In addition to a standard serial CPU implementation, BEAGLE includes two other CPU-based implementations that exploit parallelism in different ways. An SSE implementation in double precision uses vector processing extensions present in many CPUs to parallelize computation across character state values. Single-precision SSE vectorization has not been a BEAGLE priority as other phylogenetic tools already provide this feature (Ronquist and Huelsenbeck 2003 (link), Swofford 2003 ) and, so, is not yet available in BEAGLE. The OpenMP implementation uses multiple threads to parallelize computation across rate categories. Although finer-scale parallelization, equivalent to that achieved for GPU devices, could be attempted, it is unlikely to yield significant speedups due to the thread synchronization overhead in the OpenMP model.
Protocol detail
BEAGLE Phylogenetic Computation Parallelization
Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link:
Access Free Full Text.
Corresponding Organization : University of California, Los Angeles
Other organizations : University of Maryland, College Park, University of California, Davis, University of Kansas, Florida State University, University of Connecticut, University of California, Berkeley, Swedish Museum of Natural History, Evolutionary Genomics (United States), Duke University
Top 5 similar protocols
Protocol cited in 180 other protocols
Variable analysis
independent variables
- CPU-based implementations that exploit parallelism in different ways
- SSE implementation in double precision
- OpenMP implementation
- Parallelization of computation across character state values
- Parallelization of computation across rate categories
- Standard serial CPU implementation
- Single-precision SSE vectorization
- Standard serial CPU implementation is used as a control
Annotations
Based on most similar protocols
Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.
Sign up for free or login to display all annotations
As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!