Development of parallel density functional program using distributed matrix to calculate all-electron canonical wavefunction of large molecules.
We developed a new parallel density-functional canonical molecular-orbital program for large molecules based on the resolution of the identity method. In this study, all huge matrices were decomposed and saved to the distributed local memory. The routines of the analytical molecular integrals and numerical integrals of the exchange-correlation terms were parallelized using the single program multiple data method. A conventional linear algebra matrix library, ScaLAPACK, was used for matrix operations, such as diagonalization, multiplication, and inversion. Anderson's mixing method was adopted to accelerate the self-consistent field (SCF) convergence. Using this program, we calculated the canonical wavefunctions of a 306-residue protein, insulin hexamer (26,790 orbitals), and a 133-residue protein, interleukin (11,909 orbitals) by the direct-SCF method. In regard to insulin hexamer, the total parallelization efficiency of the first SCF iteration was estimated to be 82% using 64 Itanium 2 processors connected at 3.2 GB/s (SGI Altix3700), and the calculation successfully converged at the 17-th SCF iteration. By adopting the update method, the computational time of the first and the final SCF loops was 229 min and 156 min, respectively. The whole computational time including the calculation before the SCF loop was 2 days and 17 h. This study put the calculations of the canonical wavefunction of 30,000 orbitals to practical use.
Inaba
Toru
T
Mechanical Engineering Research Laboratory, Hitachi Ltd., Japan.
Sato
Fumitoshi
F