NDLI: Energy efficient biomolecular simulations with FPGA-based reconfigurable computing

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Energy efficient biomolecular simulations with FPGA-based reconfigurable computing

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Energy efficient biomolecular simulations with FPGA-based reconfigurable computing

Content Provider	ACM Digital Library
Author	Nallamuthu, Ananth Agarwal, Pratul K. Hampton, Scott Alam, Sadaf R. Smith, Melissa C.
Abstract	Reconfigurable computing (RC) is being investigated as a hardware solution for improving time-to-solution for biomolecular simulations. A number of popular molecular dynamics (MD) codes are used to study various aspects of biomolecules. These codes are now capable of simulating nanosecond time-scale trajectories per day on conventional microprocessor-based hardware, but biomolecular processes often occur at the microsecond time-scale or longer. A wide gap exists between the desired and achievable simulation capability; therefore, there is considerable interest in alternative algorithms and hardware for improving the time-to-solution of MD codes. The fine-grain parallelism provided by Field Programmable Gate Arrays (FPGA) combined with their low power consumption make them an attractive solution for improving the performance of MD simulations. In this work, we use an FPGA-based coprocessor to accelerate the compute-intensive calculations of LAMMPS, a popular MD code, achieving up to 5.5 fold speed-up on the non-bonded force computations of the particle mesh Ewald method and up to 2.2 fold speed-up in overall time-to-solution, and potentially an increase by a factor of 9 in power-performance efficiencies for the pair-wise computations. The results presented here provide an example of the multi-faceted benefits to an application in a heterogeneous computing environment.
Starting Page	83
Ending Page	84
Page Count	2
File Format	PDF
ISBN	9781450300445
DOI	10.1145/1787275.1787294
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2010-05-17
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Lammps Fpga Molecular dynamics Reconfigurable computing Biomolecular simulations
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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