Parallel Fock matrix construction program for molecular orbital calculation—Specific computer with a hierarchical network

Umeda, Hiroaki; Inadomi, Yuichi; Honda, Hiroki; Nagashima, Umpei

doi:10.1002/jcc.21108

Cited by 3 publications

(3 citation statements)

References 15 publications

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“…Also for electronic structure calculations special processors have been designed; namely ERIC, the ERI Calculation specific chip-multiprocessor 135 or the molecular orbital calculation specific embedded high performance computing (EHPC) system. 136 Almost all special processor types mentioned here accelerate the electronic structure calculations by parallelization of the ERI calculation. This is the reason for the success of GPUs but also of high performance clusters like, for instance, the IBM Blue Gene series.…”

Section: Technical Aspects: Parallelization and Special Hardwarementioning

confidence: 99%

Real‐time quantum chemistry

Haag

Reiher

2012

Int J of Quantum Chemistry

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Significant progress in the development of efficient and fast algorithms for quantum chemical calculations has been made in the past two decades. The main focus has always been the desire to be able to treat ever larger molecules or molecular assemblies-especially linear and sublinear scaling techniques are devoted to the accomplishment of this goal. However, as many chemical reactions are rather local, they usually involve only a limited number of atoms so that models of about 200 (or even less) atoms embedded in a suitable environment are sufficient to study their mechanisms. Thus, the system size does not need to be enlarged, but remains constant for reactions of this type that can be described by less than 200 atoms. The question then arises how fast one can obtain the quantum chemical results. This question is not directly answered by linear-scaling techniques. In fact, ideas such as haptic quantum chemistry (HQC) or interactive quantum chemistry require an immediate provision of quantum chemical information which demands the calculation of data in ' 'real time.' ' In this perspective, we aim at a definition of real-time quantum chemistry, explore its realm and eventually discuss applications in the field of HQC. For the latter, we elaborate whether a direct approach is possible by virtue of real-time quantum chemistry.

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Section: Technical Aspects: Parallelization and Special Hardwarementioning

confidence: 99%

Real‐time quantum chemistry

Haag

Reiher

2012

Int J of Quantum Chemistry

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“…In the field of classical molecular dynamics simulations, the so‐called ANTON processor developed by Shaw et al140 is a successful attempt to build such a special purpose processor. Also, for electronic structure calculations special processors have been designed; namely ERIC, the ERI Calculation specific chip‐multiprocessor141 or the molecular orbital calculation specific embedded high performance computing system 142…”

Section: Methods To Accelerate Electronic Structure Calculationsmentioning

confidence: 99%

Novel use of a disposable digital pressure transducer to increase the safety of pericardiocentesis

Visweswaran

Lightfoot

Gilchrist

2012

Cathet Cardio Intervent

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Cardiac tamponade represents a medical emergency necessitating emergent pericardiocentesis. Use of two-dimensional echocardiography (ECHO) has improved the safety of pericardiocentesis, but procedural challenges may occur when performed in an emergent manner outside of the catheterization laboratory without availability of fluoroscopy and readily available pressure transducers. The most problematic situation is the initial finding of bloody fluid on aspiration where intrapericardial versus intravascular location of the needle must be determined. We report two cases of cardiac tamponade managed with the use of a novel, disposable lightweight digital pressure transducer to directly measure intrapericardial pressures during an ECHO guided pericardiocentesis. In both cases the fluid initially encountered was grossly bloody and rapid definition of whether this was pericardial fluid versus an inappropriately located needle in the vascular space was critical. This type of novel, disposable self contained manometer has the potential to further minimize complications associated with pericardiocentesis. It offers a cost effective alternative and answers questions about the shifting point of service for pericardiocentesis from the invasive cath lab to less costly locations (Drummond, et al., J Am Soc Echocardiogr 1998;11:433-435).

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“…24 Here, (ij|kl) denotes a two-electron integral with four atomic orbital indices i, j, k, and l, and with N being the number of atomic orbitals. The pseudocode is shown in Figure 1, where the statements requiring RMA are indicated in bold italic statements.…”

Section: Distributed Parallel Fock Matrix Constructionmentioning

confidence: 99%

Parallel Fock matrix construction with distributed shared memory model for the FMO‐MO method

et al. 2010

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A parallel Fock matrix construction program for FMO-MO method has been developed with the distributed shared memory model. To construct a large-sized Fock matrix during FMO-MO calculations, a distributed parallel algorithm was designed to make full use of local memory to reduce communication, and was implemented on the Global Array toolkit. A benchmark calculation for a small system indicates that the parallelization efficiency of the matrix construction portion is as high as 93% at 1,024 processors. A large FMO-MO application on the epidermal growth factor receptor (EGFR) protein (17,246 atoms and 96,234 basis functions) was also carried out at the HF/6-31G level of theory, with the frontier orbitals being extracted by a Sakurai-Sugiura eigensolver. It takes 11.3 h for the FMO calculation, 49.1 h for the Fock matrix construction, and 10 min to extract 94 eigen-components on a PC cluster system using 256 processors.

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Parallel Fock matrix construction program for molecular orbital calculation—Specific computer with a hierarchical network

Cited by 3 publications

References 15 publications

Real‐time quantum chemistry

Real‐time quantum chemistry

Novel use of a disposable digital pressure transducer to increase the safety of pericardiocentesis

Parallel Fock matrix construction with distributed shared memory model for the FMO‐MO method

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