Beast-Sapelo2

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Revision as of 09:53, 9 December 2021 by Ben (talk | contribs) (Document how to use this in OOD rather than xqlogin)
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Category

Bioinformatics

Program On

Sapelo2

Version

1.10.4, 2.6.2, 2.6.3

Author / Distributor

BEAST2 BEAST

Description

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. More information: http://beast2.org/; http://beast.community/

Running Program

Versions with CPU support

  • version 1.10.4, installed in /apps/eb/Beast/1.10.4-GCC-8.3.0. This version of Beast is using beagle-lib v3.0.1 with CPU support.

To use this version of Beast, please first load the module with 

module load Beast/1.10.4-GCC-8.3.0
  • version 2.6.2, installed in /apps/eb/Beast/2.6.2-GCC-8.3.0. This version of Beast is using beagle-lib v3.0.1 with CPU support.

To use this version of Beast, please first load the module with 

module load Beast/2.6.2-GCC-8.3.0
  • version 2.6.3, installed in /apps/eb/Beast/2.6.3-foss-2019b. This version of Beast is using beagle-lib v3.0.1 with CPU support.

To use this version of Beast, please first load the module with 

module load Beast/2.6.3-foss-2019b

Versions with CPU and GPU support

  • version 2.6.3 with CPU and GPU support, installed in /apps/eb/Beast/2.6.3-fosscuda-2019b. This version of Beast is using beagle-lib/3.1.2 with GPU support.

To use this version of Beast, please first load the module with 

module load Beast/2.6.3-fosscuda-2019b

please note: beagle-lib/3.1.2 with GPU support was built for NVDIA Tesla V100 GPU device (SM70), but it also works for K20Xm, K40m, and P100 GPU nodes.

Run Beast in an interactive session

Beast is a X window program with graphic interface. It has to be run in an interactive session. Please refer to X Desktop Sessions in Open OnDemand.

  1. Start an X Desktop Session via Open OnDemand
  2. Open the Terminal application in your X Desktop session (icon at the bottom of the Desktop or via the "Applications" button in the top left)
  3. ml Beast/2.6.3-foss-2019b
  4. beauti ...
  5. beast ...
  • beast/beauti in this app is set to 16GB max heap memory. If larger memory is needed, please contact us.

Run Beast with CPU support in a batch job

Example job submission script (sub.sh) to run version 2.6.3 in a batch job: 

#!/bin/bash
#SBATCH --job-name=testBeast-CPU        
#SBATCH --partition=batch            
#SBATCH --ntasks=1                  	
#SBATCH --cpus-per-task=8        
#SBATCH --mem=40gb                    
#SBATCH --time=120:00:00           
#SBATCH --output=log.%j.out     
#SBATCH --error=log.%j.err          
#SBATCH --mail-user=username@uga.edu  
#SBATCH --mail-type=ALL   

cd $SLURM_SUBMIT_DIR

ml Beast/2.6.3-foss-2019b

beast -threads 8 [options]

Example of submission to the queue: 

sbatch  sub.sh

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well.

Run Beast with GPU support in a batch job

Example job submission script (sub.sh) to run version 2.6.3 with GPU support in a batch job: 

#!/bin/bash
#SBATCH --job-name=testBeast-GPU
#SBATCH --partition=gpu_p
#SBATCH --gres=gpu:P100:1
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=20gb
#SBATCH --time=120:00:00
#SBATCH --output=log.%j.out
#SBATCH --error=log.%j.err
#SBATCH --mail-user=username@uga.edu  
#SBATCH --mail-type=ALL   

cd $SLURM_SUBMIT_DIR

ml Beast/2.6.3-fosscuda-2019b

beast -threads 4 -beagle -beagle_GPU [options]

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well. Please note, you can also use #SBATCH --gres=gpu:K40:1 or #SBATCH --gres=gpu:K20:1 to run the job on a K40 or a K20 GPU node.

Example of submission to the queue: 

sbatch  sub.sh

Documentation

 
ml Beast/2.6.3-foss-2019b 
beast -help

  Usage: beast [-window] [-options] [-working] [-seed] [-prefix <PREFIX>] [-statefile <STATEFILE>] [-overwrite] [-resume] [-validate] [-errors <i>] [-threads <i>] [-java] [-noerr] [-loglevel <LEVEL>] [-instances <i>] [-beagle] [-beagle_info] [-beagle_order <order>] [-beagle_CPU] [-beagle_GPU] [-beagle_SSE] [-beagle_single] [-beagle_double] [-beagle_scaling <default|none|dynamic|always>] [-help] [-version] [-strictversions] [-D <DEFINITIONS>] [-DF <DEFINITIONFILE>] [-DFout <DEFINITIONRESULTFILE>] [-sampleFromPrior] [<input-file-name>]
    -window Provide a console window
    -options Display an options dialog
    -working Change working directory to input file's directory
    -seed Specify a random number generator seed
    -prefix Specify a prefix for all output log filenames
    -statefile Specify the filename for storing/restoring the state
    -overwrite Allow overwriting of log files
    -resume Allow appending of log files
    -validate Parse the XML, but do not run -- useful for debugging XML
    -errors Specify maximum number of numerical errors before stopping
    -threads The number of computational threads to use (default 1), -1 for number of cores
    -java Use Java only, no native implementations
    -noerr Suppress all output to standard error
    -loglevel error,warning,info,debug,trace
    -instances divide site patterns amongst number of threads (use with -threads option)
    -beagle Use beagle library if available
    -beagle_info BEAGLE: show information on available resources
    -beagle_order BEAGLE: set order of resource use
    -beagle_CPU BEAGLE: use CPU instance
    -beagle_GPU BEAGLE: use GPU instance if available
    -beagle_SSE BEAGLE: use SSE extensions if available
    -beagle_single BEAGLE: use single precision if available
    -beagle_double BEAGLE: use double precision if available
    -beagle_scaling BEAGLE: specify scaling scheme to use
    -help Print this information and stop
    -version Print version and stop
    -strictversions Use only package versions as specified in the 'required' attribute
    -D attribute-value pairs to be replaced in the XML, e.g., -D "arg1=10,arg2=20"
    -DF as -D, but attribute-value pairs defined in file in JSON format
    -DFout BEAST XML file written when -DF option is used
    -sampleFromPrior samples from prior for MCMC analysis (by adding sampleFromPrior="true" in the first run element)

  Example: beast test.xml
  Example: beast -window test.xml
  Example: beast -help

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Installation

Source codes download from BEAST2

System

64-bit Linux

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