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van Dam, Hubertus JJ

Publications and source records attributed to van Dam, Hubertus JJ.

Theoretical studies of the global minima and polarizabilities of small lithium clusters

Lithium clusters Lin (n=1-20) have been investigated with density functional theory (DFT) and coupled—cluster (CC) methods. The global-minimum structures are located via an improved basin---hopping algorithm and the lowest energy Lin isomers are confirmed with DFT geometry optimizations, CCSD(T) energy calculations, and by comparing simulated and experimental polarizabilities. The tetrahedral Li4 structure is found to be the basic building block of lithium clusters Lin (n=6-20). Simulated polarizabilities, including thermal effects at room temperature, are in good agreement with measured isotropic polarizabilities.

clusters↗

On the Suitability of MPI as a PGAS Runtime

Partitioned Global Address Space (PGAS) models are emerging as a popular alternative to MPI models for designing scalable applications. At the same time, MPI remains a ubiquitous communication subsystem due to its standardization, high performance, and availability on leading platforms. In this paper, we explore the suitability of using MPI as a scalable PGAS communication subsystem. We focus on the Remote Memory Access (RMA) communication in PGAS models which typically includes {\em get, put,} and {\em atomic memory operations}. We perform an in-depth exploration of design alternatives based on MPI. These alternatives include using a semantically-matching interface such as MPI-RMA, as well as not-so-intuitive interfaces such as MPI two-sided with a combination of multi-threading and dynamic process management. With an in-depth exploration of these alternatives and their shortcomings, we propose a novel design which is facilitated by the data-centric view in PGAS models. This design leverages a combination of highly tuned MPI two-sided semantics and an automatic, user-transparent split of MPI communicators to provide asynchronous progress. We implement the asynchronous progress ranks approach and other approaches within the Communication Runtime for Exascale which is a communication subsystem for Global Arrays. Our performance evaluation spans pure communication benchmarks, graph community detection and sparse matrix-vector multiplication kernels, and a computational chemistry application. The utility of our proposed PR-based approach is demonstrated by a 2.17x speed-up on 1008 processors over the other MPI-based designs.

Computational modeling↗

A Case for Soft Error Detection and Correction in Computational Chemistry

High performance computing platforms are expected to deliver 10(18) floating operations per second by the year 2022 through the deployment of millions of cores. Even if every core is highly reliable the sheer number of the them will mean that the mean time between failures will become so short that most applications runs will suffer at least one fault. In particular soft errors caused by intermittent incorrect behavior of the hardware are a concern as they lead to silent data corruption. In this paper we investigate the impact of soft errors on optimization algorithms using Hartree-Fock as a particular example. Optimization algorithms iteratively reduce the error in the initial guess to reach the intended solution. Therefore they may intuitively appear to be resilient to soft errors. Our results show that this is true for soft errors of small magnitudes but not for large errors. We suggest error detection and correction mechanisms for different classes of data structures. The results obtained with these mechanisms indicate that we can correct more than 95% of the soft errors at moderate increases in the computational cost.

Computational chemistry↗

Noniterative Multireference Coupled Cluster Methods on Heterogeneous CPU-GPU Systems

A novel parallel algorithm for non-iterative multireference coupled cluster (MRCC) theories, which merges recently introduced reference-level parallelism (RLP) [K. Bhaskaran-Nair, J.Brabec, E. Aprà, H.J.J. van Dam, J. Pittner, K. Kowalski, J. Chem. Phys. 137, 094112 (2012)] with the possibility of accelerating numerical calculations using graphics processing unit (GPU) is presented. We discuss the performance of this algorithm on the example of the MRCCSD(T) method (iterative singles and doubles and perturbative triples), where the corrections due to triples are added to the diagonal elements of the MRCCSD (iterative singles and doubles) effective Hamiltonian matrix. The performance of the combined RLP/GPU algorithm is illustrated on the example of the Brillouin-Wigner (BW) and Mukherjee (Mk) state-specific MRCCSD(T) formulations.

Brillouin-Wigner↗