Beast-Sapelo2
Category
Bioinformatics
Program On
Sapelo2
Version
1.10.4, 2.6.2, 2.6.3
Author / Distributor
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 only
- version 1.8.4 with CPU support, installed in /usr/local/apps/eb/Beast/1.8.4-foss-2016b. This version of Beast is using beagle-lib/2.1.2. This version of Beast only works on AMD nodes (it does not work on the Intel that are on Sapelo2). To use this version, please request the AMD node feature for the job.
To use this version of Beast, please first load the module with
module load Beast/1.8.4-foss-2016b
- version 2.4.8pre with CPU support, installed in /usr/local/apps/eb/Beast/2.4.8pre-foss-2016b. This version of Beast is using beagle-lib/2.1.2.
To use this version of Beast, please first load the module with
module load Beast/2.4.8pre-foss-2016b
- version 2.4.8 with CPU support, installed in /usr/local/apps/eb/Beast/2.4.8-foss-2016b. This version of Beast is using beagle-lib/2.1.2.
To use this version of Beast, please first load the module with
module load Beast/2.4.8-foss-2016b
Versions with CPU and GPU support
- version 1.10.1 with CPU and GPU support, installed in /usr/local/apps/eb/Beast/1.10.1-foss-2018a. This version of Beast is using beagle-lib/3.0.1 with GPU support.
To use this version of Beast, please first load the module with
module load Beast/1.10.1-foss-2018a
- version 1.10.3 with CPU and GPU support, installed in /usr/local/apps/eb/Beast/1.10.3-foss-2018a. This version of Beast is using beagle-lib/3.0.1 with GPU support.
To use this version of Beast, please first load the module with
module load Beast/1.10.3-foss-2018a
- version 1.10.4 with CPU and GPU support, installed in /usr/local/apps/eb/Beast/1.10.4-foss-2018a. This version of Beast is using beagle-lib/3.1.1 with GPU support.
To use this version of Beast, please first load the module with
module load Beast/1.10.4-foss-2018a
- version 2.4.8 with CPU and GPU support, installed in /usr/local/apps/eb/Beast/2.4.8-foss-2018a. This version of Beast is using beagle-lib/2.1.2 with GPU support.
To use this version of Beast, please first load the module with
module load Beast/2.4.8-foss-2018a
- version 2.5.0 with CPU and GPU support, installed in /usr/local/apps/eb/Beast/2.5.0-foss-2018a. This version of Beast is using beagle-lib/3.0.1 with GPU support.
To use this version of Beast, please first load the module with
module load Beast/2.5.0-foss-2018a
- version 2.5.1 with CPU and GPU support, installed in /usr/local/apps/eb/Beast/2.5.1-fosscuda-2018b. This version of Beast is using beagle-lib/3.0.2 with GPU support.
To use this version of Beast, please first load the module with
module load Beast/2.5.1-fosscuda-2018b
- version 2.6.3 with CPU and GPU support, installed in /usr/local/apps/eb/Beast/2.5.1-foss-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-foss-2019b
please note: version 1.10.1, 1.10.3, 2.4.8, 2.5.0, and 2.5.1 with GPU support were built for NVDIA Tesla P100 GPU devices (sm_60) but these programs also work on the K20Xm and the K40m GPU nodes.
Beast is a X window program with graphic interface. It has to be run on the Interactive node! Please refer to Run interactive Jobs and Run X window Jobs.
Start X Terminal (Mac), X window (Windows) at the local computer first, then
xqlogin module load Beast/2.4.8pre-foss-2016b beauti ... beast ... exit
- beast/beauti in this app is set to 64GB max memory. If larger memory needed, please contact us.
Run Beast with CPU support
Example job submission script (bt-CPU.sh) to run version 2.4.8pre in a batch job:
#PBS -S /bin/bash #PBS -q batch #PBS -l nodes=1:ppn=4 #PBS -l walltime=480:00:00 #PBS -l mem=80gb cd $PBS_O_WORKDIR module load Beast/2.4.8pre-foss-2016b beast -threads 4 [options]
Example of submission to the queue:
qsub bt-CPU.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
Example job submission script (bt-GPU.sh) to run version 2.5.0 in a batch job:
#PBS -S /bin/bash #PBS -q gpu_q #PBS -l nodes=1:ppn=2:gpus=1:default #PBS -l walltime=240:00:00 #PBS -l mem=80gb cd $PBS_O_WORKDIR module load Beast/2.5.0-foss-2018a beast -beagle_GPU [options]
Example of submission to the queue:
qsub bt-GPU.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. Note that Beast runs multiple processes concurrently on the GPU device, so it is important to select the "Default" GPU compute mode, as it is done on line 3 of this sample script.
Documentation
module load Beast/2.4.8pre-foss-2016b
beast -help
Checking out /home/pakala/.beast/2.4/BEAST/lib
jardir = /usr/local/apps/eb/Beast/2.4.8pre-foss-2016b/lib/launcher.jar
Checking out /usr/local/apps/eb/Beast/2.4.8pre-foss-2016b/lib
Loaded URL file:/usr/local/apps/eb/Beast/2.4.8pre-foss-2016b/lib/beast.jar
Loading package BEAST v2.4.8
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] [<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
Example: beast test.xml
Example: beast -window test.xml
Example: beast -help
Installation
Source codes download from BEAST2
System
64-bit Linux