WMTrace : a lightweight memory allocation tracker and analysis framework

The diverging gap between processor and memory performance has been a well discussed aspect of computer architecture literature for some years. The use of multi-core processor designs has, however, brought new problems to the design of memory architectures - increased core density without matched improvement in memory capacity is reduc- ing the available memory per parallel process. Multiple cores accessing memory simultaneously degrades performance as a result of resource con- tention for memory channels and physical DIMMs. These issues combine to ensure that memory remains an on-going challenge in the design of parallel algorithms which scale. In this paper we present WMTrace, a lightweight tool to trace and analyse memory allocation events in parallel applications. This tool is able to dynamically link to pre-existing application binaries requiring no source code modification or recompilation. A post-execution analysis stage enables in-depth analysis of traces to be performed allowing memory allocations to be analysed by time, size or function. The second half of this paper features a case study in which we apply WMTrace to five parallel scientific applications and benchmarks, demonstrating its effectiveness at recording high-water mark memory consumption as well as memory use per-function over time. An in-depth analysis is provided for an unstructured mesh benchmark which reveals significant memory allocation imbalance across its participating processes

Transportation noise pollution - Control and abatement

Control and abatement of transportation noise pollutio

Contact of Single Asperities with Varying Adhesion: Comparing Continuum Mechanics to Atomistic Simulations

Atomistic simulations are used to test the equations of continuum contact mechanics in nanometer scale contacts. Nominally spherical tips, made by bending crystals or cutting crystalline or amorphous solids, are pressed into a flat, elastic substrate. The normal displacement, contact radius, stress distribution, friction and lateral stiffness are examined as a function of load and adhesion. The atomic scale roughness present on any tip made of discrete atoms is shown to have profound effects on the results. Contact areas, local stresses, and the work of adhesion change by factors of two to four, and the friction and lateral stiffness vary by orders of magnitude. The microscopic factors responsible for these changes are discussed. The results are also used to test methods for analyzing experimental data with continuum theory to determine information, such as contact area, that can not be measured directly in nanometer scale contacts. Even when the data appear to be fit by continuum theory, extracted quantities can differ substantially from their true values

Recent advances in managing HIV-associated cryptococcal meningitis

The recent development of highly sensitive and specific point-of-care tests has made it possible to diagnose HIV-associated cryptococcal meningitis within minutes. However, diagnostic advances have not been matched by new antifungal drugs and treatment still relies on old off-patent drugs: amphotericin B, flucytosine and fluconazole. Cryptococcal meningitis treatment is divided in three phases: induction, consolidation and maintenance. The induction phase, aimed at drastically reducing cerebrospinal fluid fungal burden, is key for patient survival. The major challenge in cryptococcal meningitis management has been the optimisation of induction phase treatment using the limited number of available medications, and major progress has recently been made. In this review, we summarise data from key trials which form the basis of current treatment recommendations for HIV-associated cryptococcal meningitis

As above, so below: whole transcriptome profiling demonstrates strong molecular similarities between avian dorsal and ventral pallial subdivisions

Over the last two decades, beginning withthe Avian Brain Nomenclature Forum in2000, major revisions have been made to our understanding of the organization andnomenclature of the avian brain. However, there are still unresolved questions on avianpallial organization, particularly whether the cells above the vestigial ventricle representdistinct populations to those below it or similar populations. To test these two hypothe-ses, we profiled the transcriptomes of the major avian pallial subdivisions dorsal and ven-tral to the vestigial ventricle boundary using RNA sequencing and a new zebra finchgenome assembly containing about 22,000annotated, complete genes. We found thatthe transcriptomes of neural populations above and below the ventricle were remarkablysimilar. Each subdivision in dorsal pallium (Wulst) had a corresponding molecular counter-part in the ventral pallium (dorsal ventricularridge). In turn, each corresponding subdivi-sion exhibited shared gene co-expression modules that contained gene sets enriched infunctional specializations, such as anatomical structure development, synaptic transmis-sion, signaling, and neurogenesis. Thesefindings are more in line with the continuumhypothesis of avian brain subdivision organization above and below the vestigial ventriclespace, with the pallium as a whole consisting offour major cell populations (intercalatedpallium, mesopallium, hyper-nidopallium, andarcopallium) instead of seven (hyperpalliumapicale, interstitial hyperpallium apicale, intercalated hyperpallium, hyperpalliumdensocellare, mesopallium, nidopallium, and arcopallium). We suggest adopting a morestreamlined hierarchical naming system thatreflects the robust similarities in geneexpression, neural connectivity motifs, and function. These findings have important impli-cations for our understanding of overall vertebrate brain evolution

Polynomial super-gl(n) algebras

We introduce a class of finite dimensional nonlinear superalgebras $L = L_{\bar{0}} + L_{\bar{1}}$ providing gradings of $L_{\bar{0}} = gl(n) \simeq sl(n) + gl(1)$. Odd generators close by anticommutation on polynomials (of degree $>1$) in the $gl(n)$ generators. Specifically, we investigate `type I' super-$gl(n)$ algebras, having odd generators transforming in a single irreducible representation of $gl(n)$ together with its contragredient. Admissible structure constants are discussed in terms of available $gl(n)$ couplings, and various special cases and candidate superalgebras are identified and exemplified via concrete oscillator constructions. For the case of the $n$-dimensional defining representation, with odd generators $Q_{a}, \bar{Q}{}^{b}$, and even generators ${E^{a}}_{b}$, $a,b = 1,...,n$, a three parameter family of quadratic super-$gl(n)$ algebras (deformations of $sl(n/1)$) is defined. In general, additional covariant Serre-type conditions are imposed, in order that the Jacobi identities be fulfilled. For these quadratic super-$gl(n)$ algebras, the construction of Kac modules, and conditions for atypicality, are briefly considered. Applications in quantum field theory, including Hamiltonian lattice QCD and space-time supersymmetry, are discussed.Comment: 31 pages, LaTeX, including minor corrections to equation (3) and reference [60