Elastic Resources Framework in IaaS, preserving performance SLAs

Elasticity in cloud systems provides the flexibility to acquire and relinquish computing resources on demand. However, in current virtualized systems resource allocation is mostly static. Resources are allocated during VM instantiation and any change in workload leading to significant increase or decrease in resources is handled by VM migration. Hence, cloud users tend to characterize their workloads at a coarse grained level which potentially leads to under-utilized VM resources or under performing application. A more flexible and adaptive resource allocation mechanism would benefit variable workloads, such as those characterized by web servers. In this paper, we present an elastic resources framework for IaaS cloud layer that addresses this need. The framework provisions for application workload forecasting engine, that predicts at run-time the expected demand, which is input to the resource manager to modulate resource allocation based on the predicted demand. Based on the prediction errors, resources can be over-allocated or under-allocated as compared to the actual demand made by the application. Over-allocation leads to unused resources and under allocation could cause under performance. To strike a good trade-off between over-allocation and under-performance we derive an excess cost model. In this model excess resources allocated are captured as over-allocation cost and under-allocation is captured as a penalty cost for violating application service level agreement (SLA). Confidence interval for predicted workload is used to minimize this excess cost with minimal effect on SLA violations. An example case-study for an academic institute web server workload is presented. Using the confidence interval to minimize excess cost, we achieve significant reduction in resource allocation requirement while restricting application SLA violations to below 2-3%.

A Stochastic Chemical Dynamic Approach to Correlate Autoimmunity and Optimal Vitamin-D Range

Motivated by several recent experimental observations that vitamin-D could interact with antigen presenting cells (APCs) and T-lymphocyte cells (T-cells) to promote and to regulate different stages of immune response, we developed a coarse grained but general kinetic model in an attempt to capture the role of vitamin-D in immunomodulatory responses. Our kinetic model, developed using the ideas of chemical network theory, leads to a system of nine coupled equations that we solve both by direct and by stochastic (Gillespie) methods. Both the analyses consistently provide detail information on the dependence of immune response to the variation of critical rate parameters. We find that although vitamin-D plays a negligible role in the initial immune response, it exerts a profound influence in the long term, especially in helping the system to achieve a new, stable steady state. The study explores the role of vitamin-D in preserving an observed bistability in the phase diagram (spanned by system parameters) of immune regulation, thus allowing the response to tolerate a wide range of pathogenic stimulation which could help in resisting autoimmune diseases. We also study how vitamin-D affects the time dependent population of dendritic cells that connect between innate and adaptive immune responses. Variations in dose dependent response of anti-inflammatory and pro-inflammatory T-cell populations to vitamin-D correlate well with recent experimental results. Our kinetic model allows for an estimation of the range of optimum level of vitamin-D required for smooth functioning of the immune system and for control of both hyper-regulation and inflammation. Most importantly, the present study reveals that an overdose or toxic level of vitamin-D or any steroid analogue could give rise to too large a tolerant response, leading to an inefficacy in adaptive immune function.

Influence of soil grading on the characteristics of cement stabilised soil compacts

The paper deals with experimental investigations aiming at specifying optimum soil grading limits for the production of cement stabilised soil bricks (CSSB). Wide range of soil grading curves encompassing both fine and coarse grained soils were considered. Strength, durability and absorption characteristics of CSSB were examined considering 14 different types of soil grading curves and three cement contents. The investigations show that there is optimum clay content for the soil mix which yields maximum compressive strength for CSSB and the optimum clay content is about 10 and 14 % for fine grained and coarse grained soils respectively. Void ratio of the compacted specimens is the lowest at the optimum clay content and therefore possesses maximum strength at that point. CSSB using fine grained soils shows higher strength and better durability characteristics when compared to the bricks using coarse grained soils.

Relaxor behaviour in BaBi4Ti4O15 ceramics fabricated using the powders obtained by mechanochemically assisted synthesis route

Mechanochemically activated reactants were found to facilitate the synthesis of fine powders comprising 200-400 nm range crystallites of BaBi4Ti4O15 at a significantly lower temperature (700 A degrees C) than that of solid-state reaction route. Reactants (CaCO3, Bi2O3 and TiO2) in stoichiometric ratio were ball milled for 48 h to obtain homogeneous mixture. The evolution of the BaBi4Ti4O15 phase was systematically followed using X-ray powder diffraction (XRD) technique. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were employed to probe its structural and microstructural details. The electron diffraction studies established the presence of correlated octahedral rotations and associated long-range polar ordering. High-resolution TEM imaging nevertheless revealed structural inhomogeneities leading to intergrowth defects. Dense BaBi4Ti4O15 ceramics with an average grain size of 0.9 mu m were fabricated using mechanochemically assisted synthesized powders at relatively low temperature (1000 A degrees C). The effect of grain size on the dielectric and relaxor behaviour of BaBi4Ti4O15 ceramics was investigated. Fine-grained ceramics (average grain size similar to 0.9 mu m) showed higher diffusion in phase transition, lower temperature of phase transition, lower Vogel-Fulcher freezing temperature and higher activation energy for the polarization reversal than those for coarse-grained ceramics (average grain size similar to 7 mu m) fabricated via the conventional solid-state reaction route.

Efficient QR Decomposition Using Low Complexity Column-wise Givens Rotation (CGR)

QR decomposition (QRD) is a widely used Numerical Linear Algebra (NLA) kernel with applications ranging from SONAR beamforming to wireless MIMO receivers. In this paper, we propose a novel Givens Rotation (GR) based QRD (GR QRD) where we reduce the computational complexity of GR and exploit higher degree of parallelism. This low complexity Column-wise GR (CGR) can annihilate multiple elements of a column of a matrix simultaneously. The algorithm is first realized on a Two-Dimensional (2 D) systolic array and then implemented on REDEFINE which is a Coarse Grained run-time Reconfigurable Architecture (CGRA). We benchmark the proposed implementation against state-of-the-art implementations to report better throughput, convergence and scalability.

Co-Exploration of NLA Kernels and Specification of Compute Elements in Distributed Memory CGRAs

Coarse Grained Reconfigurable Architectures (CGRA) are emerging as embedded application processing units in computing platforms for Exascale computing. Such CGRAs are distributed memory multi- core compute elements on a chip that communicate over a Network-on-chip (NoC). Numerical Linear Algebra (NLA) kernels are key to several high performance computing applications. In this paper we propose a systematic methodology to obtain the specification of Compute Elements (CE) for such CGRAs. We analyze block Matrix Multiplication and block LU Decomposition algorithms in the context of a CGRA, and obtain theoretical bounds on communication requirements, and memory sizes for a CE. Support for high performance custom computations common to NLA kernels are met through custom function units (CFUs) in the CEs. We present results to justify the merits of such CFUs.

PLUTO plus : Near-Complete Modeling of Affine Transformations for Parallelism and Locality

Affine transformations have proven to be very powerful for loop restructuring due to their ability to model a very wide range of transformations. A single multi-dimensional affine function can represent a long and complex sequence of simpler transformations. Existing affine transformation frameworks like the Pluto algorithm, that include a cost function for modern multicore architectures where coarse-grained parallelism and locality are crucial, consider only a sub-space of transformations to avoid a combinatorial explosion in finding the transformations. The ensuing practical tradeoffs lead to the exclusion of certain useful transformations, in particular, transformation compositions involving loop reversals and loop skewing by negative factors. In this paper, we propose an approach to address this limitation by modeling a much larger space of affine transformations in conjunction with the Pluto algorithm's cost function. We perform an experimental evaluation of both, the effect on compilation time, and performance of generated codes. The evaluation shows that our new framework, Pluto+, provides no degradation in performance in any of the Polybench benchmarks. For Lattice Boltzmann Method (LBM) codes with periodic boundary conditions, it provides a mean speedup of 1.33x over Pluto. We also show that Pluto+ does not increase compile times significantly. Experimental results on Polybench show that Pluto+ increases overall polyhedral source-to-source optimization time only by 15%. In cases where it improves execution time significantly, it increased polyhedral optimization time only by 2.04x.

Re-examination of compaction characteristics of fine-grained soils

Standard Proctor compaction test data were generated for 3 soils with liquid limit water contents ranging from 48% to 84%. It has been established that by defining a soil by its liquid limit and coarse fraction, the path of compaction for a specific compactive effort can be predicted via a simple density-water content-liquid limit relationship. (Abstract quotes from original text)

A divide and conquer strategy for scaling weather simulations with multiple regions of interest

Accurate and timely prediction of weather phenomena, such as hurricanes and flash floods, require high-fidelity compute intensive simulations of multiple finer regions of interest within a coarse simulation domain. Current weather applications execute these nested simulations sequentially using all the available processors, which is sub-optimal due to their sub-linear scalability. In this work, we present a strategy for parallel execution of multiple nested domain simulations based on partitioning the 2-D processor grid into disjoint rectangular regions associated with each domain. We propose a novel combination of performance prediction, processor allocation methods and topology-aware mapping of the regions on torus interconnects. Experiments on IBM Blue Gene systems using WRF show that the proposed strategies result in performance improvement of up to 33% with topology-oblivious mapping and up to additional 7% with topology-aware mapping over the default sequential strategy.

Development of a global inundation map at high spatial resolution from topographic downscaling of coarse-scale remote sensing data

Large-scale estimates of the area of terrestrial surface waters have greatly improved over time, in particular through the development of multi-satellite methodologies, but the generally coarse spatial resolution (tens of kms) of global observations is still inadequate for many ecological applications. The goal of this study is to introduce a new, globally applicable downscaling method and to demonstrate its applicability to derive fine resolution results from coarse global inundation estimates. The downscaling procedure predicts the location of surface water cover with an inundation probability map that was generated by bagged derision trees using globally available topographic and hydrographic information from the SRTM-derived HydroSHEDS database and trained on the wetland extent of the GLC2000 global land cover map. We applied the downscaling technique to the Global Inundation Extent from Multi-Satellites (GIEMS) dataset to produce a new high-resolution inundation map at a pixel size of 15 arc-seconds, termed GIEMS-D15. GIEMS-D15 represents three states of land surface inundation extents: mean annual minimum (total area, 6.5 x 10(6) km(2)), mean annual maximum (12.1 x 10(6) km(2)), and long-term maximum (173 x 10(6) km(2)); the latter depicts the largest surface water area of any global map to date. While the accuracy of GIEMS-D15 reflects distribution errors introduced by the downscaling process as well as errors from the original satellite estimates, overall accuracy is good yet spatially variable. A comparison against regional wetland cover maps generated by independent observations shows that the results adequately represent large floodplains and wetlands. GIEMS-D15 offers a higher resolution delineation of inundated areas than previously available for the assessment of global freshwater resources and the study of large floodplain and wetland ecosystems. The technique of applying inundation probabilities also allows for coupling with coarse-scale hydro-climatological model simulations. (C) 2014 Elsevier Inc All rights reserved.

Stress-state permeability relationships for clays with coarse fraction

In standard laboratory consolidation tests, only the fraction of soil passing through a particular size of the sieve, called the matrix material, is used. This size is usually restricted to 1/10 of the height of the consolidation ring. Particles larger than this size that are removed before the test may consist of gravel, fragments of rock, or other coarse materials. Hence, it is not possible to estimate the compressibility and permeability of the total material based on the compressibility and permeability behavior obtained from laboratory consolidation tests on the matrix material. In the present investigation an attempt has been made to estimate the compressibility and permeability behavior of the total material based on the compressibility and permeability behavior of the matrix material. The results indicate that the presence of coarse particles will reduce the compressibility of the soil in proportion to the coarse fraction present in the whole soil and will not affect the permeability of the soil for the range investigated. If the coarse fraction exceeds the Limiting percentage, the void ratio-vertical effective stress path will also start to deviate from the predicted path. An expression has been developed to estimate approximately the deviating pressure, and it is found to depend on the soil type as well as the percent clay fraction.

Stability of Dimeric Interface in Banana Lectin: Insight from Molecular Dynamics Simulations

Banana lectin (Banlec) is a homodimeric non-glycosylated protein. It exhibits the b-prism I structure. High-temperature molecular dynamics simulations have been utilized to monitor and understand early stages of thermally induced unfolding of Banlec. The present study elucidates the behavior of the dimeric protein at four different temperatures and compares the structural and conformational changes to that of the minimized crystal structure. The process of unfolding was monitored by following the radius of gyration, the rms deviation of each residue, change in relative solvent accessibility and the pattern of inter- and intra-subunit interactions. The overall study demonstrates that the Banlec dimer is a highly stable structure, and the stability is mostly contributed by interfacial interactions. It maintains its overall conformation during high-temperature (400–500 K) simulations, with only the unstructured loop regions acquiring greater momentum under such condition. Nevertheless, at still higher temperatures (600 K) the tertiary structure is gradually lost which later extends to loss of secondary structural elements. The pattern of hydrogen bonding within the subunit and at the interface across different stages has been analyzed and has provided rationale for its intrinsic high stability.

CMC simulations of lifted turbulent jet flame in a vitiated coflow

Lifted turbulent jet diffusion flame is simulated using Conditional Moment Closure (CMC). Specifically, the burner configuration of Cabra et al. [R. Cabra, T. Myhrvold, J.Y. Chen. R.W. Dibble, A.N. Karpetis, R.S. Barlow, Proc. Combust. Inst. 29 (2002) 1881-1887] is chosen to investigate H-2/N-2 jet flame supported by a vitiated coflow of products of lean H-2/air combustion. A 2D, axisymmetric flow-model fully coupled with the scalar fields, is employed. A detailed chemical kinetic scheme is included, and first order CIVIC is applied. Simulations are carried out for different jet velocities and coflow temperatures (T-c) The predicted liftoff generally agrees with experimental data, as well as joint-PDF results. Profiles of mean scalar fluxes in the mixture fraction space, for T-c = 1025 and 1080 K reveal that (1) Inside the flame zone, the chemical term balances the molecular diffusion term, and hence the Structure is of a diffusion flamelet for both cases. (2) In the pre-flame zone, the structure depends on the coflow temperature: for the 1025 K case, the chemical term being small, the advective term balances the axial turbulent diffusion term. However, for the 1080 K case. the chemical term is large and balances the advective term, the axial turbulent diffusion term being small. It is concluded that, lift-off is controlled (a) by turbulent premixed flame propagation for low coflow temperature while (b) by autoignition for high coflow temperature. (C) 2009 The Combustion Institute. Published by Elsevier Inc. All rights reserved.

Numerical simulations of void growth near a notch tip in ductile single crystals

The objective of this work is to study the growth of a cylindrical void ahead of a notch tip in ductile FCC single crystals under mode I, plane strain, small scale yielding (SSY) conditions. To this end, finite element simulations are performed within crystal plasticity framework neglecting elastic anisotropy. Attention is focussed on the effects of crystal hardening, ratio of void diameter to spacing from the notch and crystal orientation on plastic flow localization in the ligament connecting the notch and the void as well as their growth. The results show strong interaction between shear bands emanating from the notch and angular sectors of single slip forming around the void leading to intense plastic strain development in the ligament. Further, the ductile fracture processes are retarded by increase in hardening of the single crystal and decrease in ratio of void diameter to spacing from the notch. Also, a strong influence of crystal orientation on near-tip void growth and plastic slip band development is observed. Finally, the synergistic, cooperative growth of multiple voids ahead of the notch tip is examined.

Allostery in tRNA Synthetases Elucidated from MD Simulations and Protein Structure Networks

tRNA synthetases (aaRS) are enzymes crucial in the translation of genetic code. The enzyme accylates the acceptor stem of tRNA by the congnate amino acid bound at the active site, when the anti-codon is recognized by the anti-codon site of aaRS. In a typical aaRS, the distance between the anti-codon region and the amino accylation site is approximately 70 Å. We have investigated this allosteric phenomenon at molecular level by MD simulations followed by the analysis of protein structure networks (PSN) of non-covalent interactions. Specifically, we have generated conformational ensembles by performing MD simulations on different liganded states of methionyl tRNA synthetase (MetRS) from Escherichia coli and tryptophenyl tRNA synthetase (TrpRS) from Human. The correlated residues during the MD simulations are identified by cross correlation maps. We have identified the amino acids connecting the correlated residues by the shortest path between the two selected members of the PSN. The frequencies of paths have been evaluated from the MD snapshots[1]. The conformational populations in different liganded states of the protein have been beautifully captured in terms of network parameters such as hubs, cliques and communities[2]. These parameters have been associated with the rigidity and plasticity of the protein conformations and can be associated with free energy landscape. A comparison of allosteric communication in MetRS and TrpRS [3] elucidated in this study highlights diverse means adopted by different enzymes to perform a similar function. The computational method described for these two enzymes can be applied to the investigation of allostery in other systems.