Full Electron Calculation Beyond 20,000 Atoms: Ground Electronic State of Photosynthetic Proteins TSUTOMU IKEGAMI, TOYOKAZU ISHIDA, DMITRI G. FEDOROV, KAZUO KI- TAURA, YUICHI INADOMI, HIROAKI UMEDA, MITSUO YOKOKAWA, and SATOSHI SEKIGUCHI National Institute of Advanced Industrial Science and Technology A full electron calculation for the photosynthetic reaction center of Rhodopseudomonas viridis was performed by using the fragment molecular orbital (FMO) method on a massive cluster computer. The target system contains 20,581 atoms and 77,754 electrons, which was divided into 1,398 fragments. According to the FMO prescription, the calculations of the fragments and pairs of the fragments were conducted to obtain the electronic state of the system. The calculation at RHF/6-31G* level of theory took 72.5 hours with 600 CPUs. The CPUs were grouped into several workers, to which the calculations of the fragments were dispatched. An uneven CPU grouping, where two types of workers are generated, was shown to be efficient. Categories and Subject Descriptors: J.2 [Computer Applications]: Physical Sciences And Engineering General Terms: Algorithms, Performance Additional Key Words and Phrases: Cluster computer, Electronic state calculation, Fragment molecular orbital, Photosynthesis 1. INTRODUCTION The algorithms in quantum chemistry have been developed in accordance with the evolution of the computer architecture. In the dawn of the computer era, when the CPU cycle was expensive, all the intermediate results were kept on disks, or even on magnetic tapes. As the performance of CPU improved and the data transfer be- tween CPU and storage devices became a bottleneck, a new algorithm was invented to store a minimal amount of intermediates on core memory, recalculating others on-the-fly. Those algorithms were further optimized to run better on shared mem- ory parallel machines, as they became available. Throughout the progress of both theory and technology, the size of molecules under the subject of the full electron calculation increased step by step. At the end of the last century, a novel fragment molecular orbital (FMO) method [Kitaura et al. 1999; Nakano et al. 2000; Nakano et al. 2002; Fedorov and Kitaura 2004; Fedorov et al. 2004] brought about another wave of changes to the electronic state calculation. In this paper, we will introduce our experiences on the FMO calculation of a photosynthetic reaction system, the largest ever application in full electron calcu- Permission to make digital or hard copies of all or part of this workfor personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage,and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or toredistribute to lists, requires prior specific permission and/or a fee. SC|05 November 12-18, 2005, Seattle, Washington, USA c ⃝2005 ACM 1-59593-061-2/05/0011...$5.00