 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.
-<!--Location-->
+<!--Modules-->
-{{App_Location|app={{#var:app}}|{{#var:ver}}}}
+==Required Modules==
-Garli 2.0 is installed in /apps/garli/2.0
+[[Modules|modules documentation]]
-==Available versions==
+===Serial===
-* 2.0
+*{{#var:app}}
-<!-- -->
+===Parallel (OpenMP)===
-{{#if: {{#var: mod}}|==Running the application using modules==
+*intel
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+*{{#var:app}}
-Available modules:
+===Parallel (MPI)===
-* garli/2.0 - the serial version of Garli (default).
+*intel
-* load the intel module to enable the OpenMP (multi-threaded) version of Garli.
+*openmpi
-* load both the intel and the openmpi modules to enable the MPI version of Garli
+*{{#var:app}}
+<!--Additional-->
-Examples:
+{{#if: {{#var: exe}}|==Additional Information==
+See [https://molevol.mbl.edu/index.php/Garli_FAQ Garli FAQ]
-Multi-threaded:
- module load intel/2012 garli
-MPI:
- module load intel/2012 openmpi/1.6 garli
-{{#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].
+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; 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  [https://molevol.mbl.edu/index.php/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,
+The MPI version of Garli is discussed in the [https://molevol.mbl.edu/index.php/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>mpiexec</code> MPI wrapper to run it. For example,
-  mpirun -np 12 Garli-mpi 12
+  mpiexec Garli-mpi 12
 |}}
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 66: / Line 45: @@
 {{#if: {{#var: pbs}}|==PBS Script Examples==
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
-{{#if: {{#var: policy}}|==Usage policy==
+{{#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==