# Introduction
Beagle_optimiser is a program written in Python that takes an XML input file prepared for BEAST, and finds the beagle option that will result in the shortest analysis time of that file. You can find out more about the program in the open laboratory notebook
at http://matstopel.se/notebook/beagle-optimiser.
# The program has the following functions:
mats@Slartibartfasts:~/project/beagle/test$ ./beagle_optimiser_0.9 -h
Usage: beagle_optimiser_0.9.2 [-r] [-q] [-d] [--nogpu] [-f] FILE [-t] NAME [-n] N -i [file1 file2 ..]
Options:
--version Show program's version number and exit.
-h, --hele Show this help message and exit.
-q, --quiet Minimum or no output to STDOUT.
-r, --run Run beast with the best speed settings immediately
after the test.
-f FILE, --file=FILE Write output to FILE [bo_output.txt].
-t NAME, --tmpdir=NAME
Name of temporary directory for output files. This
directory will be removed after the beagle tests are
done if the --dev flag was not invoked [.bss_tmp].
-n N, --ngen=N Chainlength for the Beast runs [10000].
--nogpu Do not use the "-Beagle_GPU" flag in the test.
-d, --dev Produce more output to STDOUT and save all temporary
files.
-i, --input Followed by one or several input files.
# Output from the program looks like this:
_______________________________________
File: benchmark1.xml
Sequences: 1441
Sites: 987
Unique patterns: 593
_______________________________________
Beast option: Time:
-beagle_SSE 199.66 seconds
-beagle_CPU 204.72 seconds
-beagle_instances 2 211.04 seconds
-beagle_instances 10 223.12 seconds
-beagle_instances 8 227.52 seconds
-beagle_instances 4 233.74 seconds
-beagle_instances 12 237.6 seconds
-beagle_instances 16 245.73 seconds
-beagle_instances 14 253.28 seconds
-beagle_GPU 263.08 seconds
Native library 386.7 seconds
-java 389.06 seconds
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# TODO
Use a random seed when the "-r" option is used.
Make BO work with MrBayes 3.2
Test different beagle options in combination (is that relevant?)