Accelerating Molecular Dynamics Simulations with Reconfigurable Computers

@article{citeulike:2771309, abstract = {With advances in reconfigurable hardware, especially field-programmable gate arrays (FPGAs), it has become possible to use reconfigurable hardware to accelerate complex applications, such as those in scientific computing. There has been a resulting development of reconfigurable computers--computers which have both general purpose processors and reconfigurable hardware, as well as memory and high-performance interconnection networks. In this paper, we describe the acceleration of molecular dynamics simulation with reconfigurable computers. We evaluate several design alternatives for the reconfigurable computer implementation. We show that a single node accelerated with reconfigurable hardware--utilizing fine-grained parallelism in the reconfigurable hardware design--is able to achieve a speed-up of about 2X over the corresponding software-only simulation. We then parallelize the application and study the effect of acceleration on performance and scalability. Specifically, we study strong scaling in which the problem size is fixed. We find that the unaccelerated version actually scales better because it spends more time in computation than the accelerated version does. However, we also find that a cluster of P accelerated nodes gives better performance than a cluster of 2P unaccelerated nodes.}, author = {Scrofano, Ronald and Gokhale, Maya B. and Trouw, Frans and Prasanna, Viktor K. }, booktitle = {Parallel and Distributed Systems, IEEE Transactions on}, citeulike-article-id = {2771309}, doi = {10.1109/TPDS.2007.70777}, journal = {Parallel and Distributed Systems, IEEE Transactions on}, keywords = {fpgasupercomputing, high-performance\_computing, molecular\_dynamics, reconfigurable\_computing}, number = {6}, pages = {764--778}, posted-at = {2008-05-08 13:57:15}, priority = {2}, title = {Accelerating Molecular Dynamics Simulations with Reconfigurable Computers}, url = {http://dx.doi.org/10.1109/TPDS.2007.70777}, volume = {19}, year = {2008} }

TY - JOUR ID - citeulike:2771309 L3 - citeulike-article-id:2771309 TI - Accelerating Molecular Dynamics Simulations with Reconfigurable Computers T2 - Parallel and Distributed Systems, IEEE Transactions on JF - Parallel and Distributed Systems, IEEE Transactions on VL - 19 IS - 6 SP - 764 EP - 778 N2 - With advances in reconfigurable hardware, especially field-programmable gate arrays (FPGAs), it has become possible to use reconfigurable hardware to accelerate complex applications, such as those in scientific computing. There has been a resulting development of reconfigurable computers--computers which have both general purpose processors and reconfigurable hardware, as well as memory and high-performance interconnection networks. In this paper, we describe the acceleration of molecular dynamics simulation with reconfigurable computers. We evaluate several design alternatives for the reconfigurable computer implementation. We show that a single node accelerated with reconfigurable hardware--utilizing fine-grained parallelism in the reconfigurable hardware design--is able to achieve a speed-up of about 2X over the corresponding software-only simulation. We then parallelize the application and study the effect of acceleration on performance and scalability. Specifically, we study strong scaling in which the problem size is fixed. We find that the unaccelerated version actually scales better because it spends more time in computation than the accelerated version does. However, we also find that a cluster of P accelerated nodes gives better performance than a cluster of 2P unaccelerated nodes. KW - fpgasupercomputing KW - high-performance_computing KW - molecular_dynamics KW - reconfigurable_computing AU - Scrofano, Ronald AU - Gokhale, Maya AU - Trouw, Frans AU - Prasanna, Viktor PY - 2008/// UR - http://dx.doi.org/10.1109/TPDS.2007.70777 ER -