RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine

Phylogenetic tree reconstruction is one of the grand challenge problems in Bioinformatics. The search for a best-scoring tree with 50 organisms, under a reasonable optimality criterion, creates a topological search space which is as large as the number of atoms in the universe. Computational phylogeny is challenging even for the most powerful supercomputers. It is also an ideal candidate for benchmarking emerging multiprocessor architectures, because it exhibits various levels of fine and coarse-grain parallelism. In this paper, we present the porting, optimization, and evaluation of RAxML on the Cell Broadband Engine. RAxML is a provably efficient, hill climbing algorithm for computing phylogenetic trees based on the Maximum Likelihood (ML) method. The algorithm uses an embarrassingly parallel search method, which also exhibits data-level parallelism and control parallelism in the computation of the likelihood functions. We present the optimization of one of the currently fastest tree search algorithms, on a real Cell blade prototype. We also investigate problems and present solutions pertaining to the optimization of floating point code, control flow, communication, scheduling, and multi-level parallelization on the Cell

Dynamic Multigrain Parallelization on the Cell Broadband Engine

This paper addresses the problem of orchestrating and scheduling parallelism at multiple levels of granularity on heterogeneous multicore processors. We present policies and mechanisms for adaptive exploitation and scheduling of multiple layers of parallelism on the Cell Broadband Engine. Our policies combine event-driven task scheduling with malleable loop-level parallelism, which is exposed from the runtime system whenever task-level parallelism leaves cores idle. We present a runtime system for scheduling applications with layered parallelism on Cell and investigate its potential with RAxML, a computational biology application which infers large phylogenetic trees, using the Maximum Likelihood (ML) method. Our experiments show that the Cell benefits significantly from dynamic parallelization methods, that selectively exploit the layers of parallelism in the system, in response to workload characteristics. Our runtime environment outperforms naive parallelization and scheduling based on MPI and Linux by up to a factor of 2.6. We are able to execute RAxML on one Cell four times faster than on a dual-processor system with Hyperthreaded Xeon processors, and 5--10\% faster than on a single-processor system with a dual-core, quad-thread IBM Power5 processor

On the design of architecture-aware algorithms for emerging applications

This dissertation maps various kernels and applications to a spectrum of programming models and architectures and also presents architecture-aware algorithms for different systems. The kernels and applications discussed in this dissertation have widely varying computational characteristics. For example, we consider both dense numerical computations and sparse graph algorithms. This dissertation also covers emerging applications from image processing, complex network analysis, and computational biology. We map these problems to diverse multicore processors and manycore accelerators. We also use new programming models (such as Transactional Memory, MapReduce, and Intel TBB) to address the performance and productivity challenges in the problems. Our experiences highlight the importance of mapping applications to appropriate programming models and architectures. We also find several limitations of current system software and architectures and directions to improve those. The discussion focuses on system software and architectural support for nested irregular parallelism, Transactional Memory, and hybrid data transfer mechanisms. We believe that the complexity of parallel programming can be significantly reduced via collaborative efforts among researchers and practitioners from different domains. This dissertation participates in the efforts by providing benchmarks and suggestions to improve system software and architectures.Ph.D.Committee Chair: Bader, David; Committee Member: Hong, Bo; Committee Member: Riley, George; Committee Member: Vuduc, Richard; Committee Member: Wills, Scot

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Broadcast-oriented wireless network-on-chip : fundamentals and feasibility

Premi extraordinari doctorat UPC curs 2015-2016, àmbit Enginyeria de les TICRecent years have seen the emergence and ubiquitous adoption of Chip Multiprocessors (CMPs), which rely on the coordinated operation of multiple execution units or cores. Successive CMP generations integrate a larger number of cores seeking higher performance with a reasonable cost envelope. For this trend to continue, however, important scalability issues need to be solved at different levels of design. Scaling the interconnect fabric is a grand challenge by itself, as new Network-on-Chip (NoC) proposals need to overcome the performance hurdles found when dealing with the increasingly variable and heterogeneous communication demands of manycore processors. Fast and flexible NoC solutions are needed to prevent communication become a performance bottleneck, situation that would severely limit the design space at the architectural level and eventually lead to the use of software frameworks that are slow, inefficient, or less programmable. The emergence of novel interconnect technologies has opened the door to a plethora of new NoCs promising greater scalability and architectural flexibility. In particular, wireless on-chip communication has garnered considerable attention due to its inherent broadcast capabilities, low latency, and system-level simplicity. Most of the resulting Wireless Network-on-Chip (WNoC) proposals have set the focus on leveraging the latency advantage of this paradigm by creating multiple wireless channels to interconnect far-apart cores. This strategy is effective as the complement of wired NoCs at moderate scales, but is likely to be overshadowed at larger scales by technologies such as nanophotonics unless bandwidth is unrealistically improved. This dissertation presents the concept of Broadcast-Oriented Wireless Network-on-Chip (BoWNoC), a new approach that attempts to foster the inherent simplicity, flexibility, and broadcast capabilities of the wireless technology by integrating one on-chip antenna and transceiver per processor core. This paradigm is part of a broader hybrid vision where the BoWNoC serves latency-critical and broadcast traffic, tightly coupled to a wired plane oriented to large flows of data. By virtue of its scalable broadcast support, BoWNoC may become the key enabler of a wealth of unconventional hardware architectures and algorithmic approaches, eventually leading to a significant improvement of the performance, energy efficiency, scalability and programmability of manycore chips. The present work aims not only to lay the fundamentals of the BoWNoC paradigm, but also to demonstrate its viability from the electronic implementation, network design, and multiprocessor architecture perspectives. An exploration at the physical level of design validates the feasibility of the approach at millimeter-wave bands in the short term, and then suggests the use of graphene-based antennas in the terahertz band in the long term. At the link level, this thesis provides an insightful context analysis that is used, afterwards, to drive the design of a lightweight protocol that reliably serves broadcast traffic with substantial latency improvements over state-of-the-art NoCs. At the network level, our hybrid vision is evaluated putting emphasis on the flexibility provided at the network interface level, showing outstanding speedups for a wide set of traffic patterns. At the architecture level, the potential impact of the BoWNoC paradigm on the design of manycore chips is not only qualitatively discussed in general, but also quantitatively assessed in a particular architecture for fast synchronization. Results demonstrate that the impact of BoWNoC can go beyond simply improving the network performance, thereby representing a possible game changer in the manycore era.Avenços en el disseny de multiprocessadors han portat a una àmplia adopció dels Chip Multiprocessors (CMPs), que basen el seu potencial en la operació coordinada de múltiples nuclis de procés. Generacions successives han anat integrant més nuclis en la recerca d'alt rendiment amb un cost raonable. Per a que aquesta tendència continuï, però, cal resoldre importants problemes d'escalabilitat a diferents capes de disseny. Escalar la xarxa d'interconnexió és un gran repte en ell mateix, ja que les noves propostes de Networks-on-Chip (NoC) han de servir un tràfic eminentment variable i heterogeni dels processadors amb molts nuclis. Són necessàries solucions ràpides i flexibles per evitar que les comunicacions dins del xip es converteixin en el pròxim coll d'ampolla de rendiment, situació que limitaria en gran mesura l'espai de disseny a nivell d'arquitectura i portaria a l'ús d'arquitectures i models de programació lents, ineficients o poc programables. L'aparició de noves tecnologies d'interconnexió ha possibilitat la creació de NoCs més flexibles i escalables. En particular, la comunicació intra-xip sense fils ha despertat un interès considerable en virtut de les seva baixa latència, simplicitat, i bon rendiment amb tràfic broadcast. La majoria de les Wireless NoC (WNoC) proposades fins ara s'han centrat en aprofitar l'avantatge en termes de latència d'aquest nou paradigma creant múltiples canals sense fils per interconnectar nuclis allunyats entre sí. Aquesta estratègia és efectiva per complementar a NoCs clàssiques en escales mitjanes, però és probable que altres tecnologies com la nanofotònica puguin jugar millor aquest paper a escales més grans. Aquesta tesi presenta el concepte de Broadcast-Oriented WNoC (BoWNoC), un nou enfoc que intenta rendibilitzar al màxim la inherent simplicitat, flexibilitat, i capacitats broadcast de la tecnologia sense fils integrant una antena i transmissor/receptor per cada nucli del processador. Aquest paradigma forma part d'una visió més àmplia on un BoWNoC serviria tràfic broadcast i urgent, mentre que una xarxa convencional serviria fluxos de dades més pesats. En virtut de la escalabilitat i del seu suport broadcast, BoWNoC podria convertir-se en un element clau en una gran varietat d'arquitectures i algoritmes poc convencionals que milloressin considerablement el rendiment, l'eficiència, l'escalabilitat i la programabilitat de processadors amb molts nuclis. El present treball té com a objectius no només estudiar els aspectes fonamentals del paradigma BoWNoC, sinó també demostrar la seva viabilitat des dels punts de vista de la implementació, i del disseny de xarxa i arquitectura. Una exploració a la capa física valida la viabilitat de l'enfoc usant tecnologies longituds d'ona milimètriques en un futur proper, i suggereix l'ús d'antenes de grafè a la banda dels terahertz ja a més llarg termini. A capa d'enllaç, la tesi aporta una anàlisi del context de l'aplicació que és, més tard, utilitzada per al disseny d'un protocol d'accés al medi que permet servir tràfic broadcast a baixa latència i de forma fiable. A capa de xarxa, la nostra visió híbrida és avaluada posant èmfasi en la flexibilitat que aporta el fet de prendre les decisions a nivell de la interfície de xarxa, mostrant grans millores de rendiment per una àmplia selecció de patrons de tràfic. A nivell d'arquitectura, l'impacte que el concepte de BoWNoC pot tenir sobre el disseny de processadors amb molts nuclis no només és debatut de forma qualitativa i genèrica, sinó també avaluat quantitativament per una arquitectura concreta enfocada a la sincronització. Els resultats demostren que l'impacte de BoWNoC pot anar més enllà d'una millora en termes de rendiment de xarxa; representant, possiblement, un canvi radical a l'era dels molts nuclisAward-winningPostprint (published version

Broadcast-oriented wireless network-on-chip : fundamentals and feasibility

Premi extraordinari doctorat UPC curs 2015-2016, àmbit Enginyeria de les TICRecent years have seen the emergence and ubiquitous adoption of Chip Multiprocessors (CMPs), which rely on the coordinated operation of multiple execution units or cores. Successive CMP generations integrate a larger number of cores seeking higher performance with a reasonable cost envelope. For this trend to continue, however, important scalability issues need to be solved at different levels of design. Scaling the interconnect fabric is a grand challenge by itself, as new Network-on-Chip (NoC) proposals need to overcome the performance hurdles found when dealing with the increasingly variable and heterogeneous communication demands of manycore processors. Fast and flexible NoC solutions are needed to prevent communication become a performance bottleneck, situation that would severely limit the design space at the architectural level and eventually lead to the use of software frameworks that are slow, inefficient, or less programmable. The emergence of novel interconnect technologies has opened the door to a plethora of new NoCs promising greater scalability and architectural flexibility. In particular, wireless on-chip communication has garnered considerable attention due to its inherent broadcast capabilities, low latency, and system-level simplicity. Most of the resulting Wireless Network-on-Chip (WNoC) proposals have set the focus on leveraging the latency advantage of this paradigm by creating multiple wireless channels to interconnect far-apart cores. This strategy is effective as the complement of wired NoCs at moderate scales, but is likely to be overshadowed at larger scales by technologies such as nanophotonics unless bandwidth is unrealistically improved. This dissertation presents the concept of Broadcast-Oriented Wireless Network-on-Chip (BoWNoC), a new approach that attempts to foster the inherent simplicity, flexibility, and broadcast capabilities of the wireless technology by integrating one on-chip antenna and transceiver per processor core. This paradigm is part of a broader hybrid vision where the BoWNoC serves latency-critical and broadcast traffic, tightly coupled to a wired plane oriented to large flows of data. By virtue of its scalable broadcast support, BoWNoC may become the key enabler of a wealth of unconventional hardware architectures and algorithmic approaches, eventually leading to a significant improvement of the performance, energy efficiency, scalability and programmability of manycore chips. The present work aims not only to lay the fundamentals of the BoWNoC paradigm, but also to demonstrate its viability from the electronic implementation, network design, and multiprocessor architecture perspectives. An exploration at the physical level of design validates the feasibility of the approach at millimeter-wave bands in the short term, and then suggests the use of graphene-based antennas in the terahertz band in the long term. At the link level, this thesis provides an insightful context analysis that is used, afterwards, to drive the design of a lightweight protocol that reliably serves broadcast traffic with substantial latency improvements over state-of-the-art NoCs. At the network level, our hybrid vision is evaluated putting emphasis on the flexibility provided at the network interface level, showing outstanding speedups for a wide set of traffic patterns. At the architecture level, the potential impact of the BoWNoC paradigm on the design of manycore chips is not only qualitatively discussed in general, but also quantitatively assessed in a particular architecture for fast synchronization. Results demonstrate that the impact of BoWNoC can go beyond simply improving the network performance, thereby representing a possible game changer in the manycore era.Avenços en el disseny de multiprocessadors han portat a una àmplia adopció dels Chip Multiprocessors (CMPs), que basen el seu potencial en la operació coordinada de múltiples nuclis de procés. Generacions successives han anat integrant més nuclis en la recerca d'alt rendiment amb un cost raonable. Per a que aquesta tendència continuï, però, cal resoldre importants problemes d'escalabilitat a diferents capes de disseny. Escalar la xarxa d'interconnexió és un gran repte en ell mateix, ja que les noves propostes de Networks-on-Chip (NoC) han de servir un tràfic eminentment variable i heterogeni dels processadors amb molts nuclis. Són necessàries solucions ràpides i flexibles per evitar que les comunicacions dins del xip es converteixin en el pròxim coll d'ampolla de rendiment, situació que limitaria en gran mesura l'espai de disseny a nivell d'arquitectura i portaria a l'ús d'arquitectures i models de programació lents, ineficients o poc programables. L'aparició de noves tecnologies d'interconnexió ha possibilitat la creació de NoCs més flexibles i escalables. En particular, la comunicació intra-xip sense fils ha despertat un interès considerable en virtut de les seva baixa latència, simplicitat, i bon rendiment amb tràfic broadcast. La majoria de les Wireless NoC (WNoC) proposades fins ara s'han centrat en aprofitar l'avantatge en termes de latència d'aquest nou paradigma creant múltiples canals sense fils per interconnectar nuclis allunyats entre sí. Aquesta estratègia és efectiva per complementar a NoCs clàssiques en escales mitjanes, però és probable que altres tecnologies com la nanofotònica puguin jugar millor aquest paper a escales més grans. Aquesta tesi presenta el concepte de Broadcast-Oriented WNoC (BoWNoC), un nou enfoc que intenta rendibilitzar al màxim la inherent simplicitat, flexibilitat, i capacitats broadcast de la tecnologia sense fils integrant una antena i transmissor/receptor per cada nucli del processador. Aquest paradigma forma part d'una visió més àmplia on un BoWNoC serviria tràfic broadcast i urgent, mentre que una xarxa convencional serviria fluxos de dades més pesats. En virtut de la escalabilitat i del seu suport broadcast, BoWNoC podria convertir-se en un element clau en una gran varietat d'arquitectures i algoritmes poc convencionals que milloressin considerablement el rendiment, l'eficiència, l'escalabilitat i la programabilitat de processadors amb molts nuclis. El present treball té com a objectius no només estudiar els aspectes fonamentals del paradigma BoWNoC, sinó també demostrar la seva viabilitat des dels punts de vista de la implementació, i del disseny de xarxa i arquitectura. Una exploració a la capa física valida la viabilitat de l'enfoc usant tecnologies longituds d'ona milimètriques en un futur proper, i suggereix l'ús d'antenes de grafè a la banda dels terahertz ja a més llarg termini. A capa d'enllaç, la tesi aporta una anàlisi del context de l'aplicació que és, més tard, utilitzada per al disseny d'un protocol d'accés al medi que permet servir tràfic broadcast a baixa latència i de forma fiable. A capa de xarxa, la nostra visió híbrida és avaluada posant èmfasi en la flexibilitat que aporta el fet de prendre les decisions a nivell de la interfície de xarxa, mostrant grans millores de rendiment per una àmplia selecció de patrons de tràfic. A nivell d'arquitectura, l'impacte que el concepte de BoWNoC pot tenir sobre el disseny de processadors amb molts nuclis no només és debatut de forma qualitativa i genèrica, sinó també avaluat quantitativament per una arquitectura concreta enfocada a la sincronització. Els resultats demostren que l'impacte de BoWNoC pot anar més enllà d'una millora en termes de rendiment de xarxa; representant, possiblement, un canvi radical a l'era dels molts nuclisAward-winningPostprint (published version

Evolutionary Genomics

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Colocation-aware Resource Management for Distributed Parallel Applications in Consolidated Clusters

Department of Computer Science and EngineeringConsolidated clusters, which run various distributed parallel applications such as big data frameworks, machine learning applications, and scienti???c applications to solve complex problems in wide range of fields, are already used commonly. Resource providers allow various applications with different characteristics to execute together to efficiently utilize their resources. There are some important issues about scheduling applications to resources. When applications share the same resources, interference between them affects their performance. The performance of applications can be improved or degraded depending on which resources are used to execute them based on various characteristics of applications and resources. Characteristics and resource requirements of applications can constrain their placement, and these constraints can be extended to constraints between applications. These issues should be considered to manage resource e???ciently and improve the performance of applications. In this thesis, we study how to manage resources e???ciently while scheduling distributed parallel applications in consolidated clusters. First, we present a holistic VM placement technique for distributed parallel applications in heterogeneous virtual cluster, aiming to maximize the e???ciency of the cluster and consequently reduce cost for service providers and users. We analyze the e???ect of heterogeneity of resource, di???erent VM con???gurations, and interference between VMs on the performance of distributed parallel applications and propose a placement technique that uses a machine learning algorithm to estimate the runtime of a distributed parallel application. Second, we present a two-level scheduling algorithms, which distribute applications to platforms then map tasks to each node. we analyze the platform and co-runner a???nities of looselycoupled applications and use them for scheduling decision. Third, we study constraint-aware VM placement in heterogeneous clusters. We present a modelofVMplacementconstraintsandconstraint-awareVMplacementalgorithms. Weanalyze the e???ect of VM placement constraint, and evaluate the performance of algorithms over various settings with simulation and experiments in a small cluster. Finally, we propose interference-awareresource management system for CNN models in GPU cluster. We analyze the e???ect of interference between CNN models. We then propose techniques to mitigate slowdown from interference for target model, and to predict performance of CNN models when they are co-located. We propose heuristic algorithm to schedule CNN models, and evaluate the techniques and algorithm from experiments in GPU cluster.clos