Computing and data processing

The applications of computers and data processing to astronomy are discussed. Among the topics covered are the emerging national information infrastructure, workstations and supercomputers, supertelescopes, digital astronomy, astrophysics in a numerical laboratory, community software, archiving of ground-based observations, dynamical simulations of complex systems, plasma astrophysics, and the remote control of fourth dimension supercomputers

Assessing gains from parallel computation on a supercomputer

We assess gains from parallel computation on Backlight supercomputer. The information transfers are expensive. We find that to make parallel computation efficient, a task per core must be sufficiently large, ranging from few seconds to one minute depending on the number of cores employed. For small problems, the shared memory programming (OpenMP) and a hybrid of shared and distributive memory programming (OpenMP&MPI) leads to a higher efficiency of parallelization than the distributive memory programming (MPI) alone.XSEDE grant TG-ASC120048; Hoover Institution and Department of Economics at Stanford University, University of Alicante, Ivie, and the Spanish Ministry of Science and Innovation under the grant ECO2012-36719

Integrating BOINC with Microsoft Excel: A case study

The convergence of conventional Grid computing with public resource computing (PRC) offers potential benefits in the enterprise setting. For this work we took the popular PRC toolkit BOINC and used it to execute a previously monolithic Microsoft Excel financial model across several commodity computers. Our experience indicates that speedup approaching linear may be realised for certain scenarios, and that this approach offers a viable route to leveraging idle desktop PCs in the enterprise

Grids and the Virtual Observatory

We consider several projects from astronomy that benefit from the Grid paradigm and associated technology, many of which involve either massive datasets or the federation of multiple datasets. We cover image computation (mosaicking, multi-wavelength images, and synoptic surveys); database computation (representation through XML, data mining, and visualization); and semantic interoperability (publishing, ontologies, directories, and service descriptions)

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