Architecture of Qbox: A scalable first-principles molecular dynamics code

被引:208
作者
Gygi, F. [1 ]
机构
[1] Univ Calif Davis, Dept Appl Sci, Davis, CA 95616 USA
关键词
D O I
10.1147/rd.521.0137
中图分类号
TP3 [计算技术、计算机技术];
学科分类号
0812 ;
摘要
We describe the architecture of Qbox, a parallel, scalable first principles molecular dynamics (FPMD) code. Qbox is a C++/ Message Passing Interface implementation of FPMD based on the plane-wave, pseudopotential method for electronic structure calculations. It is built upon well-optimized parallel numerical libraries, such as Basic Linear Algebra Communication Subprograms (BLACS) and Scalable Linear Algebra Package (ScaLAPACK), and also features an Extensible Markup Language (XML) interface built on the Apache Xerces-C library. We describe various choices made in the design of Qbox that led to excellent scalability on large parallel computers. In particular, we discuss the case of the IBM Blue Gene/L (TM) platform on which Qbox was run using up to 65,536 nodes. Future design challenges,for upcoming petascale computers are also discussed. Examples of applications of Qbox to a variety of first-principles simulations of solids, liquids, and nanostructures are briefly described.
引用
收藏
页码:137 / 144
页数:8
相关论文
共 31 条
[1]  
Adiga Narasimha R, 2002, SC 02, DOI [10.1109/SC.2002.10017, DOI 10.1109/SC.2002.10017]
[2]   A first principles simulation of rigid water [J].
Allesch, M ;
Schwegler, E ;
Gygi, F ;
Galli, G .
JOURNAL OF CHEMICAL PHYSICS, 2004, 120 (11) :5192-5198
[3]   ITERATIVE PROCEDURES FOR NONLINEAR INTEGRAL EQUATIONS [J].
ANDERSON, DG .
JOURNAL OF THE ACM, 1965, 12 (04) :547-&
[4]  
[Anonymous], P INT C AC SPEECH SI
[5]  
[Anonymous], EFFECTIVE C 50 SPECI
[6]  
*AP, AP XML PROJ XERC C V
[7]  
Belonoshko AB, 1996, AM MINERAL, V81, P303
[8]  
Blackford L. S., 1997, ScaLAPACK user's guide
[9]   UNIFIED APPROACH FOR MOLECULAR-DYNAMICS AND DENSITY-FUNCTIONAL THEORY [J].
CAR, R ;
PARRINELLO, M .
PHYSICAL REVIEW LETTERS, 1985, 55 (22) :2471-2474
[10]   Carbon under extreme conditions: Phase boundaries and electronic properties from first-principles theory [J].
Correa, AA ;
Bonev, SA ;
Galli, G .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (05) :1204-1208