Large-scale ab initio calculations based on three levels of parallelization

被引:157
作者
Bottin, Francois [1 ,2 ]
Leroux, Stephane [1 ]
Knyazev, Andrew [3 ]
Zerah, Gilles [1 ]
机构
[1] CEA, DAM Ile France, Dept Phys Theor & Appl, F-91680 Bruyeres Le Chatel, France
[2] ENS, CNRS, UMR 8536, LRC,Ctr Math & Leurs Applicat, Cachan, France
[3] Univ Colorado, Dept Math Sci, Denver, CO 80217 USA
基金
美国国家科学基金会;
关键词
density functional theory; ABINIT; eigenvalue; LOBPCG; SCALAPACK; FFT; parallelization; MPI; supercomputing;
D O I
10.1016/j.commatsci.2007.07.019
中图分类号
T [工业技术];
学科分类号
08 ;
摘要
We suggest and implement a parallelization scheme based on an efficient multiband eigenvalue solver, called the locally optimal block preconditioned conjugate gradient (LOBPCG) Method, and using an optimized three-dimensional (3D) fast Fourier transform (FFT) in the ab initio plane-wave code ABINIT. In addition to the standard data partitioning over processors corresponding to different k-points, we introduce data partitioning with respect to blocks of bands as well as spatial partitioning in the Fourier space of coefficients over the plane waves basis set used in ABINIT. This k-points-multiband-FFT parallelization avoids any collective communications on the whole set of processors relying instead on one-dimensional communications only. For a single k-point, super-linear scaling is achieved for up to 100 processors due to an extensive use of hardware-optimized BLAS, LAPACK and SCALAPACK routines, mainly in the LOBPCG routine. We observe good performance up to 200 processors. With 10 k-points our three-way data partitioning results in linear scaling up to 1000 processors for a practical system used for testing. (C) 2007 Elsevier B.V. All rights reserved.
引用
收藏
页码:329 / 336
页数:8
相关论文
共 36 条
[21]   Competing stabilization mechanism for the polar ZnO(0001)-Zn surface [J].
Kresse, G ;
Dulub, O ;
Diebold, U .
PHYSICAL REVIEW B, 2003, 68 (24)
[22]   AN ITERATION METHOD FOR THE SOLUTION OF THE EIGENVALUE PROBLEM OF LINEAR DIFFERENTIAL AND INTEGRAL OPERATORS [J].
LANCZOS, C .
JOURNAL OF RESEARCH OF THE NATIONAL BUREAU OF STANDARDS, 1950, 45 (04) :255-282
[23]   Melting of lithium hydride under pressure [J].
Ogitsu, T ;
Schwegler, E ;
Gygi, F ;
Galli, G .
PHYSICAL REVIEW LETTERS, 2003, 91 (17) :175502-175502
[24]   ITERATIVE MINIMIZATION TECHNIQUES FOR ABINITIO TOTAL-ENERGY CALCULATIONS - MOLECULAR-DYNAMICS AND CONJUGATE GRADIENTS [J].
PAYNE, MC ;
TETER, MP ;
ALLAN, DC ;
ARIAS, TA ;
JOANNOPOULOS, JD .
REVIEWS OF MODERN PHYSICS, 1992, 64 (04) :1045-1097
[25]   CONVERGENCE ACCELERATION OF ITERATIVE SEQUENCES - THE CASE OF SCF ITERATION [J].
PULAY, P .
CHEMICAL PHYSICS LETTERS, 1980, 73 (02) :393-398
[26]   Surface reconstructions on InN and GaN polar and nonpolar surfaces [J].
Segev, David ;
Van de Walle, Chris G. .
SURFACE SCIENCE, 2007, 601 (04) :L15-L18
[27]   Implementation of linear-scaling plane wave density functional theory on parallel computers [J].
Skylaris, CK ;
Haynes, PD ;
Mostofi, AA ;
Payne, MC .
PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS, 2006, 243 (05) :973-988
[28]   Introducing ONETEP: Linear-scaling density functional simulations on parallel computers [J].
Skylaris, CK ;
Haynes, PD ;
Mostofi, AA ;
Payne, MC .
JOURNAL OF CHEMICAL PHYSICS, 2005, 122 (08)
[29]   AB-INITIO MOLECULAR-DYNAMICS STUDY OF FIRST-ORDER PHASE-TRANSITIONS - MELTING OF SILICON [J].
SUGINO, O ;
CAR, R .
PHYSICAL REVIEW LETTERS, 1995, 74 (10) :1823-1826
[30]   SOLUTION OF SCHRODINGER-EQUATION FOR LARGE SYSTEMS [J].
TETER, MP ;
PAYNE, MC ;
ALLAN, DC .
PHYSICAL REVIEW B, 1989, 40 (18) :12255-12263