Difference between revisions of "GARLI"
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| + | __NOTOC__ | ||
| + | __NOEDITSECTION__ | ||
| + | [[Category:Software]][[Category:Phylogenetics]][[Category:Biology]] | ||
| + | {|<!--Main settings - REQUIRED--> | ||
| + | |{{#vardefine:app|garli}} | ||
| + | |{{#vardefine:url|https://www.nescent.org/wg_garli/Main_Page}} | ||
| + | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | ||
| + | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
| + | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | ||
| + | |{{#vardefine:policy|}} <!--Enable policy section --> | ||
| + | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | ||
| + | |{{#vardefine:faq|}} <!--Enable FAQ section --> | ||
| + | |{{#vardefine:citation|}} <!--Enable Reference/Citation section --> | ||
| + | |} | ||
| + | <!-- ######## Template Body ######## --> | ||
| + | <!--Description--> | ||
| + | {{#if: {{#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. | ||
| + | <!--Modules--> | ||
| + | ==Required Modules== | ||
| + | [[Modules|modules documentation]] | ||
| + | ===Serial=== | ||
| + | *{{#var:app}} | ||
| + | ===Parallel (OpenMP)=== | ||
| + | *intel | ||
| + | *{{#var:app}} | ||
| + | ===Parallel (MPI)=== | ||
| + | *intel | ||
| + | *openmpi | ||
| + | *{{#var:app}} | ||
| + | <!--Additional--> | ||
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
| + | See [https://molevol.mbl.edu/index.php/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 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://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, | ||
| + | mpiexec Garli-mpi 12 | ||
| + | |}} | ||
| + | {{#if: {{#var: conf}}|==Configuration== | ||
| + | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
| + | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
| + | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| + | {{#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== | ||
| + | WRITE PERFORMANCE TESTING RESULTS HERE|}} | ||
| + | {{#if: {{#var: faq}}|==FAQ== | ||
| + | *'''Q:''' **'''A:'''|}} | ||
| + | {{#if: {{#var: citation}}|==Citation== | ||
| + | If you publish research that uses {{{app}}} you have to cite it as follows: | ||
| + | WRITE CITATION HERE | ||
| + | |}} | ||
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
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