A Class of Parallel Tiled Linear Algebra Algorithms for Multicore Architectures

As multicore systems continue to gain ground in the High Performance Computing world, linear algebra algorithms have to be reformulated or new algorithms have to be developed in order to take advantage of the architectural features on these new processors. Fine grain parallelism becomes a major requirement and introduces the necessity of loose synchronization in the parallel execution of an operation. This paper presents an algorithm for the Cholesky, LU and QR factorization where the operations can be represented as a sequence of small tasks that operate on square blocks of data. These tasks can be dynamically scheduled for execution based on the dependencies among them and on the availability of computational resources. This may result in an out of order execution of the tasks which will completely hide the presence of intrinsically sequential tasks in the factorization. Performance comparisons are presented with the LAPACK algorithms where parallelism can only be exploited at the level of the BLAS operations and vendor implementations

Fine-Grained Multithreading for the Multifrontal QR Factorization of Sparse Matrices

International audienceThe advent of multicore processors represents a disruptive event in the history of computer science as conventional parallel programming paradigms are proving incapable of fully exploiting their potential for concurrent computations. The need for different or new programming models clearly arises from recent studies which identify fine-granularity and dynamic execution as the keys to achieving high efficiency on multicore systems. This work presents an approach to the parallelization of the multifrontal method for the $QR$ factorization of sparse matrices specifically designed for multicore based systems. High efficiency is achieved through a fine-grained partitioning of data and a dynamic scheduling of computational tasks relying on a dataflow parallel programming model. Experimental results show that an implementation of the proposed approach achieves higher performance and better scalability than existing equivalent software

Oxidative Stress in Cardiovascular Inflammation: Its Involvement in Autoimmune Responses

Recently, it has become clear that atherosclerosis is a chronic inflammatory disease in which inflammation and immune responses play a key role. Accelerated atherosclerosis has been reported in patients with autoimmune diseases, suggesting an involvement of autoimmune mechanisms in atherogenesis. Different self-antigens or modified self-molecules have been identified as target of humoral and cellular immune responses in patients with atherosclerotic disease. Oxidative stress, increasingly reported in these patients, is the major event causing structural modification of proteins with consequent appearance of neoepitopes. Self-molecules modified by oxidative events can become targets of autoimmune reactions, thus sustaining the inflammatory mechanisms involved in endothelial dysfunction and plaque development. In this paper, we will summarize the best characterized autoantigens in atherosclerosis and their possible role in cardiovascular inflammation

Implementing multifrontal sparse solvers for multicore architectures with Sequential Task Flow runtime systems

International audienceTo face the advent of multicore processors and the ever increasing complexity of hardware architectures, programming models based on DAG parallelism regained popularity in the high performance, scientific computing community. Modern runtime systems offer a programming interface that complies with this paradigm and powerful engines for scheduling the tasks into which the application is decomposed. These tools have already proved their effectiveness on a number of dense linear algebra applications. This paper evaluates the usability and effectiveness of runtime systems based on the Sequential Task Flow model for complex applications , namely, sparse matrix multifrontal factorizations which feature extremely irregular workloads, with tasks of different granularities and characteristics and with a variable memory consumption. Most importantly, it shows how this parallel programming model eases the development of complex features that benefit the performance of sparse, direct solvers as well as their memory consumption. We illustrate our discussion with the multifrontal QR factorization running on top of the StarPU runtime system. ACM Reference Format: Emmanuel Agullo, Alfredo Buttari, Abdou Guermouche and Florent Lopez, 2014. Implementing multifrontal sparse solvers for multicore architectures with Sequential Task Flow runtime system

Multifrontal QR Factorization for Multicore Architectures over Runtime Systems

International audienceTo face the advent of multicore processors and the ever increasing complexity of hardware architectures, programming models based on DAG parallelism regained popularity in the high performance, scientific computing community. Modern runtime systems offer a programming interface that complies with this paradigm and powerful engines for scheduling the tasks into which the application is decomposed. These tools have already proved their effectiveness on a number of dense linear algebra applications. This paper evaluates the usability of runtime systems for complex applications, namely, sparse matrix multifrontal factorizations which constitute extremely irregular workloads, with tasks of different granularities and characteristics and with a variable memory consumption. Experimental results on real-life matrices show that it is possible to achieve the same efficiency as with an ad hoc scheduler which relies on the knowledge of the algorithm. A detailed analysis shows the performance behavior of the resulting code and possible ways of improving the effectiveness of runtime systems

Chronic and acute alcohol exposure prevents monocyte-derived dendritic cells from maturing in response to microbial stimuli

Gli alcolisti sono soggetti immunocompromessi per stile di vita caratterizzati da una disregolazione del sistema immunitario e quindi da una maggiore suscettibilità all’insorgenza di malattie infettive. L’alcol interferisce con le funzioni di cellule e molecole del sistema immunitario, compromettendo i meccanismi dell’immunità innata ed acquisita, umorale e cellulare, e determinando alterate risposte infiammatorie spesso associate a danni organo-specifici. Tuttavia i meccanismi che determinano la disfunzione immunitaria non sono ancora del tutto chiariti. Studi clinici e sperimentali hanno messo in evidenza che l’abuso cronico di alcol è associato ad una aumentata incidenza di infezioni polmonari da Streptococcus pneumoniae e Mycobacterium tuberculosis, di infezioni epatiche da HBV e HCV. L'associazione tra abuso d’alcol ed aumento dei decessi per infezioni è nota da più di 75 anni, ma solo negli ultimi 15 anni seri sforzi investigativi sono stati fatti per comprendere il ruolo dell’abuso alcolico nelle disfunzioni immunitarie. Gli alcolisti, la cui maggioranza ricade nella fascia socioeconomica povera, spesso soffrono condizioni di sovraffollamento e d’accesso limitato alle cure sanitarie, che possono aumentare la probabilità di contrarre e diffondere malattie infettive. Inoltre, molti alcolisti soffrono di malnutrizione e di malattie epatiche condizioni che possono compromettere il sistema immunitario e la sua capacità di resistere all’infezione. Le disfunzioni immunitarie indotte dall’alcol dipendono da vari fattori, tra cui la dose d’alcol e la durata d’esposizione (cronica vs acuta), dalla presenza e caratteristiche d’altri stimoli come le molecole microbiche. I difetti a carico delle cellule presentanti l'antigene (APC) sembrano giocare un ruolo fondamentale nell’alterazioni delle risposte dell’immunità cellulo-mediata e nella riduzione della proliferazione linfocitaria antigene specifica. Le cellule dendritiche (CD), cellule professionali presentanti l’antigene, sono tra le più potenti APCs, il loro grado di maturazione fenotipica e funzionale regola il grado e la tipologia della risposta immune che porta all’attivazione e la tolleranza. Tra gli obbiettivi della ricerca sugli effetti dell’alcol sulla salute umana, c’è grande necessità di sviluppare approcci multimodali in grado di modulare e recuperare la funzionalità del sistema immune dai danni indotti dall’abuso di alcol. Lo scopo principale della presente tesi è stato quello di approfondire lo studio dei meccanismi molecolari e cellulari indotti dall’alcol sulle cellule dell’immunità innata al fine di promuovere un’immunità protettiva specifica. Per raggiungere questi obiettivi specifici è stato valutato i) il grado d’alterazione dell’immunità innata in soggetti immunocompromessi per abuso d’alcol (esposizione cronica) ed il grado d’alterazione di monociti e CD esposte in vitro all’etanolo (esposizione acuta); ii) l’efficacia del trattamento in vitro con cromoglicato sodico di monociti e CD come strategia adiuvante ad uso umano nel modello di differenziazione e maturazione delle CD. In particolare, sono stati studiati gli effetti in vivo dell’esposizione cronica all’alcol sulla capacità dei monociti, ottenuti da soggetti alcolisti, di differenziare e maturare in vitro in CD funzionali. Per ampliare le attuali informazioni sui cambiamenti indotti dall’esposizione acuta all’alcol sulle cellule dendritiche è stato valutato il grado di alterazione delle CD esposte in vitro all’etanolo dopo induzione del processo di maturazione. In questo studio sono state allestite colture di CD generate da soggetti alcolisti cronici e da soggetti sani non bevitori. Mediante tecniche di immunochimica e di citometria a flusso è stata eseguita una caratterizzazione fenotipica e funzionale delle CD generate da monociti in presenza dei fattori di crescita IL-4 e GM-CSF. Le cellule dendritiche sono state caratterizzate a livello fenotipico e funzionale prima e dopo stimolazione con LPS (endocitosi, migrazione, produzione di citochine, capacità allostimolatoria), E’ stato inoltre valutata la capacità di cellule dendritiche esposte in vitro all’etanolo di polarizzare linfociti T naïve ed il tipo di polarizzazione indotto. Come possibile approccio alla prevenzione degli effetti negativi dell’alcol sul sistema immunitario, è stata valutata la capacità del cromoglicato, farmaco utilizzato nella terapia anti-allergica e noto per la sua capacità di stabilizzare la polarità delle membrane cellulari, di esercitare in vitro un effetto adiuvante sulla funzionalità dei monociti e CD esposte all’etanolo. Per questo scopo abbiamo valutato in vitro l’attività del cromoglicato sul fenotipo e la funzione delle CD esposte all’etanolo, nel modello di differenziazione e di maturazione delle CD. I risultati della presente tesi dimostrano come l'esposizione cronica e acuta all'alcol, anche a dosi moderate, influenza in vitro la maturazione fenotipica e funzionale delle cellule dendritiche in risposta ad uno stimolo maturativo microbico, quale LPS, suggerendo una ridotta capacità degli alcolisti cronici a controllare le infezioni. Inoltre, i risultati della presente tesi mettono in evidenza il possibile ruolo di adiuvante del cromoglicato nel processo di differenziazione e maturazione delle CD, suggerendo come questo farmaco possa rappresentare uno strategia innovativa in grado di ripristinare la corretta funzionalità dell’immunità innata nei soggetti alcolisti e in tal modo migliorare la capacità del sistema immunitario a resistere all’infezioni.Research demonstrating alcohol's adverse effects on functions of the immune system supports clinical evidence of an increased incidence of infectious diseases, such as pneumoniae, tuberculosis and hepatitis C, as well as a greater susceptibility to cancer in humans chronically abusing alcohol. While the association of alcohol abuse with increased deaths from infections was made over 75 years ago, only in the past 15 years has serious investigative efforts been made to understand the role of alcoholic exposure on immune dysfunction. Among the many alcoholics whose socioeconomic status is poor, overcrowded living conditions and limited access to health care may increase the likelihood of contracting and spreading disease. In addition, many alcoholics suffer from malnutrition and liver disease, conditions that may themselves compromise the immune system's capacity to resist infection. Evidence from human and animal studies in vivo as well as from experiments in vitro suggests that alcohol abuse may exert adverse immunomodulatory effects on innate and adaptive immune responses. Alcohol-induced immune dysfunctions depend on various factors including the dose and duration of alcohol exposure (chronic vs acute) and on the presence and characteristics of additional stimuli such as microbial molecules. Defects of antigen presenting cells (APC) appear to be pivotal in the alcohol-induced alterations of cell-mediated immunity and in decreased antigen (Ag)-specific T cell proliferation. Dendritic cells (DCs) are the most potent APCs. The functional state of DC maturation and their activation degree control immunity and tolerance. The complex nature of the linkage between alcohol consumption, altered host immune responses, and infection remains controversial and incompletely understood. Most importantly, there is a need to develop a multimodal approach, including components of immune modulation and immune restoration, to repair possible damages in the host defence system induced by alcohol ingestion. In this study we addressed this research need in: 1) to understand how alcohol exposure induces immune alterations that contribute to the occurrence of particular kinds of infectious diseases showing a higher incidence in alcohol abuser population than in the general population and 2) to develop strategies to reduce the occurrence of alcohol-induced immune alterations. To clarify the immunological effects exerted by alcohol abuse on human monocyte-derived DCs we investigated whether in vivo chronic alcohol exposure alters the ability of monocytes from alcoholics to differentiate and mature in vitro into functional DCs. To extend current information on direct alcohol-induced changes in DCs, we evaluated whether in vitro acute ethanol (EtOH) treatment of differentiated immature DCs (iDCs) generated from chronic alcoholics and healthy control subjects impairs DC maturation. Using immunochemical and cytofluorimetric analysis we determined the phenotype and functions (endocytosis, migration, cytokine production and allostimulatory ability) of monocyte-derived DCs and analyzed the ability of iDCs to respond to the microbial product lipopolysaccharide (LPS). We also wanted to find out whether EtOH-treated antigen-stimulated DCs correctly primed naïve T lymphocytes, thus inducing T helper 1 (Th1) cell polarization. As a possible approach in the prevention of alcohol's adverse effects on the immune system we investigated whether cromoglycate-like’ anti-allergic drugs -- by their well established property to stabilize membrane lipid polarity -- might exert in vitro an adjuvant effect on monocytes and DCs exposed to EtOH. For this purpose we evaluated in vitro activity of cromoglycate on DC phenotype and function exposed to EtOH in the well-established model of DC differentiation and maturation. Our results showed that alcoholics’ monocytes differentiated into immature DCs with an altered phenotype and functions (alc-iDCs). Alc-iDCs showed fewer CD1a+ cells, weaker CD86 expression and higher HLA-DR expression associated with lower endocytosis and allostimulatory functions than did iDCs from healthy subjects (control-iDCs). Despite these impairments, alc-iDCs produced tumour necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6) in large amounts. LPS stimulation failed to induce full phenotypical and functional alc-iDC maturation. In vitro acute EtOH exposure also prevented alc-iDCs and control-iDCs from maturing in response to LPS. T-cell priming experiments showed that EtOH treatment prevented LPS-stimulated control-DCs from priming and polarizing naïve allogeneic T cells into T helper 1 (Th1) cells, thus favouring a predominant T helper 2 (Th2) environment. Furthermore, this thesis establishes a new adjuvant effect of cromoglycate on the level of DC differentiation and maturation and suggests that cromoglycate may represent an innovative strategy to reverse the impaired immune response in alcoholics thus improving the immune system's capacity to resist infection

Exploiting a Parametrized Task Graph model for the parallelization of a sparse direct multifrontal solver

International audienceThe advent of multicore processors requires to reconsider the design of high performance computing libraries to embrace portable and effective techniques of parallel software engineering. One of the most promising approaches consists in abstracting an application as a directed acyclic graph (DAG) of tasks. While this approach has been popularized for shared memory environments by the OpenMP 4.0 standard where dependencies between tasks are automatically inferred, we investigate an alternative approach, capable of describing the DAG of task in a distributed setting, where task dependencies are explicitly encoded. So far this approach has been mostly used in the case of algorithms with a regular data access pattern and we show in this study that it can be efficiently applied to a higly irregular numerical algorithm such as a sparse multifrontal QR method. We present the resulting implementation and discuss the potential and limits of this approach in terms of productivity and effectiveness in comparison with more common parallelization techniques. Although at an early stage of development, preliminary results show the potential of the parallel programming model that we investigate in this work

Scheduling data flow program in xkaapi: A new affinity based Algorithm for Heterogeneous Architectures

Efficient implementations of parallel applications on heterogeneous hybrid architectures require a careful balance between computations and communications with accelerator devices. Even if most of the communication time can be overlapped by computations, it is essential to reduce the total volume of communicated data. The literature therefore abounds with ad-hoc methods to reach that balance, but that are architecture and application dependent. We propose here a generic mechanism to automatically optimize the scheduling between CPUs and GPUs, and compare two strategies within this mechanism: the classical Heterogeneous Earliest Finish Time (HEFT) algorithm and our new, parametrized, Distributed Affinity Dual Approximation algorithm (DADA), which consists in grouping the tasks by affinity before running a fast dual approximation. We ran experiments on a heterogeneous parallel machine with six CPU cores and eight NVIDIA Fermi GPUs. Three standard dense linear algebra kernels from the PLASMA library have been ported on top of the Xkaapi runtime. We report their performances. It results that HEFT and DADA perform well for various experimental conditions, but that DADA performs better for larger systems and number of GPUs, and, in most cases, generates much lower data transfers than HEFT to achieve the same performance