The science clusters are used by Museum research scientists, postdoctoral fellows, graduate and undergraduate students whose work relies heavily on high-end capability computing in areas of biology, genomics, astrophysics, and anthropology.
Museum scientists are at the forefront of developing and utilizing cutting-edge approaches in computing paradigms to address problems of broad application in the biological and physical sciences. For instance, researchers in Invertebrate Zoology have developed and implemented phylogenetic algorithms that are used by scientists around the world. While those in Astrophysics, in collaborations with scientists world-wide, use high-resolution numerical simulation techniques to bring life to the Hayden Planetarium Space Shows.
Further, as part of the core mission of the Museum, to educate, train and disseminate information, the clusters are leveraged to promote the significance of high-performance computing within today's society for science and engineering through our educational programs.
High-performance computing at the Museum has a long history, beginning with homebrew clusters assembled by curators and graduate students.
The Museum computing facility consists of several high-performance computing platforms: two Intel XEON multi-node Linux clusters, one AMD multi-core server and a six node special-purpose GRavity PipelinE (GRAPE) machines. The clusters are used primarily to run scientific applications extending phylogenetic analysis in computational biology to large-scale astrophysics simulations.
Enyo is a cluser of 33 Intel Xeon 3.0GHz dual-core, dual-processors (128 processors), L2 cache, 64-bit and 1TB shared storage. Each node has a total of 16GB RAM. The system is configured with Infiniband switch fabric, Linux Cent OS, and Scyld Clusterware cluster management solution.
Demeter is a cluster of 127 Intel Xeon 2.8GHz dual-core (256 processors), diskless nodes, 4GB RAM per node and 32-bit. The system is configured with Myrinet switch fabric and 100MB Ethernet, Linux RedHat and NimbusOS cluster management solution. At the time of acquisition in 2002, Demeter ranked number 107 on the Top 500 list of supercomputers.
Eve is an AMD Opteron 846 2.2GHz, 8-way server and 64-bit. It has 128GB RAM and runs Linux Cent OS This machine is used mainly for testing and development.
- GRavity PipelinE (GRAPE) machines are purposely used for computing gravitational forces at speeds of several teraflops. Each board is connected to a Linux host server.
The computer clusters are used intensively for research that relies heavily on high-end capability computing in biology, genomics, astrophysics, and anthropology.
The Division of Anthropology at the Museum has recently begun to rely on the use of tools more familiar in biological evolution and systematics due to advances in both data acquisition and databasing, and interpretive models based on a tree/network framework. The research of Anthropology curator Peter Whiteley employs an anthro-informatic approach, utilizing computational and phylogenetic tools to build on databases of human kinship variants, and test hypotheses about kinship system transformation and evolution.
The Museum's biological science divisions (Invertebrate Zoology, Vertebrate Zoology, and Paleontology) are involved in a broad variety of research projects concerning the evolutionary relationships of creatures of immense diversity, ranging from viruses, foraminifera, and sponges to arthropods, and vertebrates. The basic problem of reconstructing evolutionary trees falls into a class of problems known at NP-hard, i.e. non-deterministic polynomial-time hard. Researchers in these divisions are at the forefront of algorithmic innovation and implementation of combinatorial heuristics.
Researchers in the Invertebrate Zoology Division, led by Chair Ward Wheeler, have developed a series of heuristics to the tree-alignment problem and chromosomal alignment. These ideas (and other existing approaches) have been implemented in our open source, freely available POY software (Varon et al., 2010; ), which was preceded by MALIGN.
Empirical and theoretical papers in astrophysics and biological sciences are available for download. Find these papers, along with relevant copyright law and acknowledgement requirements, on our Publications page.