ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community.

BACKGROUND: The advent of Next Generation Sequencing (NGS) technologies and the concomitant reduction in sequencing costs allows unprecedented high throughput profiling of biological systems in a cost-efficient manner. Modern biological experiments are increasingly becoming both data and computationally intensive and the wealth of publicly available biological data is introducing bioinformatics into the "Big Data" era. For these reasons, the effective application of High Performance Computing (HPC) architectures is becoming progressively more recognized also by bioinformaticians. Here we describe HPC resources provisioning pilot programs dedicated to bioinformaticians, run by the Italian Node of ELIXIR (ELIXIR-IT) in collaboration with CINECA, the main Italian supercomputing center. RESULTS: Starting from April 2016, CINECA and ELIXIR-IT launched the pilot Call "ELIXIR-IT HPC@CINECA", offering streamlined access to HPC resources for bioinformatics. Resources are made available either through web front-ends to dedicated workflows developed at CINECA or by providing direct access to the High Performance Computing systems through a standard command-line interface tailored for bioinformatics data analysis. This allows to offer to the biomedical research community a production scale environment, continuously updated with the latest available versions of publicly available reference datasets and bioinformatic tools. Currently, 63 research projects have gained access to the HPC@CINECA program, for a total handout of ~ 8 Millions of CPU/hours and, for data storage, ~ 100 TB of permanent and ~ 300 TB of temporary space. CONCLUSIONS: Three years after the beginning of the ELIXIR-IT HPC@CINECA program, we can appreciate its impact over the Italian bioinformatics community and draw some considerations. Several Italian researchers who applied to the program have gained access to one of the top-ranking public scientific supercomputing facilities in Europe. Those investigators had the opportunity to sensibly reduce computational turnaround times in their research projects and to process massive amounts of data, pursuing research approaches that would have been otherwise difficult or impossible to undertake. Moreover, by taking advantage of the wealth of documentation and training material provided by CINECA, participants had the opportunity to improve their skills in the usage of HPC systems and be better positioned to apply to similar EU programs of greater scale, such as PRACE. To illustrate the effective usage and impact of the resources awarded by the program - in different research applications - we report five successful use cases, which have already published their findings in peer-reviewed journals.

M100 ExaData: a data collection campaign on the CINECA's Marconi100 Tier-0 supercomputer.

Supercomputers are the most powerful computing machines available to society. They play a central role in economic, industrial, and societal development. While they are used by scientists, engineers, decision-makers, and data-analyst to computationally solve complex problems, supercomputers and their hosting datacenters are themselves complex power-hungry systems. Improving their efficiency, availability, and resiliency is vital and the subject of many research and engineering efforts. Still, a major roadblock hinders researchers: dearth of reliable data describing the behavior of production supercomputers. In this paper, we present the result of a ten-year-long project to design a monitoring framework (EXAMON) deployed at the Italian supercomputers at CINECA datacenter. We disclose the first holistic dataset of a tier-0 Top10 supercomputer. It includes the management, workload, facility, and infrastructure data of the Marconi100 supercomputer for two and half years of operation. The dataset (published via Zenodo) is the largest ever made public, with a size of 49.9TB before compression. We also provide open-source software modules to simplify access to the data and provide direct usage examples.

Molecular field theory with atomistic modeling for the curvature elasticity of nematic liquid crystals.

Liquid crystals oppose a restoring force to distortions of the main alignment axis, the so-called director. For nematics this behavior is characterized by the three elastic moduli associated with the splay (K(11)), twist (K(22)), and bend (K(33)) modes; in addition, two moduli for mixed splay-bend (k(13)) and saddle-splay (k(24)) can be defined. The elastic constants are material properties which depend on the mesogen structure, but the relation between molecular features and deformations on a much longer scale has not been fully elucidated. The prediction of elastic properties is a challenge for theoretical and computational methods: atomistic simulations require large samples and must be integrated by statistical thermodynamics models to connect intermolecular correlations and elastic response. Here we present a molecular field theory, wherein expressions for the elastic constants of nematics are derived starting from a simple form of the single molecule orientational distribution function; this is parametrized according to the amount of molecular surface aligned to the nematic director. Such a model allows a detailed account of the chemical structure; moreover the conformational freedom, which is a common feature of mesogens, can be easily included. Given the atomic coordinates, the elastic constants can be calculated without any adjustable parameter at a low computational cost. The example of 4-n-pentyl,4(')-cyanobiphenyl (5CB) is used to illustrate the capability of the developed methodology; even for this mesogen, which is usually taken as a prototypal rodlike system, we predict a significant dependence of the elastic moduli on the molecular conformation. We show that good estimates of magnitude and temperature dependence of the elastic constants are obtained, provided that the molecular geometry is correctly taken into account.

A quasidegenerate formulation of the second order n-electron valence state perturbation theory approach.

The n-electron valence state perturbation theory (NEVPT) is reformulated in a quasidegenerate (QD) approach. The new theory allows the treatment of cases where the proximity of the energies causes artifacts in the zero order description. Problems of quasidegeneration are relevant in the dynamics involving regions at avoided crossings (or conical intersections) and in spectroscopy where the energies and oscillator strengths can be strongly influenced by the mixing of states of different nature. Two test cases are analyzed concerning (a) the ionic-neutral avoided crossing in LiF and (b) the valence/Rydberg mixing in the excited states of ethene. The QD-NEVPT2 is shown to be a useful tool for such systems.