Generalizing Amdahl’s Law for Power and Energy

Extending Amdahl\u27s law to identify optimal power-performance configurations requires considering the interactive effects of power, performance, and parallel overhead

Iso-energy-efficiency: An approach to power-constrained parallel computation

Future large scale high performance supercomputer systems require high energy efficiency to achieve exaflops computational power and beyond. Despite the need to understand energy efficiency in high-performance systems, there are few techniques to evaluate energy efficiency at scale. In this paper, we propose a system-level iso-energy-efficiency model to analyze, evaluate and predict energy-performance of data intensive parallel applications with various execution patterns running on large scale power-aware clusters. Our analytical model can help users explore the effects of machine and application dependent characteristics on system energy efficiency and isolate efficient ways to scale system parameters (e.g. processor count, CPU power/frequency, workload size and network bandwidth) to balance energy use and performance. We derive our iso-energy-efficiency model and apply it to the NAS Parallel Benchmarks on two power-aware clusters. Our results indicate that the model accurately predicts total system energy consumption within 5% error on average for parallel applications with various execution and communication patterns. We demonstrate effective use of the model for various application contexts and in scalability decision-making

PowerPack: Energy Profiling and Analysis of High-Performance Systems and Applications

Energy efficiency is a major concern in modern high-performance computing system design. In the past few years, there has been mounting evidence that power usage limits system scale and computing density, and thus, ultimately system performance. However, despite the impact of power and energy on the computer systems community, few studies provide insight to where and how power is consumed on high-performance systems and applications. In previous work, we designed a framework called PowerPack that was the first tool to isolate the power consumption of devices including disks, memory, NICs, and processors in a high-performance cluster and correlate these measurements to application functions. In this work, we extend our framework to support systems with multicore, multiprocessor-based nodes, and then provide in-depth analyses of the energy consumption of parallel applications on clusters of these systems. These analyses include the impacts of chip multiprocessing on power and energy efficiency, and its interaction with application executions. In addition, we use PowerPack to study the power dynamics and energy efficiencies of dynamic voltage and frequency scaling (DVFS) techniques on clusters. Our experiments reveal conclusively how intelligent DVFS scheduling can enhance system energy efficiency while maintaining performance

Electrochemical probing of selective haemoglobin binding in hydrogel-based molecularly imprinted polymers

An electrochemical method has been developed for the probing of hydrogel-based molecularly imprinted polymers (HydroMIPs) on the surface of a glassy carbon electrode. HydroMIPs designed for bovine haemoglobin selectivity were electrochemically characterised and their rebinding properties were monitored using cyclic voltammetry. The electrochemical reduction of bovine oxyhaemoglobin (BHb) in solution was observed to occur at ?0.460 V vs (Ag/AgCl) in 150 mM phosphate buffer solution (PBS). When the protein was selectively bound to the MIP, the electrochemical reduction of oxyhaemoglobin could be observed at a similar peak potential of ?0.480 V vs (Ag/AgCl). When analysing the non-imprinted control polymer (NIP) interfaced at the electrode, which contained no protein, the peak reduction potential corresponded to that observed for dissolved oxygen in solution (?0.65 V vs (Ag/AgCl)). MIP and NIP (in the absence of protein) were interfaced at the electrode and protein allowed to diffuse through the polymers from the bulk solution end to the electrode. It was observed that whereas NIP exhibited a protein response within 10 min of protein exposure, up to 45 min of exposure time was required in the case of the MIP before a protein response could be obtained. Our results suggest that due to the selective nature of the MIP, BHb arrival at the electrode via diffusion is delayed by the MIP due to attractive selective interactions with exposed cavities, but not the NIP which is devoid of selective cavities

Power and energy profiling of scientific applications on distributed systems

Abstract , by node (for each of 32 nodes), and by system scale (2, 4, 8, 16, and 32 node

Reversible Silencing of CFTR Chloride Channels by Glutathionylation

The cystic fibrosis transmembrane conductance regulator (CFTR) is a phosphorylation- and ATP-dependent chloride channel that modulates salt and water transport across lung and gut epithelia. The relationship between CFTR and oxidized forms of glutathione is of potential interest because reactive glutathione species are produced in inflamed epithelia where they may be modulators or substrates of CFTR. Here we show that CFTR channel activity in excised membrane patches is markedly inhibited by several oxidized forms of glutathione (i.e., GSSG, GSNO, and glutathione treated with diamide, a strong thiol oxidizer). Three lines of evidence indicate that the likely mechanism for this inhibitory effect is glutathionylation of a CFTR cysteine (i.e., formation of a mixed disulfide with glutathione): (a) channels could be protected from inhibition by pretreating the patch with NEM (a thiol alkylating agent) or by lowering the bath pH; (b) inhibited channels could be rescued by reducing agents (e.g., DTT) or by purified glutaredoxins (Grxs; thiol disulfide oxidoreductases) including a mutant Grx that specifically reduces mixed disulfides between glutathione and cysteines within proteins; and (c) reversible glutathionylation of CFTR polypeptides in microsomes could be detected biochemically under the same conditions. At the single channel level, the primary effect of reactive glutathione species was to markedly inhibit the opening rates of individual CFTR channels. CFTR channel inhibition was not obviously dependent on phosphorylation state but was markedly slowed when channels were first “locked open” by a poorly hydrolyzable ATP analogue (AMP-PNP). Consistent with the latter finding, we show that the major site of inhibition is cys-1344, a poorly conserved cysteine that lies proximal to the signature sequence in the second nucleotide binding domain (NBD2) of human CFTR. This region is predicted to participate in ATP-dependent channel opening and to be occluded in the nucleotide-bound state of the channel based on structural comparisons to related ATP binding cassette transporters. Our results demonstrate that human CFTR channels are reversibly inhibited by reactive glutathione species, and support an important role of the region proximal to the NBD2 signature sequence in ATP-dependent channel opening

Impedance adaptation for optimal robot–environment interaction

In this paper, impedance adaptation is investigated for robots interacting with unknown environments. Impedance control is employed for the physical interaction between robots and environments, subject to unknown and uncertain environments dynamics. The unknown environments are described as linear systems with unknown dynamics, based on which the desired impedance model is obtained. A cost function that measures the tracking error and interaction force is defined, and the critical impedance parameters are found to minimize it. Without requiring the information of the environments dynamics, the proposed impedance adaptation is feasible in a large number of applications where robots physically interact with unknown environments. The validity of the proposed method is verified through simulation studies

Rapid Transition towards the Division of Labor via Evolution of Developmental Plasticity

A crucial step in several major evolutionary transitions is the division of labor between components of the emerging higher-level evolutionary unit. Examples include the separation of germ and soma in simple multicellular organisms, appearance of multiple cell types and organs in more complex organisms, and emergence of casts in eusocial insects. How the division of labor was achieved in the face of selfishness of lower-level units is controversial. I present a simple mathematical model describing the evolutionary emergence of the division of labor via developmental plasticity starting with a colony of undifferentiated cells and ending with completely differentiated multicellular organisms. I explore how the plausibility and the dynamics of the division of labor depend on its fitness advantage, mutation rate, costs of developmental plasticity, and the colony size. The model shows that the transition to differentiated multicellularity, which has happened many times in the history of life, can be achieved relatively easily. My approach is expandable in a number of directions including the emergence of multiple cell types, complex organs, or casts of eusocial insects

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi

Electrodeposited lead dioxide coatings

Lead dioxide coatings on inert substrates such as titanium and carbon now offer new opportunities for a material known for 150 years. It is now recognised that electrodeposition allows the preparation of stable coatings with different phase structures and a wide range of surface morphologies. In addition, substantial modification to the physical properties and catalytic activities of the coatings are possible through doping and the fabrication of nanostructured deposits or composites. In addition to applications as a cheap anode material in electrochemical technology, lead dioxide coatings provide unique possibilities for probing the dependence of catalytic activity on layer composition and structure (critical review, 256 references)