Vector optimization of amber 3.0 on the NEC SX-2/400 supercomputer |
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| Affiliation: | 1. Department of Environmental Engineering, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea;2. Korea Gas Research Institute New Energy Technology Research Center, Sinhang-daero 960, Yeonsu-gu, Incheon, 21993, Republic of Korea;1. College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang, Henan, 464000, PR China;2. Henan Province Key Laboratory of Utilization of Non Metallic Mineral in the South of Henan, Xinyang Normal University, Xinyang, Henan, 464000, PR China;3. State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering, Ningxia University, Yinchuan, 750021, PR China;1. Department of Physics, Faculty of Science, Firat University, 23119 Elazig, Turkey;2. Research and Application Center, Kastamonu University, 37100 Kastamonu, Turkey;3. Department of Chemistry, Faculty of Science, Firat University, 23119 Elazig, Turkey;1. College of Chemistry, Chemical Engineering and Materials Science, Zaozhuang University, Zaozhuang, 277160, PR China;2. School of Environment and Technology, Nanjing Institute of Technology, Nanjing, 211167, PR China;3. College of Chemical and Environmental Engineering, Shandong University of Science and Tehnnology, Qingdao, 266590, PR China;1. Fuel Cell Research Center, Korea Institute of Science and Technology (KIST), 39-1 Hawolgok, Seongbuk-gu, Seoul 136-791, Republic of Korea;2. Department of Environmental Engineering, Chungbuk National University, 52 Naesudong-ro, Heungdeok-gu, Cheongju, Chungbuk 361-763, Republic of Korea;3. Department of Clean Energy and Chemical Engineering, University of Science Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 305-350, Republic of Korea;4. Department of Materials Engineering and Convergence Technology, Enginerring Research Institute, Gyeongsang National University, Jinju 660-701, Republic of Korea |
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| Abstract: | The AMBER 3.0 molecular mechanics and molecular dynamics programs have been ported to and vectorized on the NEC SX-2/400 supercomputer. A detailed discussion of the vector enhancement of the AMBER non-bonded pair list generation subroutine is presented. Automatic vectorization using the FORT77SX compiler yielded speed-up factors of 1.2 to 1.5 over unvectorized code. Recoding of key portions of the program, as described in this paper, yielded speed-up factors of 1.8-2.7. The perturbation molecular dynamics program, PERDYN, now runs up to 35 times faster on the SX-2/400 than the VAX optimized version of the same program runs on the VAX 8650. |
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