Brook Auto: High-Level Certification-Friendly Programming for GPU-powered Automotive Systems

Modern automotive systems require increased performance to implement Advanced Driving Assistance Systems (ADAS). GPU-powered platforms are promising candidates for such computational tasks, however current low-level programming models challenge the accelerator software certification process, while they limit the hardware selection to a fraction of the available platforms. In this paper we present Brook Auto, a high-level programming language for automotive GPU systems which removes these limitations. We describe the challenges and solutions we faced in its implementation, as well as a complete evaluation in terms of performance and productivity, which shows the effectiveness of our method.This work has been partially supported by the Spanish Ministry of Science and Innovation under grant TIN2015-65316-P and the HiPEAC Network of Excellence.Peer ReviewedPostprint (author's final draft

Towards general purpose computations on low-end mobile GPUs

GPUs traditionally offer high computational capabilities, frequently higher than their CPU counterparts. While high-end mobile GPUs vendors introduced recently general purpose APIs, such as OpenCL, to leverage their computational power, the vast majority of the mobile devices lack such support. Despite that their graphics APIs have similarities with desktop graphics APIs, they have significant differences, which prevent the use of well-known techniques that offer general-purpose computations over such interfaces. In this paper we show how these obstacles can be overcome, in order to achieve general purpose programmability of these devices. As a proof of concept we implemented our proposal on a real embedded platform (Raspberry Pi) based on Broadcom's VideoCore IV GPU, obtaining a speedup of 7.2× over the CPU.This work has been partially supported by the Spanish Ministry of Science and Innovation under grant TIN2015-65316-P and the HiPEAC Network of Excellence. Leonidas Kosmidis is also funded by the Spanish Ministry of Education under the FPU grant AP2010-4208.Postprint (author's final draft

Sensing Stemness

Purpose of review: Hematopoietic stem cells (HSCs) are formed embryonically during a dynamic developmental process and later reside in adult hematopoietic organs in a quiescent state. In response to their changing environment, HSCs have evolved diverse mechanisms to cope with intrinsic and extrinsic challenges. This review intends to discuss how HSCs and other stem cells co-opted DNA and RNA innate immune pathways to fine-tune developmental processes.Recent findings: Innate immune receptors for nucleic acids like the RIG-I-like family receptors and members of DNA sensing pathways are expressed in HSCs and other stem cells. Even though the "classic" role of these receptors is recognition of foreign DNA or RNA from pathogens, it was recently shown that cellular transposable element (TE) RNA or R-loops activate such receptors, serving as endogenous triggers of inflammatory signaling that can shape HSC formation during development and regeneration.Summary: Endogenous TEs and R-loops activate RNA and DNA sensors, which trigger distinct inflammatory signals to fine-tune stem cell decisions. This phenomenon could have broad implications for diverse somatic stem cells, for a variety of diseases and during aging

Small molecule screen in zebrafish and HSC expansion

The zebrafish (Danio rerio) has emerged as a valuable model organism that is amenable for large-scale chemical and genetic screens. The ability of zebrafish to produce large quantities of synchronized, externally fertilized, transparent embryos makes them ideal for screens, which often are not possible in mammalian models. Signaling pathways important for hematopoiesis are well conserved between zebrafish and mammals, making many targets identified in zebrafish screens applicable to mammals. Hematopoiesis in zebrafish occurs in two waves: the primitive or embryonic wave and the definitive or adult wave. Definitive hematopoietic stem cells arise in the aorta-gonad-mesonephros region (AGM) and express conserved markers such as runx1 and c-myb that allow for the detection of stem cells by whole-mount in situ hybridization (WISH). In this protocol, we will discuss a chemical screen in zebrafish embryos to detect compounds that expand or deplete hematopoietic stem cells (HSCs) in vivo. This type of screen represents a powerful tool to study HSCs in zebrafish

Zebrafish Globin Switching Occurs in Two Developmental Stages and Is Controlled by the LCR

Globin gene switching is a complex, highly regulated process allowing expression of distinct globin genes at specific developmental stages. Here, for the first time, we have characterized all of the zebrafish globins based on the completed genomic sequence. Two distinct chromosomal loci, termed major (chromosome 3) and minor (chromosome 12), harbor the globin genes containing α/β pairs in a 5′–3′ to 3′–5′ orientation. Both these loci share synteny with the mammalian α-globin locus. Zebrafish globin expression was assayed during development and demonstrated two globin switches, similar to human development. A conserved regulatory element, the locus control region (LCR), was revealed by analyzing DNase I hypersensitive sites, H3K4 trimethylation marks and GATA1 binding sites. Surprisingly, the position of these sites with relation to the globin genes is evolutionarily conserved, despite a lack of overall sequence conservation. Motifs within the zebrafish LCR include CACCC, GATA, and NFE2 sites, suggesting functional interactions with known transcription factors but not the same LCR architecture. Functional homology to the mammalian α-LCR MCS-R2 region was confirmed by robust and specific reporter expression in erythrocytes of transgenic zebrafish. Our studies provide a comprehensive characterization of the zebrafish globin loci and clarify the regulation of globin switching.Stem Cell and Regenerative Biolog

DO-178C certification of general-purpose GPU software: review of existing methods and future directions

—General-Purpose GPU software is considered for use in avionics to satisfy the increased computational requirements of future systems. Therefore, it needs to be certified following the DO-178C guidance as all airborne software. In this work, we review the existing methods in the literature, we analyse their advantages and disadvantages, and we discuss how they can be combined to obtain certification with lower effort and cost. Our focus is restricted on application-level software, under the premise that successful completion of verification of avionics graphics GPU software products has been demonstrated, so their GPU compiler has been considered acceptable for these already DO-178C certified products, or existing qualified GPU compilers exist. Finally, we discuss upcoming solutions for certified general purpose GPU computing .This work was performed within the Airbus TANIAGPU Project ADS (E/200) in collaboration with the project partners Airbus Defence and Space, Madrid, Spain and CoreAVI, Canada. It was also partially supported by the European Space Agency (ESA) through the GPU4S (GPU for Space) activity, the Spanish Ministry of Economy and Competitiveness under grants PID2019-107255GB and FJCI-2017-34095 (Spanish State Research Agency / http://dx.doi.org/10.13039/501100011033) and the HiPEAC Network of Excellence.Peer ReviewedPostprint (author's final draft

Evaluation of SYCL’s suitability for high-performance critical systems

Upcoming safety critical systems require high performance processing, which can be provided by multi-cores and embedded GPUs found in several Systems-on-chip (SoC) targeting these domains. So far, only low-level programming models and APIs, such as CUDA or OpenCL have been evaluated. In this paper, we evaluate the effectiveness of a higher level programming model, SYCL, for critical applications executed in such embedded platforms. In particular, we are interested in two aspects: performance and programmability. In order to conduct our study, we use the open source GPU4S Bench benchmarking suite for space and an open source pedestrian detection application representing the automotive sector, which we port into SYCL and analyse their behavior. We perform our evaluation on a high-performance platform featuring an NVIDIA GTX 1080Ti as well as a representative embedded platform, the NVIDIA Xavier AGX which is considered a good candidate for future safety critical systems in both domains and we compare our results with other programming models. Our results show that in several cases SYCL is able to obtain performance close to highly optimised code using CUDA or NVIDIA libraries, with significantly lower development effort and complexity, which confirms the suitability of SYCL for programming high-performance safety critical systems.This work was funded by the Ministerio de Ciencia e Innovacion - Agencia Estatal de Investigacion (PID2019-107255GB-C21 and IJC-2020-045931-I MCIN/AEI/10.13039/501100011033), the European Commission’s Horizon 2020 programme under the UP2DATE project (grant agreement 871465) and the HiPEAC Network of Excellence.Peer ReviewedPostprint (author's final draft

A Reporter Screen in a Human Haploid Cell Line Identifies CYLD as a Constitutive Inhibitor of NF-κB

The development of forward genetic screens in human haploid cells has the potential to transform our understanding of the genetic basis of cellular processes unique to man. So far, this approach has been limited mostly to the identification of genes that mediate cell death in response to a lethal agent, likely due to the ease with which this phenotype can be observed. Here, we perform the first reporter screen in the near-haploid KBM7 cell line to identify constitutive inhibitors of NF-κB. CYLD was the only currently known negative regulator of NF-κB to be identified, thus uniquely distinguishing this gene. Also identified were three genes with no previous known connection to NF-κB. Our results demonstrate that reporter screens in haploid human cells can be applied to investigate the many complex signaling pathways that converge upon transcription factors