Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well exploited with a combination of SIMD, multi-threading, and MPI-based SPMD/MPMD parallelism, while GPUs can be used as accelerators to compute interactions offloaded from the CPU. Here we evaluate which hardware produces trajectories with GROMACS 4.6 or 5.0 in the most economical way. We have assembled and benchmarked compute nodes with various CPU/GPU combinations to identify optimal compositions in terms of raw trajectory production rate, performance-to-price ratio, energy efficiency, and several other criteria. Though hardware prices are naturally subject to trends and fluctuations, general tendencies are clearly visible. Adding any type of GPU significantly boosts a node's simulation performance. For inexpensive consumer-class GPUs this improvement equally reflects in the performance-to-price ratio. Although memory issues in consumer-class GPUs could pass unnoticed since these cards do not support ECC memory, unreliable GPUs can be sorted out with memory checking tools. Apart from the obvious determinants for cost-efficiency like hardware expenses and raw performance, the energy consumption of a node is a major cost factor. Over the typical hardware lifetime until replacement of a few years, the costs for electrical power and cooling can become larger than the costs of the hardware itself. Taking that into account, nodes with a well-balanced ratio of CPU and consumer-class GPU resources produce the maximum amount of GROMACS trajectory over their lifetime

Metascheduling of HPC Jobs in Day-Ahead Electricity Markets

High performance grid computing is a key enabler of large scale collaborative computational science. With the promise of exascale computing, high performance grid systems are expected to incur electricity bills that grow super-linearly over time. In order to achieve cost effectiveness in these systems, it is essential for the scheduling algorithms to exploit electricity price variations, both in space and time, that are prevalent in the dynamic electricity price markets. In this paper, we present a metascheduling algorithm to optimize the placement of jobs in a compute grid which consumes electricity from the day-ahead wholesale market. We formulate the scheduling problem as a Minimum Cost Maximum Flow problem and leverage queue waiting time and electricity price predictions to accurately estimate the cost of job execution at a system. Using trace based simulation with real and synthetic workload traces, and real electricity price data sets, we demonstrate our approach on two currently operational grids, XSEDE and NorduGrid. Our experimental setup collectively constitute more than 433K processors spread across 58 compute systems in 17 geographically distributed locations. Experiments show that our approach simultaneously optimizes the total electricity cost and the average response time of the grid, without being unfair to users of the local batch systems.Comment: Appears in IEEE Transactions on Parallel and Distributed System

Robust optimization for energy transactions in multi-microgrids under uncertainty

Independent operation of single microgrids (MGs) faces problems such as low self-consumption of local renewable energy, high operation cost and frequent power exchange with the grid. Interconnecting multiple MGs as a multi-microgrid (MMG) is an effective way to improve operational and economic performance. However, ensuring the optimal collaborative operation of a MMG is a challenging problem, especially under disturbances of intermittent renewable energy. In this paper, the economic and collaborative operation of MMGs is formulated as a unit commitment problem to describe the discrete characteristics of energy transaction combinations among MGs. A two-stage adaptive robust optimization based collaborative operation approach for a residential MMG is constructed to derive the scheduling scheme which minimizes the MMG operating cost under the worst realization of uncertain PV output. Transformed by its KKT optimality conditions, the reformulated model is efficiently solved by a column-and-constraint generation (C&CG) method. Case studies verify the effectiveness of the proposed model and evaluate the benefits of energy transactions in MMGs. The results show that the developed MMG operation approach is able to minimize the daily MMG operating cost while mitigating the disturbances of uncertainty in renewable energy sources. Compared to the non-interactive model, the proposed model can not only reduce the MMG operating cost but also mitigate the frequent energy interaction between the MMG and the grid

A Taxonomy of Data Grids for Distributed Data Sharing, Management and Processing

Data Grids have been adopted as the platform for scientific communities that need to share, access, transport, process and manage large data collections distributed worldwide. They combine high-end computing technologies with high-performance networking and wide-area storage management techniques. In this paper, we discuss the key concepts behind Data Grids and compare them with other data sharing and distribution paradigms such as content delivery networks, peer-to-peer networks and distributed databases. We then provide comprehensive taxonomies that cover various aspects of architecture, data transportation, data replication and resource allocation and scheduling. Finally, we map the proposed taxonomy to various Data Grid systems not only to validate the taxonomy but also to identify areas for future exploration. Through this taxonomy, we aim to categorise existing systems to better understand their goals and their methodology. This would help evaluate their applicability for solving similar problems. This taxonomy also provides a "gap analysis" of this area through which researchers can potentially identify new issues for investigation. Finally, we hope that the proposed taxonomy and mapping also helps to provide an easy way for new practitioners to understand this complex area of research.Comment: 46 pages, 16 figures, Technical Repor

A review of microgrid development in the United States – A decade of progress on policies, demonstrations, controls, and software tools

Microgrids have become increasingly popular in the United States. Supported by favorable federal and local policies, microgrid projects can provide greater energy stability and resilience within a project site or community. This paper reviews major federal, state, and utility-level policies driving microgrid development in the United States. Representative U.S. demonstration projects are selected and their technical characteristics and non-technical features are introduced. The paper discusses trends in the technology development of microgrid systems as well as microgrid control methods and interactions within the electricity market. Software tools for microgrid design, planning, and performance analysis are illustrated with each tool's core capability. Finally, the paper summarizes the successes and lessons learned during the recent expansion of the U.S. microgrid industry that may serve as a reference for other countries developing their own microgrid industries