Things have been quite on the blog, but not because there has not been a lot to say. In fact, there has been so much happening that I have had not the idle cycles to write about them.
Recently got a chance to meet one of the D.E.Shaw Research scientists and got an insight into what they are doing. Prior to forming D.E. Shaw Research, David Shaw founded D.E. Shaw & Co., a hedge fund which is one of the most successful quantitative analysis shops. Since 2001, David Shaw has been doing full time research as part of D.E.Shaw Research. D.E. Shaw Research develops both algorithms and customized machine architectures for molecular dynamic simulations such as protein folding. The result is the Anton Supercomputer, a heavily customized machine with 512 specialized computing nodes specifically designed for particle interaction simulations.
Basically, each of the 512 nodes consists of a heavily pipelined special-purpose ASIC that is designed to compute the particle force interactions (using an algorithm called the NT method), along with a general-purpose processor that supports a limited instruction set. Communication is heavily optimized to reduce the amount of data exchanged between nodes. The processors are connected into a 3D toroidal hypercube and each processor "owns" a set of particles corresponding to a particular cube of space. One of these is to be hosted at the Pittsburgh Supercomputing Center.
The ability to perform long, accurate Molecular Dynamics (MD) simulations involving proteins and other biological macro-molecules could in principle provide answer to some of the most important outstanding questions in the field of biology, chemistry and medicine.
Recently got a chance to meet one of the D.E.Shaw Research scientists and got an insight into what they are doing. Prior to forming D.E. Shaw Research, David Shaw founded D.E. Shaw & Co., a hedge fund which is one of the most successful quantitative analysis shops. Since 2001, David Shaw has been doing full time research as part of D.E.Shaw Research. D.E. Shaw Research develops both algorithms and customized machine architectures for molecular dynamic simulations such as protein folding. The result is the Anton Supercomputer, a heavily customized machine with 512 specialized computing nodes specifically designed for particle interaction simulations.
Basically, each of the 512 nodes consists of a heavily pipelined special-purpose ASIC that is designed to compute the particle force interactions (using an algorithm called the NT method), along with a general-purpose processor that supports a limited instruction set. Communication is heavily optimized to reduce the amount of data exchanged between nodes. The processors are connected into a 3D toroidal hypercube and each processor "owns" a set of particles corresponding to a particular cube of space. One of these is to be hosted at the Pittsburgh Supercomputing Center.
The ability to perform long, accurate Molecular Dynamics (MD) simulations involving proteins and other biological macro-molecules could in principle provide answer to some of the most important outstanding questions in the field of biology, chemistry and medicine.
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