OP2-Clang : a source-to-source translator using Clang/LLVM LibTooling

Domain Specific Languages or Active Library frameworks have recently emerged as an important method for gaining performance portability, where an application can be efficiently executed on a wide range of HPC architectures without significant manual modifications. Embedded DSLs such as OP2, provides an API embedded in general purpose languages such as C/C++/Fortran. They rely on source-to-source translation and code refactorization to translate the higher-level API calls to platform specific parallel implementations. OP2 targets the solution of unstructured-mesh computations, where it can generate a variety of parallel implementations for execution on architectures such as CPUs, GPUs, distributed memory clusters and heterogeneous processors making use of a wide range of platform specific optimizations. Compiler tool-chains supporting source-to-source translation of code written in mainstream languages currently lack the capabilities to carry out such wide-ranging code transformations. Clang/LLVM’s Tooling library (LibTooling) has long been touted as having such capabilities but have only demonstrated its use in simple source refactoring tasks. In this paper we introduce OP2-Clang, a source-to-source translator based on LibTooling, for OP2’s C/C++ API, capable of generating target parallel code based on SIMD, OpenMP, CUDA and their combinations with MPI. OP2-Clang is designed to significantly reduce maintenance, particularly making it easy to be extended to generate new parallelizations and optimizations for hardware platforms. In this research, we demonstrate its capabilities including (1) the use of LibTooling’s AST matchers together with a simple strategy that use parallelization templates or skeletons to significantly reduce the complexity of generating radically different and transformed target code and (2) chart the challenges and solution to generating optimized parallelizations for OpenMP, SIMD and CUDA. Results indicate that OP2-Clang produces near-identical parallel code to that of OP2’s current source-to-source translator. We believe that the lessons learnt in OP2-Clang can be readily applied to developing other similar source-to-source translators, particularly for DSLs

OP2-Clang : a source-to-source translator using Clang/LLVM LibTooling

Domain Specific Languages or Active Library frameworks have recently emerged as an important method for gaining performance portability, where an application can be efficiently executed on a wide range of HPC architectures without significant manual modifications. Embedded DSLs such as OP2, provides an API embedded in general purpose languages such as C/C++/Fortran. They rely on source-to-source translation and code refactorization to translate the higher-level API calls to platform specific parallel implementations. OP2 targets the solution of unstructured-mesh computations, where it can generate a variety of parallel implementations for execution on architectures such as CPUs, GPUs, distributed memory clusters and heterogeneous processors making use of a wide range of platform specific optimizations. Compiler tool-chains supporting source-to-source translation of code written in mainstream languages currently lack the capabilities to carry out such wide-ranging code transformations. Clang/LLVM’s Tooling library (LibTooling) has long been touted as having such capabilities but have only demonstrated its use in simple source refactoring tasks. In this paper we introduce OP2-Clang, a source-to-source translator based on LibTooling, for OP2’s C/C++ API, capable of generating target parallel code based on SIMD, OpenMP, CUDA and their combinations with MPI. OP2-Clang is designed to significantly reduce maintenance, particularly making it easy to be extended to generate new parallelizations and optimizations for hardware platforms. In this research, we demonstrate its capabilities including (1) the use of LibTooling’s AST matchers together with a simple strategy that use parallelization templates or skeletons to significantly reduce the complexity of generating radically different and transformed target code and (2) chart the challenges and solution to generating optimized parallelizations for OpenMP, SIMD and CUDA. Results indicate that OP2-Clang produces near-identical parallel code to that of OP2’s current source-to-source translator. We believe that the lessons learnt in OP2-Clang can be readily applied to developing other similar source-to-source translators, particularly for DSLs

BioTIME: A database of biodiversity time series for the Anthropocene

Motivation: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. Main types of variables included: The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. Spatial location and grain: BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km(2) (158 cm(2)) to 100 km(2) (1,000,000,000,000 cm(2)). Time period and grainBio: TIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. Major taxa and level of measurement: BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates

Early evolution of the extraordinary Nova Del 2013 (V339 Del)

We determine the temporal evolution of the luminosity L(WD), radius R(WD) and effective temperature Teff of the white dwarf (WD) pseudophotosphere of V339 Del from its discovery to around day 40. Another main objective was studying the ionization structure of the ejecta. These aims were achieved by modelling the optical/near-IR spectral energy distribution (SED) using low-resolution spectroscopy (3500 - 9200 A), UBVRcIc and JHKLM photometry. During the fireball stage (Aug. 14.8 - 19.9, 2013), Teff was in the range of 6000 - 12000 K, R(WD) was expanding non-uniformly in time from around 66 to around 300 (d/3 kpc) R(Sun), and L(WD) was super-Eddington, but not constant. After the fireball stage, a large emission measure of 1.0-2.0E+62 (d/3 kpc)**2 cm**(-3) constrained the lower limit of L(WD) to be well above the super-Eddington value. The evolution of the H-alpha line and mainly the transient emergence of the Raman-scattered O VI 1032 A line suggested a biconical ionization structure of the ejecta with a disk-like H I region persisting around the WD until its total ionization, around day 40. It is evident that the nova was not evolving according to the current theoretical prediction. The unusual non-spherically symmetric ejecta of nova V339 Del and its extreme physical conditions and evolution during and after the fireball stage represent interesting new challenges for the theoretical modelling of the nova phenomenon.Comment: 14 pages, 9 figures, 3 tables, accepted for Astronomy and Astrophysic

Evidence for directional selection at a novel major histocompatibility class I marker in wild common frogs (Rana temporaria) exposed to a viral pathogen (Ranavirus).

(c) 2009 Teacher et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Whilst the Major Histocompatibility Complex (MHC) is well characterized in the anuran Xenopus, this region has not previously been studied in another popular model species, the common frog (Rana temporaria). Nor, to date, have there been any studies of MHC in wild amphibian host-pathogen systems. We characterise an MHC class I locus in the common frog, and present primers to amplify both the whole region, and specifically the antigen binding region. As no more than two expressed haplotypes were found in over 400 clones from 66 individuals, it is likely that there is a single class I locus in this species. This finding is consistent with the single class I locus in Xenopus, but contrasts with the multiple loci identified in axolotls, providing evidence that the diversification of MHC class I into multiple loci likely occurred after the Caudata/Anura divergence (approximately 350 million years ago) but before the Ranidae/Pipidae divergence (approximately 230 mya). We use this locus to compare wild populations of common frogs that have been infected with a viral pathogen (Ranavirus) with those that have no history of infection. We demonstrate that certain MHC supertypes are associated with infection status (even after accounting for shared ancestry), and that the diseased populations have more similar supertype frequencies (lower F(ST)) than the uninfected. These patterns were not seen in a suite of putatively neutral microsatellite loci. We interpret this pattern at the MHC locus to indicate that the disease has imposed selection for particular haplotypes, and hence that common frogs may be adapting to the presence of Ranavirus, which currently kills tens of thousands of amphibians in the UK each year

Environmental variables, habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus

Coastal lagoons are semi-isolated ecosystems exposed to wide fluctuations of environmental conditions and showing habitat fragmentation. These features may play an important role in separating species into different populations, even at small spatial scales. In this study, we evaluate the concordance between mitochondrial (previous published data) and nuclear data analyzing the genetic variability of Pomatoschistus marmoratus in five localities, inside and outside the Mar Menor coastal lagoon (SE Spain) using eight microsatellites. High genetic diversity and similar levels of allele richness were observed across all loci and localities, although significant genic and genotypic differentiation was found between populations inside and outside the lagoon. In contrast to the FST values obtained from previous mitochondrial DNA analyses (control region), the microsatellite data exhibited significant differentiation among samples inside the Mar Menor and between lagoonal and marine samples. This pattern was corroborated using Cavalli-Sforza genetic distances. The habitat fragmentation inside the coastal lagoon and among lagoon and marine localities could be acting as a barrier to gene flow and contributing to the observed genetic structure. Our results from generalized additive models point a significant link between extreme lagoonal environmental conditions (mainly maximum salinity) and P. marmoratus genetic composition. Thereby, these environmental features could be also acting on genetic structure of coastal lagoon populations of P. marmoratus favoring their genetic divergence. The mating strategy of P. marmoratus could be also influencing our results obtained from mitochondrial and nuclear DNA. Therefore, a special consideration must be done in the selection of the DNA markers depending on the reproductive strategy of the species

RNAstructure: software for RNA secondary structure prediction and analysis

<p>Abstract</p> <p>Background</p> <p>To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence.</p> <p>Results</p> <p>RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained.</p> <p>Conclusion</p> <p>The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at <url>http://rna.urmc.rochester.edu/RNAstructure.html</url>.</p

Evidence for Mito-Nuclear and Sex-Linked Reproductive Barriers between the Hybrid Italian Sparrow and Its Parent Species

Studies of reproductive isolation between homoploid hybrid species and their parent species have rarely been carried out. Here we investigate reproductive barriers between a recently recognized hybrid bird species, the Italian sparrow Passer italiae and its parent species, the house sparrow P. domesticus and Spanish sparrow P. hispaniolensis. Reproductive barriers can be difficult to study in hybrid species due to lack of geographical contact between taxa. However, the Italian sparrow lives parapatrically with the house sparrow and both sympatrically and parapatrically with the Spanish sparrow. Through whole-transcriptome sequencing of six individuals of each of the two parent species we identified a set of putatively parent species-diagnostic single nucleotide polymorphism (SNP) markers. After filtering for coverage, genotyping success (>97%) and multiple SNPs per gene, we retained 86 species-informative, genic, nuclear and mitochondrial SNP markers from 84 genes for analysis of 612 male individuals. We show that a disproportionately large number of sex-linked genes, as well as the mitochondria and nuclear genes with mitochondrial function, exhibit sharp clines at the boundaries between the hybrid and the parent species, suggesting a role for mito-nuclear and sex-linked incompatibilities in forming reproductive barriers. We suggest that genomic conflict via interactions between mitochondria and sex-linked genes with mitochondrial function ("mother's curse") at one boundary and centromeric drive at the other may best explain our findings. Hybrid speciation in the Italian sparrow may therefore be influenced by mechanisms similar to those involved in non-hybrid speciation, but with the formation of two geographically separated species boundaries instead of one. Spanish sparrow alleles at some loci have spread north to form reproductive barriers with house sparrows, while house sparrow alleles at different loci, including some on the same chromosome, have spread in the opposite direction to form barriers against Spanish sparrows

Electron Transfer Function versus Oxygen Delivery: A Comparative Study for Several Hexacoordinated Globins Across the Animal Kingdom

Caenorhabditis elegans globin GLB-26 (expressed from gene T22C1.2) has been studied in comparison with human neuroglobin (Ngb) and cytoglobin (Cygb) for its electron transfer properties. GLB-26 exhibits no reversible binding for O2 and a relatively low CO affinity compared to myoglobin-like globins. These differences arise from its mechanism of gaseous ligand binding since the heme iron of GLB-26 is strongly hexacoordinated in the absence of external ligands; the replacement of this internal ligand, probably the E7 distal histidine, is required before binding of CO or O2 as for Ngb and Cygb. Interestingly the ferrous bis-histidyl GLB-26 and Ngb, another strongly hexacoordinated globin, can transfer an electron to cytochrome c (Cyt-c) at a high bimolecular rate, comparable to those of inter-protein electron transfer in mitochondria. In addition, GLB-26 displays an unexpectedly rapid oxidation of the ferrous His-Fe-His complex without O2 actually binding to the iron atom, since the heme is oxidized by O2 faster than the time for distal histidine dissociation. These efficient mechanisms for electron transfer could indicate a family of hexacoordinated globin which are functionally different from that of pentacoordinated globins

Population Genetic Differences along a Latitudinal Cline between Original and Recently Colonized Habitat in a Butterfly

BACKGROUND: Past and current range or spatial expansions have important consequences on population genetic structure. Habitat-use expansion, i.e. changing habitat associations, may also influence genetic population parameters, but has been less studied. Here we examined the genetic population structure of a Palaeartic woodland butterfly Pararge aegeria (Nymphalidae) which has recently colonized agricultural landscapes in NW-Europe. Butterflies from woodland and agricultural landscapes differ in several phenotypic traits (including morphology, behavior and life history). We investigated whether phenotypic divergence is accompanied by genetic divergence between populations of different landscapes along a 700 km latitudinal gradient. METHODOLOGY/PRINCIPAL FINDINGS: Populations (23) along the latitudinal gradient in both landscape types were analyzed using microsatellite and allozyme markers. A general decrease in genetic diversity with latitude was detected, likely due to post-glacial colonization effects. Contrary to expectations, agricultural landscapes were not less diverse and no significant bottlenecks were detected. Nonetheless, a genetic signature of recent colonization is reflected in the absence of clinal genetic differentiation within the agricultural landscape, significantly lower gene flow between agricultural populations (3.494) than between woodland populations (4.183), and significantly higher genetic differentiation between agricultural (0.050) than woodland (0.034) pairwise comparisons, likely due to multiple founder events. Globally, the genetic data suggest multiple long distance dispersal/colonization events and subsequent high intra- and inter-landscape gene flow in this species. Phosphoglucomutase deviated from other enzymes and microsatellite markers, and hence may be under selection along the latitudinal gradient but not between landscape types. Phenotypic divergence was greater than genetic divergence, indicating directional selection on some flight morphology traits. MAIN CONCLUSIONS/SIGNIFICANCE: Clinal differentiation characterizes the population structure within the original woodland habitat. Genetic signatures of recent habitat expansion remain, notwithstanding high gene flow. After differentiation through drift was excluded, both latitude and landscape were significant factors inducing spatially variable phenotypic variation