Amdahl's law and parallelization of the FMLSQ program on the Intel Nehalem architecture

被引：1
|
作者：
Strokopytov, Boris V. [1 ,2 ]
Dorovatovsky, Pavel V. [1 ,2 ]
Trofimov, Anton A. [1 ]
Polyakov, Konstantin M. [1 ,2 ]
机构：
[1] VA Engelhardt Mol Biol Inst, Moscow 119991, Russia
[2] Russian Res Ctr, Kurchatov Inst, Moscow 123182, Russia
来源：
JOURNAL OF APPLIED CRYSTALLOGRAPHY | 2011年 / 44卷
关键词：
MACROMOLECULAR STRUCTURES; EFFICIENT CALCULATION; REFINEMENT; MATRIX; EQUATIONS; BINDING; FFT;
D O I：
10.1107/S0021889811020218
中图分类号：
O6 [化学];
学科分类号：
0703 ;
摘要：
This paper highlights a parallelization of the FMLSQ program, which allows full-matrix least-squares refinement of large macromolecular structures. The detailed elapsed time profiling of FMLSQ and analysis of its execution on two different Intel architectures has led to a dramatic speedup due to parallelization of all stages of the algorithm. Amdahl's law proved to be very useful during this analysis. It has been shown that processor memory bandwidth may be more important than raw processing power for parallel crystallographic calculations. The new parallelized version of the program has been tested on several protein structures at high resolution. Requirements for a computing architecture intended for full-matrix refinement are discussed in detail.
引用
收藏
页码：672 / 680
页数：9
相关论文
共 50 条
  • [1] Computer Architecture and Amdahl's Law
    Amdahl, Gene M.
    [J]. COMPUTER, 2013, 46 (12) : 38 - 46
  • [2] Next generation Intel® micro-architecture (Nehalem) clocking architecture
    Kurd, Nasser
    Douglas, Jonathan
    Mosalikanti, Praveen
    Kumar, Rajesh
    [J]. 2008 SYMPOSIUM ON VLSI CIRCUITS, DIGEST OF TECHNICAL PAPERS, 2008, : 62 - 63
  • [3] Next generation Intel® micro-architecture (Nehalem) clocking architecture
    Kurd, Nasser
    Douglas, Jonathan
    Mosalikanti, Praveen
    Kumar, Rajesh
    [J]. 2008 IEEE SYMPOSIUM ON VLSI CIRCUITS, 2008, : 49 - 50
  • [4] On the Parallelization Approaches for Intel MIC Architecture
    Atanassov, E.
    Gurov, T.
    Karaivanova, A.
    Ivanovska, S.
    Durchova, M.
    Dimitrov, D.
    [J]. APPLICATION OF MATHEMATICS IN TECHNICAL AND NATURAL SCIENCES (AMITANS'16), 2016, 1773
  • [5] Using Amdahl's law as a metric to drive code parallelization: Two case studies
    Horoi, M
    Enbody, RJ
    [J]. INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 2001, 15 (01): : 75 - 80
  • [6] Next Generation Intel® Core™ Micro-Architecture (Nehalem) Clocking
    Kurd, Nasser
    Mosalikanti, Praveen
    Neidengard, Mark
    Douglas, Jonathan
    Kumar, Rajesh
    [J]. IEEE JOURNAL OF SOLID-STATE CIRCUITS, 2009, 44 (04) : 1121 - 1129
  • [7] Parallelization of Adaboost Algorithm on Intel MIC Architecture
    Luo, Haibiao
    Yuan, Haojie
    Cheng, Shendong
    Li, Ying
    Yuan, Feng
    Wei, Mingzhu
    [J]. PROCEEDINGS OF THE 2016 INTERNATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE: TECHNOLOGIES AND APPLICATIONS, 2016, 127
  • [8] Break Amdahl's Law!
    Sutter, Herb
    [J]. DR DOBBS JOURNAL, 2008, 33 (02): : 74 - +
  • [9] Amdahl's Law for Tail Latency
    Delimitrou, Christina
    Kozyrakis, Christos
    [J]. COMMUNICATIONS OF THE ACM, 2018, 61 (08) : 65 - 72
  • [10] Amdahl's law in the multicore era
    Hill, Mark D.
    Marty, Michael R.
    [J]. COMPUTER, 2008, 41 (07) : 33 - +
12345