RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data

This is the peer reviewed version of the following article: Computer Methods and Programs in Biomedine 138 (2016): 73-81, which has been published in final form at http://dx.doi.org/10.1016/j.cmpb.2016.10.008Background and objective To facilitate routine analysis and to improve the reproducibility of the results, next-generation sequencing (NGS) analysis requires intuitive, efficient and integrated data processing pipelines. Methods We have selected well-established software to construct a suite of automated and parallelized workflows to analyse NGS data for DNA-seq (single-nucleotide variants (SNVs) and indels), CNA-seq, bisulfite-seq and ChIP-seq experiments. Results Here, we present RUbioSeq+, an updated and extended version of RUbioSeq, a multiplatform application that incorporates a suite of automated and parallelized workflows to analyse NGS data. This new version includes: (i) an interactive graphical user interface (GUI) that facilitates its use by both biomedical researchers and bioinformaticians, (ii) a new pipeline for ChIP-seq experiments, (iii) pair-wise comparisons (case–control analyses) for DNA-seq experiments, (iv) and improvements in the parallelized and multithreaded execution options. Results generated by our software have been experimentally validated and accepted for publication. Conclusions RUbioSeq+ is free and open to all users at http://rubioseq.bioinfo.cnio.es/.M.R-C is funded by the BLUEPRINT Consortium (FP7/ 2007-2013) under grant agreement number 282510. J.M.F is funded by the INB Node 2 - CNIO, a member of Proteored - PRB2-ISCIII and is supported by grant PT13/0001, of the PE I+D+i 2013-2016, funded by ISCIII and FEDER. H.L-F is funded by a postdoctoral fellowship from the Xunta de Galicia. F.F-R and D.G-P are funded by the European Union's Seventh Framework Programme FP7/REGPOT 2012 2013.1 under grant agreement n° 316265 (BIOCAPS) and the "Platform of integration of intelligent techniques for analysis of biomedical information" project (TIN2013-47153-C3-3-R) financed by the Spanish Ministry of Economy and Competitiveness C.FT is funded by the "Spanish National Youth Guarantee Implementation Plan” (2013/2016) financed by the Spanish Ministry of Economy and Competitivenes

Integrated Design and Implementation of Embedded Control Systems with Scilab

Embedded systems are playing an increasingly important role in control engineering. Despite their popularity, embedded systems are generally subject to resource constraints and it is therefore difficult to build complex control systems on embedded platforms. Traditionally, the design and implementation of control systems are often separated, which causes the development of embedded control systems to be highly time-consuming and costly. To address these problems, this paper presents a low-cost, reusable, reconfigurable platform that enables integrated design and implementation of embedded control systems. To minimize the cost, free and open source software packages such as Linux and Scilab are used. Scilab is ported to the embedded ARM-Linux system. The drivers for interfacing Scilab with several communication protocols including serial, Ethernet, and Modbus are developed. Experiments are conducted to test the developed embedded platform. The use of Scilab enables implementation of complex control algorithms on embedded platforms. With the developed platform, it is possible to perform all phases of the development cycle of embedded control systems in a unified environment, thus facilitating the reduction of development time and cost.Comment: 15 pages, 14 figures; Open Access at http://www.mdpi.org/sensors/papers/s8095501.pd

Investigación de un modelo de sistema no determinista multiproceso

La gestión de sistemas cuyo comportamiento no es determinista es uno de los problemas más importantes de la teoría de la gestión moderna. Hoy en día, los sistemas con complejidad estructural y de comportamiento prevalecen en todas las áreas de la actividad humana y, por lo tanto, su investigación es de suma importancia. Tales sistemas, a diferencia de los sistemas deterministas, se denominan no deterministas. Se caracterizan por un comportamiento difícil de predecir, determinado tanto por influencias aleatorias externas como dentro de los propios sistemas. Un claro ejemplo de un sistema no determinista son las multitudes de personas, fábricas y redes y sistemas informáticos. El problema del comportamiento no determinista directamente en el contexto de las actividades profesionales puede verse utilizando un ejemplo de construcción de analizadores sintácticos. El objetivo del artículo es diseñaruna clase de sistemas orientados a elementos de soporte de un modelo de eventos discretos. El objetivo de la investigación es simular modelos de eventos discretos. El tema de investigación es la creación de un modelo de evento discreto basado en el comportamiento de un autómata de estado finito indeterminado. Durante la preparación del trabajo, se desarrolló e implementó prácticamente un algoritmo para la aplicación, que materializa el principio de trabajar con hilos. Los resultados obtenidos en el artículo tienen como objetivo resolver el problema del procesamiento de datos en paralelo basado en el paralelismo del comportamiento de NFA (autómata finito no determinista) al leer los caracteres de la cadena de entrada. Como resultado, esto debería tener un impacto positivo en la regulación de los procesos de simulación de un sistema no determinista, aumentando su eficiencia y estabilidad. En conclusión, se divulga el algoritmo del trabajo de la aplicación y se extraen conclusiones sobre la efectividad y eficiencia de su desarroll

Investigación de un modelo de sistema no determinista multiproceso

Managing the systems which behaviour is non-deterministic is one of the most important problems in modern management theory. Today, systems with structural and behavioural complexity are prevalent in all areas of human activity, and therefore, their research is of the utmost importance. Such systems, as opposed to deterministic systems, are called non-deterministic. They are characterised by difficult predictable behaviour determined both by external random influences, and within the systems themselves. A clear example of a non-deterministic system is crowds of people, factories, and computer networks and systems. The problem of non-deterministic behaviour directly within the context of professional activities can be seen using an example of building syntactic analysers. The aim of the paper is to design a class of systems oriented towards supporting elements of a discrete event model. The target of research is to simulate discrete event models. The subject of research is a creation of a discrete event model based on the behaviour of an undetermined finite state automaton. During the preparation of the paper, there was developed and practically implemented an algorithm for the application, which materializes the principle of working with threads. The results obtained in the paper are aimed at solving the problem of parallel data processing based on the parallelism of NFA's (non-deterministic finite automaton) behaviour when reading the input string characters. As a result, this should have a positive impact on the regulation of the simulation processes of a non-deterministic system, increasing its efficiency and stability. In conclusion, the algorithm of the application work is disclosed and conclusions about the effectiveness and efficiency of its development are drawn.La gestión de sistemas cuyo comportamiento no es determinista es uno de los problemas más importantes de la teoría de la gestión moderna. Hoy en día, los sistemas con complejidad estructural y de comportamiento prevalecen en todas las áreas de la actividad humana y, por lo tanto, su investigación es de suma importancia. Tales sistemas, a diferencia de los sistemas deterministas, se denominan no deterministas. Se caracterizan por un comportamiento difícil de predecir, determinado tanto por influencias aleatorias externas como dentro de los propios sistemas. Un claro ejemplo de un sistema no determinista son las multitudes de personas, fábricas y redes y sistemas informáticos. El problema del comportamiento no determinista directamente en el contexto de las actividades profesionales puede verse utilizando un ejemplo de construcción de analizadores sintácticos. El objetivo del artículo es diseñar una clase de sistemas orientados a elementos de soporte de un modelo de eventos discretos. El objetivo de la investigación es simular modelos de eventos discretos. El tema de investigación es la creación de un modelo de evento discreto basado en el comportamiento de un autómata de estado finito indeterminado. Durante la preparación del trabajo, se desarrolló e implementó prácticamente un algoritmo para la aplicación, que materializa el principio de trabajar con hilos. Los resultados obtenidos en el artículo tienen como objetivo resolver el problema del procesamiento de datos en paralelo basado en el paralelismo del comportamiento de NFA (autómata finito no determinista) al leer los caracteres de la cadena de entrada. Como resultado, esto debería tener un impacto positivo en la regulación de los procesos de simulación de un sistema no determinista, aumentando su eficiencia y estabilidad. En conclusión, se divulga el algoritmo del trabajo de la aplicación y se extraen conclusiones sobre la efectividad y eficiencia de su desarrollo

Recent developments in GEANT 4

Fil: Depaola, Gerardo Osvaldo. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomía, Física y Computación; Argentina.GEANT4 is a software toolkit for the simulation of the passage of particles through matter. It is used by a large number of experiments and projects in a variety of application domains, including high energy physics, astrophysics and space science, medical physics and radiation protection. Over the past several years, major changes have been made to the toolkit in order to accommodate the needs of these user communities, and to efficiently exploit the growth of computing power made available by advances in technology. The adaptation of GEANT4 to multithreading, advances in physics, detector modeling and visualization, extensions to the toolkit, including biasing and reverse Monte Carlo, and tools for physics and release validation are discussed here.info:eu-repo/semantics/publishedVersionFil: Depaola, Gerardo Osvaldo. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomía, Física y Computación; Argentina.Física de Partículas y Campo

Improving the User Experience of the rCUDA Remote GPU Virtualization Framework

Graphics processing units (GPUs) are being increasingly embraced by the high-performance computing community as an effective way to reduce execution time by accelerating parts of their applications. remote CUDA (rCUDA) was recently introduced as a software solution to address the high acquisition costs and energy consumption of GPUs that constrain further adoption of this technology. Specifically, rCUDA is a middleware that allows a reduced number of GPUs to be transparently shared among the nodes in a cluster. Although the initial prototype versions of rCUDA demonstrated its functionality, they also revealed concerns with respect to usability, performance, and support for new CUDA features. In response, in this paper, we present a new rCUDA version that (1) improves usability by including a new component that allows an automatic transformation of any CUDA source code so that it conforms to the needs of the rCUDA framework, (2) consistently features low overhead when using remote GPUs thanks to an improved new communication architecture, and (3) supports multithreaded applications and CUDA libraries. As a result, for any CUDA-compatible program, rCUDA now allows the use of remote GPUs within a cluster with low overhead, so that a single application running in one node can use all GPUs available across the cluster, thereby extending the single-node capability of CUDA. Copyright © 2014 John Wiley & Sons, Ltd.This work was funded by the Generalitat Valenciana under Grant PROMETEOII/2013/009 of the PROMETEO program phase II. The author from Argonne National Laboratory was supported by the US Department of Energy, Office of Science, under Contract No. DE-AC02-06CH11357. The authors are also grateful for the generous support provided by Mellanox Technologies.Reaño González, C.; Silla Jiménez, F.; Castello Gimeno, A.; Peña Monferrer, AJ.; Mayo Gual, R.; Quintana Ortí, ES.; Duato Marín, JF. (2015). Improving the User Experience of the rCUDA Remote GPU Virtualization Framework. Concurrency and Computation: Practice and Experience. 27(14):3746-3770. https://doi.org/10.1002/cpe.3409S374637702714NVIDIA NVIDIA industry cases http://www.nvidia.es/object/tesla-case-studiesFigueiredo, R., Dinda, P. A., & Fortes, J. (2005). Guest Editors’ Introduction: Resource Virtualization Renaissance. Computer, 38(5), 28-31. doi:10.1109/mc.2005.159Duato J Igual FD Mayo R Peña AJ Quintana-Ortí ES Silla F An efficient implementation of GPU virtualization in high performance clusters Euro-Par 2009 Workshops, ser. LNCS, 6043 Delft, Netherlands, 385 394Duato J Peña AJ Silla F Mayo R Quintana-Ortí ES Performance of CUDA virtualized remote GPUs in high performance clusters International Conference on Parallel Processing, Taipei, Taiwan 2011 365 374Duato J Peña AJ Silla F Fernández JC Mayo R Quintana-Ortí ES Enabling CUDA acceleration within virtual machines using rCUDA International Conference on High Performance Computing, Bangalore, India 2011 1 10Shi, L., Chen, H., Sun, J., & Li, K. (2012). vCUDA: GPU-Accelerated High-Performance Computing in Virtual Machines. IEEE Transactions on Computers, 61(6), 804-816. doi:10.1109/tc.2011.112Gupta V Gavrilovska A Schwan K Kharche H Tolia N Talwar V Ranganathan P GViM: GPU-accelerated virtual machines 3rd Workshop on System-Level Virtualization for High Performance Computing, Nuremberg, Germany 2009 17 24Giunta G Montella R Agrillo G Coviello G A GPGPU transparent virtualization component for high performance computing clouds Euro-Par 2010 - Parallel Processing, 6271 Ischia, Italy, 379 391Zillians VGPU http://www.zillians.com/vgpuLiang TY Chang YW GridCuda: a grid-enabled CUDA programming toolkit Proceedings of the 25th IEEE International Conference on Advanced Information Networking and Applications Workshops (WAINA), Biopolis, Singapore 2011 141 146Barak A Ben-Nun T Levy E Shiloh A Apackage for OpenCL based heterogeneous computing on clusters with many GPU devices Workshop on Parallel Programming and Applications on Accelerator Clusters, Heraklion, Crete, Greece 2010 1 7Xiao S Balaji P Zhu Q Thakur R Coghlan S Lin H Wen G Hong J Feng W-C VOCL: an optimized environment for transparent virtualization of graphics processing units Proceedings of InPar, San Jose, California, USA 2012 1 12Kim J Seo S Lee J Nah J Jo G Lee J SnuCL: an OpenCL framework for heterogeneous CPU/GPU clusters Proceedings of the 26th International Conference on Supercomputing, Venice, Italy 2012 341 352NVIDIA The NVIDIA CUDA Compiler Driver NVCC Version 5, NVIDIA 2012Quinlan D Panas T Liao C ROSE http://rosecompiler.org/Free Software Foundation, Inc. GCC, the GNU Compiler Collection http://gcc.gnu.org/LLVM Clang: a C language family frontend for LLVM http://clang.llvm.org/Martinez G Feng W Gardner M CU2CL: a CUDA-to-OpenCL Translator for Multi- and Many-core Architectures http://eprints.cs.vt.edu/archive/00001161/01/CU2CL.pdfLLVM The LLVM compiler infrastructure http://llvm.org/Reaño C Peña AJ Silla F Duato J Mayo R Quintana-Orti ES CU2rCU: towards the complete rCUDA remote GPU virtualization and sharing solution Proceedings of the 19th International Conference on High Performance Computing (HiPC), Pune, India 2012 1 10NVIDIA The NVIDIA GPU Computing SDK Version 4, NVIDIA 2011Sandia National Labs LAMMPS molecular dynamics simulator http://lammps.sandia.gov/Citrix Systems, Inc. Xen http://xen.org/Peña AJ Virtualization of accelerators in high performance clusters Ph.D. Thesis, 2013NVIDIA CUDA profiler user's guide version 5, NVIDIA 2012Igual, F. D., Chan, E., Quintana-Ortí, E. S., Quintana-Ortí, G., van de Geijn, R. A., & Van Zee, F. G. (2012). The FLAME approach: From dense linear algebra algorithms to high-performance multi-accelerator implementations. Journal of Parallel and Distributed Computing, 72(9), 1134-1143. doi:10.1016/j.jpdc.2011.10.014Slurm workload manager http://slurm.schedmd.co

GeantV: Results from the prototype of concurrent vector particle transport simulation in HEP

Full detector simulation was among the largest CPU consumer in all CERN experiment software stacks for the first two runs of the Large Hadron Collider (LHC). In the early 2010's, the projections were that simulation demands would scale linearly with luminosity increase, compensated only partially by an increase of computing resources. The extension of fast simulation approaches to more use cases, covering a larger fraction of the simulation budget, is only part of the solution due to intrinsic precision limitations. The remainder corresponds to speeding-up the simulation software by several factors, which is out of reach using simple optimizations on the current code base. In this context, the GeantV R&D project was launched, aiming to redesign the legacy particle transport codes in order to make them benefit from fine-grained parallelism features such as vectorization, but also from increased code and data locality. This paper presents extensively the results and achievements of this R&D, as well as the conclusions and lessons learnt from the beta prototype.Comment: 34 pages, 26 figures, 24 table