Tuning Parallel Applications in Parallel

Auto-tuning has recently received significant attention from the High Performance Computing community. Most auto-tuning approaches are specialized to work either on specific domains such as dense linear algebra and stencil computations, or only at certain stages of program execution such as compile time and runtime. Real scientific applications, however, demand a cohesive environment that can efficiently provide auto-tuning solutions at all stages of application development and deployment. Towards that end, we describe a unified end-to-end approach to auto-tuning scientific applications. Our system, Active Harmony, takes a search-based collaborative approach to auto-tuning. Application programmers, library writers and compilers collaborate to describe and export a set of performance related tunable parameters to the Active Harmony system. These parameters define a tuning search-space. The auto-tuner monitors the program performance and suggests adaptation decisions. The decisions are made by a central controller using a parallel search algorithm. The algorithm leverages parallel architectures to search across a set of optimization parameter values. Different nodes of a parallel system evaluate different configurations at each timestep. Active Harmony supports runtime adaptive code-generation and tuning for parameters that require new code (e.g. unroll factors). Effectively, we merge traditional feedback directed optimization and just-in-time compilation. This feature also enables application developers to write applications once and have the auto-tuner adjust the application behavior automatically when run on new systems. We evaluated our system on multiple large-scale parallel applications and showed that our system can improve the execution time by up to 46% compared to the original version of the program. Finally, we believe that the success of any auto-tuning research depends on how effectively application developers, domain-experts and auto-tuners communicate and work together. To that end, we have developed and released a simple and extensible language that standardizes the parameter space representation. Using this language, developers and researchers can collaborate to export tunable parameters to the tuning frameworks. Relationships (e.g. ordering, dependencies, constraints, ranking) between tunable parameters and search-hints can also be expressed

Baryon Inhomogeneity Generation in the Quark-Gluon Plasma Phase

We discuss the possibility of generation of baryon inhomogeneities in a quark-gluon plasma phase due to moving Z(3) interfaces. By modeling the dependence of effective mass of the quarks on the Polyakov loop order parameter, we study the reflection of quarks from collapsing Z(3) interfaces and estimate resulting baryon inhomogeneities in the context of the early universe. We argue that in the context of certain low energy scale inflationary models, it is possible that large Z(3) walls arise at the end of the reheating stage. Collapse of such walls could lead to baryon inhomogeneities which may be separated by large distances near the QCD scale. Importantly, the generation of these inhomogeneities is insensitive to the order, or even the existence, of the quark-hadron phase transition. We also briefly discuss the possibility of formation of quark nuggets in this model, as well as baryon inhomogeneity generation in relativistic heavy-ion collisions.Comment: 11 pages, 2 figures, revtex4, more detailed discussion added about formation and evolution of Z(3)domain walls in the univers

queue: Customized large-scale clock frequency scaling

Abstract-We examine the scalability of a set of techniques related to Dynamic Voltage-Frequency Scaling (DVFS) on HPC systems to reduce the energy consumption of scientific applications through an application-aware analysis and runtime framework, Green Queue. Green Queue supports making CPU clock frequency changes in response to intra-node and internode observations about application behavior. Our intra-node approach reduces CPU clock frequencies and therefore power consumption while CPUs lacks computational work due to inefficient data movement. Our inter-node approach reduces clock frequencies for MPI ranks that lack computational work. We investigate these techniques on a set of large scientific applications on 1024 cores of Gordon, an Intel Sandybridgebased supercomputer at the San Diego Supercomputer Center. Our optimal intra-node technique showed an average measured energy savings of 10.6% and a maximum of 21.0% over regular application runs. Our optimal inter-node technique showed an average 17.4% and a maximum of 31.7% energy savings

Recent Developments in the General Atomic and Molecular Electronic Structure System

A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized

Comparative analysis of knowledge and management practices of insect pests of maize among IPM adopters and non-adopters in Sindhupalchok, Nepal

Integrated pest management (IPM) is a decision-based approach that involves optimizing the pest population below the economic threshold by the coordinated use of multiple tactics in an economically and environmentally sound manner. The adoption of IPM in farming practices prevents long-term pest damage by combining biological control, modification of cultural practices, habitual manipulation, and use of resistant varieties. In Nepal, mostly in hilly regions, haphazard chemical pesticide application has inevitable effects on human health, the environment, and the ecosystem. The haphazard chemical pesticide application in Sindhupalchok, Nepal originated mostly due to a knowledge gap in the identification of the stages of the lifecycle of pests, and the distinction between beneficial and harmful insects.  To compare the effectiveness of management practices between IPM adopters and non-adopters this study was framed for six months in Sangachokgadi municipality, Sindhupalchok, Nepal.  The knowledge gap among the maize growers in Sindhupalchok was assessed using both primary and secondary data collection methods. For primary data collection a comprehensive and structured questionnaire, face-to-face interview, phone call interview, and Key Informant Interview was conducted. Similarly, secondary data was collected from various articles and publications from Maize Zone, the Ministry of Agriculture and Livestock Development (MoALD), Nepal Agriculture Research Council (NARC), and National Maize Research Program (NMRP). The collected data were then analyzed (descriptive statistics, chi-square test, and indexing) by using computer software packages i.e., Statistical Package for Social Science (SPSS) version 26, and Microsoft Excel 2010. The analyzed data revealed maize growers adopting IPM practices for crop management are known to have significantly better knowledge of the life cycle of pests, were able to distinguish between beneficial and harmful insects, and had knowledge of appropriate fertilizer doses.  Further, the findings revealed IPM adopters had better knowledge of chemical pesticide handling which could minimize the chemical hazards among the farmers