Does BEAGLE truly avail itself of multiple cores or only GPU?

[griffinia]

Will I see any advantage to trying to get BEAGLE installed on our 32-
core Open-SUSE Linux parallel server, or does BEAGLE only use the GPU
in addition to a single core. And does it only work with Nvidia
graphics processors? Sorry if this sounds naive, but I am new to
parallel processing and our IT specialist is useless.

Thanks,
Alan

[Marc Suchard]

BEAGLE supports multi-core CPUs, SSE-vectorization and NVidia GPUs.
Possible command-lines:

beast -beagle -beagle_XXX -beagle_instances Y <XML filename>

where XXX is either CPU, SSE or GPU and Y is the number of CPU-cores/
instances to use.

If you use BEAGLE in your analyses, please reference:

Suchard, M.A. and Rambaut, A. (2009). Many-core algorithms for
statistical phylogenetics. Bioinformatics, 25, 1370-1376.

A formal release publication for BEAGLE 1.0 should be submitted soon,
at which time that manuscript should be referenced as well. The
release publication will describe the recently added SSE-
vectorization.

best, Marc

[Aaron Darling]

Hi Alan,

In addition to what Marc mentioned, BEAGLE can also use OpenMP to
parallelize across multiple CPU cores. A single beagle instance can
currently compute likelihoods for multiple rate categories (think gamma
across site rate heterogeneity) using multiple cores. However, I can't
comment on whether current BEAST releases support the use of BEAGLE in
this way.