Beast
BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies 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 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.
More information can be found on Beast2’s homepage.
Running Beast
To run Beast load one of the available modules, discoverable with:
$ module spider beast
CPU job script
The following script can be used to run Beast on CPUs only.
Note
The script requests a full node’s worth of CPUs on Saga, --cpus-per-task, you
should test for your self with your own input to see if this is necessary. The
same is also true for the --mem-per-cpu parameter, other input might require
more or less memory.
#!/bin/bash
#SBATCH --account=nn<NNNN>k
#SBATCH --job-name=beast_cpu
#SBATCH --time=04:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=40
#SBATCH --mem-per-cpu=1G
## Recommended safety settings:
set -o errexit # Make bash exit on any error
set -o nounset # Treat unset variables as errors
module --quiet purge
module load Beast/2.6.7-GCC-10.3.0-CUDA-11.3.1
module list
beast -beagle_cpu -threads $SLURM_CPUS_PER_TASK test.xml
GPU job script
Beast supports GPU acceleration through a GPU accelerated version of
beagle-lib. If your input
supports it, using GPUs should improve the performance, but always test before
submitting long running jobs as GPU jobs “cost” more than pure CPU jobs.
#!/bin/bash
#SBATCH --account=nn<NNNN>k
#SBATCH --job-name=beast_cpu
#SBATCH --time=00:30:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=4G
#SBATCH --partition=accel
#SBATCH --gpus=1
## Recommended safety settings:
set -o errexit # Make bash exit on any error
set -o nounset # Treat unset variables as errors
module --quiet purge
module load Beast/2.6.7-GCC-10.3.0-CUDA-11.3.1
module list
beast -beagle_gpu test.xml
Performance increase
Some timing examples are listed below for the example sequences in test.xml,
linked above. The requested resources are chosen based on billing units, see
Projects and accounting, where one GPU is the equivalent of six CPU cores.
Then the memory is chosen such that it will not be the determining factor for
the overall billing. Note that CPU-hrs is what your job is billed, i.e. what
you pay for the job.
Configuration |
CPUs |
GPUs |
MEM |
Runtime |
Speedup |
Billing |
CPU-hrs |
|---|---|---|---|---|---|---|---|
Reference |
1 |
0 |
4G |
13716.573s |
1.0 |
1 |
3.8 |
1 GPU equivalent |
6 |
0 |
6G |
4328.023s |
3.2 |
6 |
7.2 |
Half normal node |
20 |
0 |
20G |
3998.535s |
3.4 |
20 |
22.2 |
Full normal node |
40 |
0 |
40G |
6103.471s |
2.3 |
40 |
67.8 |
1 GPU |
1 |
1 |
4G |
1174.682s |
11.7 |
6 |
2.0 |
2 GPUs |
2 |
2 |
8G |
4153.796s |
3.3 |
12 |
13.8 |
The impression we get from the above data is that Beast is well suited for
running on GPUs, but limited to a single GPU. By using GPU acceleration for our
test example we reduce our CPU hour spending (2.0 compared to 3.8) while
also seeing an increase in performance (lower total runtime). In other words,
using GPUs is both cheaper and faster than using the pure CPU implementation.
License information
Beast 2 is available under the GNU Lesser General Public License (LGPL) version 2.1.
It is the user’s responsibility to make sure they adhere to the license agreements.
Citation
The homepage contains information about how to cite Beast.