A System Development Kit for Big Data Applications on FPGA-based Clusters: The EVEREST Approach

Modern big data workflows are characterized by computationally intensive kernels. The simulated results are often combined with knowledge extracted from AI models to ultimately support decision-making. These energy-hungry workflows are increasingly executed in data centers with energy-efficient hardware accelerators since FPGAs are well-suited for this task due to their inherent parallelism. We present the H2020 project EVEREST, which has developed a system development kit (SDK) to simplify the creation of FPGA-accelerated kernels and manage the execution at runtime through a virtualization environment. This paper describes the main components of the EVEREST SDK and the benefits that can be achieved in our use cases.Comment: Accepted for presentation at DATE 2024 (multi-partner project session

Characterization of DNA repair deficient strains of Chlamydomonas reinhardtii generated by insertional mutagenesis.

While the mechanisms governing DNA damage response and repair are fundamentally conserved, cross-kingdom comparisons indicate that they differ in many aspects due to differences in life-styles and developmental strategies. In photosynthetic organisms these differences have not been fully explored because gene-discovery approaches are mainly based on homology searches with known DDR/DNA repair proteins. Here we performed a forward genetic screen in the green algae Chlamydomonas reinhardtii to identify genes deficient in DDR/DNA repair. We isolated five insertional mutants that were sensitive to various genotoxic insults and two of them exhibited altered efficiency of transgene integration. To identify genomic regions disrupted in these mutants, we established a novel adaptor-ligation strategy for the efficient recovery of the insertion flanking sites. Four mutants harbored deletions that involved known DNA repair factors, DNA Pol zeta, DNA Pol theta, SAE2/COM1, and two neighbouring genes encoding ERCC1 and RAD17. Deletion in the last mutant spanned two Chlamydomonas-specific genes with unknown function, demonstrating the utility of this approach for discovering novel factors involved in genome maintenance

Molecular characterization of <i>aph7</i>″ insertions.

<p>(A) Southern analysis of <i>aph7</i>″ insertions in individual mutants. The restriction enzymes used for each experiment are indicated; positions of the restriction sites within the <i>aph7</i>″ construct probe used for hybridization are depicted in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105482#pone-0105482-g001" target="_blank">Figure 1A</a>. (B) Structure of the hairpin adaptor with a blunt end; examples of hairpins with ends compatible with selected restriction enzymes are indicated. (C) PCR products, separated in agarose gels and stained with ethidium bromide, that were generated after two rounds of nested PCR from a genomic library produced by <i>Pst</i>I digest.</p

Transformation efficiency of <i>C. reinhardtii</i> mutants.

<p>(A) Transformation efficiency calculated as the frequency of Arg-prototrophic transformants per a total number of transformed cells normalized to 1 pmol of pUCARG7.8 construct used for transformation. (B) Efficiency of homology-driven integration estimated as a ratio between the transformation efficiencies obtained with the pUCBM20ΔARG and pUCARG7.8 constructs. (A, B) C = <i>cw15-302 arg2</i>; standard errors of three independent experiments are indicated (N = 3). (C) Growth curves of the Z12 strain and selected Z12 Arg-prototrophic revertants in TAP liquid media with or without Arg. <i>cw15-302 arg2</i> cells complemented with the <i>ARG7</i> construct were used as an Arg-prototrophic control (C-ARG7).</p

Structure of insertion sites.

<p>Black arrows represent the aph7″ insert, red arrows indicate homologues to known DNA repair genes, blue arrows represent genes unrelated to DNA repair, and green boxes depict DNA fragments that were co-transformed to the insertion sites from ectopic locations. Sequences at the insert borders are indicated.</p

Sensitivity of <i>C. reinhardtii</i> mutant strains to genotoxic treatments.

<p>(A) Structure of the <i>aph7"</i> construct used for the insertional mutagenesis. Primers (arrows), restriction sites and the region used as a probe for Southern hybridization are indicated. (B) Growth curves of mutant and the parental <i>cw15-302 arg2</i> strains (denoted as C) in TAP liquid media supplemented with zeocin, MMC or MMS. (C) Growth of mutant strains on TAP plates exposed to increasing dose of UV-C or HU. Pictures were taken five days after inoculation.</p

Relative sensitivity to genotoxic treatments in respect to other mutants and the control strain <i>cw15-302 arg2</i> (+++ high sensitivity, ++ intermediate sensitivity, + mild sensitivity, −no sensitivity).

<p>Relative sensitivity to genotoxic treatments in respect to other mutants and the control strain <i>cw15-302 arg2</i> (+++ high sensitivity, ++ intermediate sensitivity, + mild sensitivity, −no sensitivity).</p

Effects of Subchronic Exposure to N,N-Diethyl-m-toluamide on Selected Biomarkers in Common Carp (Cyprinus carpio L.)

DEET (N,N-diethyl-m-toluamide) is the most common active ingredient in the insect repellents commonly detected in European groundwater. The aim of this study was to investigate the effect of subchronic DEET exposure on biochemical and haematological parameters, antioxidant enzymes, including catalase, glutathione peroxidase, glutathione reductase, and glutathione S-transferase, and the amount of thiobarbituric acid reactive substances (TBARS) in common carp (Cyprinus carpio L.). Two specific proinflammatory and anti-inflammatory cytokine genes were selected to assess an immunological status of the fish. Fish were exposed for 28 days to three concentrations of DEET (1.0 g/L, 0.1 mg/L, and 1.0 mg/L) where 1 g/L is corresponding to the concentration found in the environment. DEET had a significant ( &lt; 0.05) effect on increased RBC, decreased mean corpuscular volume (MCV), and mean corpuscular haemoglobin value (MCH) compared to control groups in the concentration of 1 mg/L. A significant decline ( &lt; 0.05) in triacylglycerols (TAG) in plasma was found in the concentration of 1 mg/L compared to the control groups. The parameters of oxidative stress in tissues of common carp were weekly affected and immunological parameters were not affected

ANTAREX - AutoTuning and adaptivity approach for energy efficient eXascale HPC systems

The main goal of the ANTAREX project is to express by a Domain Specific Language (DSL) the application self-adaptivity and to runtime manage and autotune applications for green and heterogeneous High Performance Computing (HPC) systems up to the Exascale level. Key innovations of the project include the introduction of a separation of concerns between self-adaptivity strategies and application functionalities. The DSL approach will allow the definition of energy-efficiency, performance, and adaptivity strategies as well as their enforcement at runtime through application autotuning and resource and power management

Autotuning and adaptivity approach for energy efficient Exascale HPC systems: The ANTAREX approach

The main goal of the ANTAREX1project is to express by a Domain Specific Language (DSL) the application self-adaptivity and to runtime manage and autotune applications for green and heterogeneous High Performance Computing (HPC) systems up to the Exascale level. Key innovations of the project include the introduction of a separation of concerns between self-adaptivity strategies and application functionalities. The DSL approach will allow the definition of energy-efficiency, performance, and adaptivity strategies as well as their enforcement at runtime through application autotuning and resource and power management