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
[1]   PROJECTOR AUGMENTED-WAVE METHOD [J].
BLOCHL, PE .
PHYSICAL REVIEW B, 1994, 50 (24) :17953-17979
[2]   ABINITIO THEORY OF THE SI(111)-(7X7) SURFACE RECONSTRUCTION - A CHALLENGE FOR MASSIVELY PARALLEL COMPUTATION [J].
BROMMER, KD ;
NEEDELS, M ;
LARSON, BE ;
JOANNOPOULOS, JD .
PHYSICAL REVIEW LETTERS, 1992, 68 (09) :1355-1358
[3]   SELF-CONSISTENT CALCULATIONS OF THE ENERGY-BANDS AND BONDING PROPERTIES OF B-12(C-3) [J].
BYLANDER, DM ;
KLEINMAN, L ;
LEE, S .
PHYSICAL REVIEW B, 1990, 42 (02) :1394-1403
[4]   High-pressure melting of lead [J].
Cricchio, F ;
Belonoshko, AB ;
Burakovsky, L ;
Preston, DL ;
Ahuja, R .
PHYSICAL REVIEW B, 2006, 73 (14)
[5]   ITERATIVE CALCULATION OF A FEW OF LOWEST EIGENVALUES AND CORRESPONDING EIGENVECTORS OF LARGE REAL-SYMMETRIC MATRICES [J].
DAVIDSON, ER .
JOURNAL OF COMPUTATIONAL PHYSICS, 1975, 17 (01) :87-94
[6]   Novel stabilization mechanism on polar surfaces: ZnO(0001)-Zn [J].
Dulub, O ;
Diebold, U ;
Kresse, G .
PHYSICAL REVIEW LETTERS, 2003, 90 (01) :4-016102
[7]   An efficient 3-dim FFT for plane wave electronic structure calculations on massively parallel machines composed of multiprocessor nodes [J].
Goedecker, S ;
Boulet, M ;
Deutsch, T .
COMPUTER PHYSICS COMMUNICATIONS, 2003, 154 (02) :105-110
[8]   First-principles computation of material properties: the ABINIT software project [J].
Gonze, X ;
Beuken, JM ;
Caracas, R ;
Detraux, F ;
Fuchs, M ;
Rignanese, GM ;
Sindic, L ;
Verstraete, M ;
Zerah, G ;
Jollet, F ;
Torrent, M ;
Roy, A ;
Mikami, M ;
Ghosez, P ;
Raty, JY ;
Allan, DC .
COMPUTATIONAL MATERIALS SCIENCE, 2002, 25 (03) :478-492
[9]   INHOMOGENEOUS ELECTRON-GAS [J].
RAJAGOPAL, AK ;
CALLAWAY, J .
PHYSICAL REVIEW B, 1973, 7 (05) :1912-1919
[10]   Car-Parrinello molecular dynamics on massively parallel computers [J].
Hutter, J ;
Curioni, A .
CHEMPHYSCHEM, 2005, 6 (09) :1788-1793