Beast-Sapelo2

Category

Bioinformatics

Program On

Sapelo2

Version

1.10.4, 2.5.1, 2.6.3, 2.7.3, 2.7.5

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 without GPU support

• version 1.10.4 installed in /apps/eb/Beast/1.10.4-GCC-11.3.0

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

module load Beast/1.10.4-GCC-11.3.0

• version 2.5.1 installed in /apps/eb/Beast/2.5.1-GCC-11.3.0

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

module load Beast/2.5.1-GCC-11.3.0

• version 2.7.5 installed in /apps/eb/Beast/2.7.5-GCC-11.3.0

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

module load Beast/2.7.5-GCC-11.3.0

Versions with CPU and GPU support

• version 1.10.4 with CPU and GPU support, installed in /apps/eb/Beast/1.10.4-GCC-11.3.0-CUDA-11.4.1. 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/1.10.4-GCC-11.3.0-CUDA-11.4.1

• version 2.6.3 with CPU and GPU support, installed in /apps/eb/Beast/2.6.3-foss-2021b-CUDA-11.4.1/. This version of Beast is using beagle-lib/4.0.0 with GPU support.

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

module load Beast/2.6.3-foss-2021b-CUDA-11.4.1

• version 2.7.3 with CPU and GPU support, installed in /apps/eb/Beast/2.7.3-foss-2021b-CUDA-11.4.1/. This version of Beast is using beagle-lib/4.0.0 with GPU support.

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

module load Beast/2.7.3-foss-2021b-CUDA-11.4.1

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/2.7.3-foss-2021b-CUDA-11.4.1
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 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:A100:1
#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/2.7.3-foss-2021b-CUDA-11.4.1 

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. You need to use #SBATCH --gres=gpu:A100:1 to run the job on a A100 GPU node.

Example of submission to the queue:

sbatch  sub.sh

Documentation

ml Beast/2.7.3-foss-2021b-CUDA-11.4.1 
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] [-version_file <VERSIONFILE>] [-packagedir <PACKAGEDIR>] [<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)
    -version_file Provide a version file containing a list of services to explicitly allow. (Useful for package development.)
    -packagedir Set user package directory instead of using the default

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


ml Beast/2.7.3-foss-2021b-CUDA-11.4.1 
beast -beagle_info

                        BEAST v2.7.3, 2002-2022
             Bayesian Evolutionary Analysis Sampling Trees
                       Designed and developed by
 Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard
                                    
                   Centre for Computational Evolution
                         University of Auckland
                       r.bouckaert@auckland.ac.nz
                        alexei@cs.auckland.ac.nz
                                    
                   Institute of Evolutionary Biology
                        University of Edinburgh
                           a.rambaut@ed.ac.uk
                                    
                    David Geffen School of Medicine
                 University of California, Los Angeles
                           msuchard@ucla.edu
                                    
                      Downloads, Help & Resources:
                           http://beast2.org/
                                    
  Source code distributed under the GNU Lesser General Public License:
                   http://github.com/CompEvol/beast2
                                    
                           BEAST developers:
   Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, 
 Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, 
Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, 
          Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie
                                    
                               Thanks to:
          Roald Forsberg, Beth Shapiro and Korbinian Strimmer


--- BEAGLE RESOURCES ---

0 : CPU (x86_64)
    Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_SSE VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU

1 : NVIDIA A100-SXM4-80GB
    Global memory (MB): 81051
    Clock speed (Ghz): 1.41
    Number of cores: 13824
    Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH COMPUTATION_ASYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_NONE THREADING_NONE PROCESSOR_GPU FRAMEWORK_CUDA

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Installation

Source codes download from BEAST2

System

64-bit Linux