SWIFT: Using task-based parallelism, fully asynchronous communication, and graph partition-based domain decomposition for strong scaling on more than 100,000 cores

We present a new open-source cosmological code, called SWIFT, designed to solve the equations of hydrodynamics using a particle-based approach (Smooth Particle Hydrodynamics) on hybrid shared / distributed-memory architectures. SWIFT was designed from the bottom up to provide excellent strong scaling on both commodity clusters (Tier-2 systems) and Top100-supercomputers (Tier-0 systems), without relying on architecture-specific features or specialized accelerator hardware. This performance is due to three main computational approaches: • Task-based parallelism for shared-memory parallelism, which provides fine-grained load balancing and thus strong scaling on large numbers of cores. • Graph-based domain decomposition, which uses the task graph to decompose the simulation domain such that the work, as opposed to just the data, as is the case with most partitioning schemes, is equally distributed across all nodes. • Fully dynamic and asynchronous communication, in which communication is modelled as just another task in the task-based scheme, sending data whenever it is ready and deferring on tasks that rely on data from other nodes until it arrives. In order to use these approaches, the code had to be re-written from scratch, and the algorithms therein adapted to the task-based paradigm. As a result, we can show upwards of 60% parallel efficiency for moderate-sized problems when increasing the number of cores 512-fold, on both x86-based and Power8-based architectures

Electromagnetic plasma modeling in circuit breaker within the finite volume method

In order to ensure the galvanic isolation of an electrical system following a manual operation or a default strike, current limitation properties of the electric arc are used, forcing a fast decrease to zero current. Modeling this process reveals complex, since it involves a large amount of physical phenomena (radiation, phase transitions, electromagnetism, fluid dynamics, plasma physics). In order to get a robust solving, enhancing strongly coupled resolution and time constants compatibility, the Finite Volume Method has been chosen. This method was first implemented on intrinsic electromagnetism problems (current flow, magnetostatics including non-linear materials, and magnetodynamics). Once validated, the models have been successfully used in the Schneider's current-interruption dedicated software, thus allowing a significantly improved simulation of Schneider Electric circuit breakers

Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits

Correct orthology assignment is a critical prerequisite of numerous comparative genomics procedures, such as function prediction, construction of phylogenetic species trees and genome rearrangement analysis. We present an algorithm for the detection of non-orthologs that arise by mistake in current orthology classification methods based on genome-specific best hits, such as the COGs database. The algorithm works with pairwise distance estimates, rather than computationally expensive and error-prone tree-building methods. The accuracy of the algorithm is evaluated through verification of the distribution of predicted cases, case-by-case phylogenetic analysis and comparisons with predictions from other projects using independent methods. Our results show that a very significant fraction of the COG groups include non-orthologs: using conservative parameters, the algorithm detects non-orthology in a third of all COG groups. Consequently, sequence analysis sensitive to correct orthology assignments will greatly benefit from these findings

Practical Evaluation of Lempel-Ziv-78 and Lempel-Ziv-Welch Tries

We present the first thorough practical study of the Lempel-Ziv-78 and the Lempel-Ziv-Welch computation based on trie data structures. With a careful selection of trie representations we can beat well-tuned popular trie data structures like Judy, m-Bonsai or Cedar

A methodology for determining amino-acid substitution matrices from set covers

We introduce a new methodology for the determination of amino-acid substitution matrices for use in the alignment of proteins. The new methodology is based on a pre-existing set cover on the set of residues and on the undirected graph that describes residue exchangeability given the set cover. For fixed functional forms indicating how to obtain edge weights from the set cover and, after that, substitution-matrix elements from weighted distances on the graph, the resulting substitution matrix can be checked for performance against some known set of reference alignments and for given gap costs. Finding the appropriate functional forms and gap costs can then be formulated as an optimization problem that seeks to maximize the performance of the substitution matrix on the reference alignment set. We give computational results on the BAliBASE suite using a genetic algorithm for optimization. Our results indicate that it is possible to obtain substitution matrices whose performance is either comparable to or surpasses that of several others, depending on the particular scenario under consideration

Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences

BACKGROUND: The estimation of the difference between two evolutionary distances within a triplet of homologs is a common operation that is used for example to determine which of two sequences is closer to a third one. The most accurate method is currently maximum likelihood over the entire triplet. However, this approach is relatively time consuming. RESULTS: We show that an alternative estimator, based on pairwise estimates and therefore much faster to compute, has almost the same statistical power as the maximum likelihood estimator. We also provide a numerical approximation for its variance, which could otherwise only be estimated through an expensive re-sampling approach such as bootstrapping. An extensive simulation demonstrates that the approximation delivers precise confidence intervals. To illustrate the possible applications of these results, we show how they improve the detection of asymmetric evolution, and the identification of the closest relative to a given sequence in a group of homologs. CONCLUSION: The results presented in this paper constitute a basis for large-scale protein cross-comparisons of pairwise evolutionary distances

Genus Hydrangea: diversity of pigments and phenolic compounds

The most important collection of Hydrangea in Europe is located in Angers (France). It consists of over 700 germplasm accessions distributed in 13 species. Originating from Asia and America, they were introduced in Europe in the 18th century for their ornamental interest but medicinal properties may also be found in this genus since extracts from H. macrophylla are already described as exhibiting anti-diabetic [1], lipid lowering and anti-oxidative [2], anti-allergic [3] and antimalarial activities [4]. Management of the collection requires botanical, genetic and biochemical studies allowing good, reliable characterization of species, subspecies and varieties. In this context, the biochemical characterization of the inflorescences was undertaken to evaluate the intra and interspecific diversities of pigments and other phenolic compounds. Inflorescences are generally white, except for three species: H. macrophylla, H. involucrata and H .aspera which exhibit rose or blue flowers. Among them only H. macrophylla was previously studied for sepal color variation [5]. In this study, 80 accessions were analyzed by means of HPLC/DAD, LC-MS/MS and NMR experiments: 46 H. macrophylla, 13 H. aspera, 6 H. involucrata, 5 H. paniculata, 3 H. quercifolia, 2 H. arborescens, 2 H. anomala, 2 H. heteromala, 1 H. scandens, 1 H. seemannii and 1 H. integrifolia. About 50 phenolic derivatives - essentially phenolic acids and flavonols (quercetin and kaempferol) - and 20 anthocyanins could be identified. The contents of pigments and other phenolic compounds appeared as very diverse both qualitatively and quantitatively and some compounds could be identified as chemospecific. On this basis, a statistical study using Principal Component Analysis allowed a clear distinction between both species and subspecies. Besides, different biological evaluations of crude extracts and secondary metabolites isolated from Hydrangea sp will also be discussed