RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs Export

@incollection{citeulike:3519492, abstract = {Inference of phylogenetic trees comprising hundreds or even thousands of organisms based on the Maximum Likelihood (ML) method is computationally extremely intensive. In order to accelerate computations we implemented RAxML-OMP, an efficient OpenMP-parallelization for Symmetric Multi-Processing machines (SMPs) based on the sequential program RAxML-V (Randomized Axelerated Maximum Likelihood). RAxML-V is a program for inference of evolutionary trees based upon the ML method and incorporates several advanced search algorithms like fast hill-climbing and simulated annealing. We assess performance of RAxML-OMP on the widely used Intel Xeon, Intel Itanium, and AMD Opteron architectures. RAxML-OMP scales particularly well on the AMD Opteron architecture and achieves even super-linear speedups for large datasets (with a length ≥ 5.000 base pairs) due to improved cache-efficiency and data locality. RAxML-OMP is freely available as open source code.}, author = {Stamatakis, Alexandros and Ott, Michael and Ludwig, Thomas}, citeulike-article-id = {3519492}, citeulike-linkout-0 = {http://dx.doi.org/10.1007/11535294_25}, citeulike-linkout-1 = {http://www.springerlink.com/content/duqxjtpev3wb1wkv}, doi = {10.1007/11535294_25}, journal = {Parallel Computing Technologies}, keywords = {comparison-ib-mx, hpc-app, raxml}, pages = {288--302}, posted-at = {2008-11-15 19:18:59}, priority = {2}, title = {RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs}, url = {http://dx.doi.org/10.1007/11535294_25}, year = {2005} }

TY - CHAP ID - citeulike:3519492 L3 - citeulike-article-id:3519492 N2 - Inference of phylogenetic trees comprising hundreds or even thousands of organisms based on the Maximum Likelihood (ML) method is computationally extremely intensive. In order to accelerate computations we implemented RAxML-OMP, an efficient OpenMP-parallelization for Symmetric Multi-Processing machines (SMPs) based on the sequential program RAxML-V (Randomized Axelerated Maximum Likelihood). RAxML-V is a program for inference of evolutionary trees based upon the ML method and incorporates several advanced search algorithms like fast hill-climbing and simulated annealing. We assess performance of RAxML-OMP on the widely used Intel Xeon, Intel Itanium, and AMD Opteron architectures. RAxML-OMP scales particularly well on the AMD Opteron architecture and achieves even super-linear speedups for large datasets (with a length ≥ 5.000 base pairs) due to improved cache-efficiency and data locality. RAxML-OMP is freely available as open source code. JF - Parallel Computing Technologies EP - 302 TI - RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs SP - 288 KW - comparison-ib-mx KW - hpc-app KW - raxml AU - Stamatakis, Alexandros AU - Ott, Michael AU - Ludwig, Thomas PY - 2005/// UR - http://dx.doi.org/10.1007/11535294_25 ER -