Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges.

The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data. This in turn requires massive computational resources. Therefore, high performance computing (HPC) platforms are highly needed as well as efficient and scalable algorithms that can take advantage of these platforms. In this paper, we survey the state-of-the-art HPC platforms for big biological data analytics. We first list the characteristics of big biological data and popular computing platforms. Then we provide a taxonomy of different biological data analysis applications and a survey of the way they have been mapped onto various computing platforms. After that, we present a case study to compare the efficiency of different computing platforms for handling the classical biological sequence alignment problem. At last we discuss the open issues in big biological data analytics

Accelerating HMMER on FPGA using Parallel Prefixes and Reductions

HMMER is a widely used tool in bioinformatics, based on Profile Hidden Markov Models. The computation kernels of HMMER i.e. MSV and P7Viterbi are very compute intensive and data dependencies restrict to sequential execution. In this paper, we propose an original parallelization scheme for HMMER by rewriting their mathematical formulation, to expose the hidden potential parallelization opportunities. Our parallelization scheme targets FPGA technology, and our architecture can achieve 10 times speedup compared with that of latest HMMER3 SSE version, while not compromising on sensitivity of original algorithm.HMMER est un outil basé sur la notion profils à base modèles de Markov cachés, qui est très largement utilisé en bio-informatique. Les parties critiques de l'algorithme (fonctions MSV et P7Viterbi) utilisées dans HMMER sont très consommatrices en temps de calcul et réputées très difficiles à paralléliser. Dans cet article, nous proposons un schéma de parallélisation original pour HMMER, basé sur une reformulation mathématique de l'algorithme qui permet de découvrir de nouvelles possibilités de parallélisation bien adaptées à des implantations matérielles dédiées. Nous avons implanté cette approche sur un accélérateur FPGA et avons mesuré des gains en performance supérieurs à 10 par rapport à l'implémentation logicielle de HMMER3, laquelle exploite pourtant déjà de manière extrêmement efficace les extensions SIMD des processeurs x8

High performance reconfigurable architectures for biological sequence alignment

Bioinformatics and computational biology (BCB) is a rapidly developing multidisciplinary field which encompasses a wide range of domains, including genomic sequence alignments. It is a fundamental tool in molecular biology in searching for homology between sequences. Sequence alignments are currently gaining close attention due to their great impact on the quality aspects of life such as facilitating early disease diagnosis, identifying the characteristics of a newly discovered sequence, and drug engineering. With the vast growth of genomic data, searching for a sequence homology over huge databases (often measured in gigabytes) is unable to produce results within a realistic time, hence the need for acceleration. Since the exponential increase of biological databases as a result of the human genome project (HGP), supercomputers and other parallel architectures such as the special purpose Very Large Scale Integration (VLSI) chip, Graphic Processing Unit (GPUs) and Field Programmable Gate Arrays (FPGAs) have become popular acceleration platforms. Nevertheless, there are always trade-off between area, speed, power, cost, development time and reusability when selecting an acceleration platform. FPGAs generally offer more flexibility, higher performance and lower overheads. However, they suffer from a relatively low level programming model as compared with off-the-shelf microprocessors such as standard microprocessors and GPUs. Due to the aforementioned limitations, the need has arisen for optimized FPGA core implementations which are crucial for this technology to become viable in high performance computing (HPC). This research proposes the use of state-of-the-art reprogrammable system-on-chip technology on FPGAs to accelerate three widely-used sequence alignment algorithms; the Smith-Waterman with affine gap penalty algorithm, the profile hidden Markov model (HMM) algorithm and the Basic Local Alignment Search Tool (BLAST) algorithm. The three novel aspects of this research are firstly that the algorithms are designed and implemented in hardware, with each core achieving the highest performance compared to the state-of-the-art. Secondly, an efficient scheduling strategy based on the double buffering technique is adopted into the hardware architectures. Here, when the alignment matrix computation task is overlapped with the PE configuration in a folded systolic array, the overall throughput of the core is significantly increased. This is due to the bound PE configuration time and the parallel PE configuration approach irrespective of the number of PEs in a systolic array. In addition, the use of only two configuration elements in the PE optimizes hardware resources and enables the scalability of PE systolic arrays without relying on restricted onboard memory resources. Finally, a new performance metric is devised, which facilitates the effective comparison of design performance between different FPGA devices and families. The normalized performance indicator (speed-up per area per process technology) takes out advantages of the area and lithography technology of any FPGA resulting in fairer comparisons. The cores have been designed using Verilog HDL and prototyped on the Alpha Data ADM-XRC-5LX card with the Virtex-5 XC5VLX110-3FF1153 FPGA. The implementation results show that the proposed architectures achieved giga cell updates per second (GCUPS) performances of 26.8, 29.5 and 24.2 respectively for the acceleration of the Smith-Waterman with affine gap penalty algorithm, the profile HMM algorithm and the BLAST algorithm. In terms of speed-up improvements, comparisons were made on performance of the designed cores against their corresponding software and the reported FPGA implementations. In the case of comparison with equivalent software execution, acceleration of the optimal alignment algorithm in hardware yielded an average speed-up of 269x as compared to the SSEARCH 35 software. For the profile HMM-based sequence alignment, the designed core achieved speed-up of 103x and 8.3x against the HMMER 2.0 and the latest version of HMMER (version 3.0) respectively. On the other hand, the implementation of the gapped BLAST with the two-hit method in hardware achieved a greater than tenfold speed-up compared to the latest NCBI BLAST software. In terms of comparison against other reported FPGA implementations, the proposed normalized performance indicator was used to evaluate the designed architectures fairly. The results showed that the first architecture achieved more than 50 percent improvement, while acceleration of the profile HMM sequence alignment in hardware gained a normalized speed-up of 1.34. In the case of the gapped BLAST with the two-hit method, the designed core achieved 11x speed-up after taking out advantages of the Virtex-5 FPGA. In addition, further analysis was conducted in terms of cost and power performances; it was noted that, the core achieved 0.46 MCUPS per dollar spent and 958.1 MCUPS per watt. This shows that FPGAs can be an attractive platform for high performance computation with advantages of smaller area footprint as well as represent economic ‘green’ solution compared to the other acceleration platforms. Higher throughput can be achieved by redeploying the cores on newer, bigger and faster FPGAs with minimal design effort

Extreme Scale De Novo Metagenome Assembly

Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art tools require big shared memory machines and cannot handle contemporary metagenome datasets that exceed Terabytes in size. In this paper, we introduce the MetaHipMer pipeline, a high-quality and high-performance metagenome assembler that employs an iterative de Bruijn graph approach. MetaHipMer leverages a specialized scaffolding algorithm that produces long scaffolds and accommodates the idiosyncrasies of metagenomes. MetaHipMer is end-to-end parallelized using the Unified Parallel C language and therefore can run seamlessly on shared and distributed-memory systems. Experimental results show that MetaHipMer matches or outperforms the state-of-the-art tools in terms of accuracy. Moreover, MetaHipMer scales efficiently to large concurrencies and is able to assemble previously intractable grand challenge metagenomes. We demonstrate the unprecedented capability of MetaHipMer by computing the first full assembly of the Twitchell Wetlands dataset, consisting of 7.5 billion reads - size 2.6 TBytes.Comment: Accepted to SC1

Fault- and Yield-Aware On-Chip Memory Design and Management

Ever decreasing device size causes more frequent hard faults, which becomes a serious burden to processor design and yield management. This problem is particularly pronounced in the on-chip memory which consumes up to 70% of a processor' s total chip area. Traditional circuit-level techniques, such as redundancy and error correction code, become less effective in error-prevalent environments because of their large area overhead. In this work, we suggest an architectural solution to building reliable on-chip memory in the future processor environment. Our approaches have two parts, a design framework and architectural techniques for on-chip memory structures. Our design framework provides important architectural evaluation metrics such as yield, area, and performance based on low level defects and process variations parameters. Processor architects can quickly evaluate their designs' characteristics in terms of yield, area, and performance. With the framework, we develop architectural yield enhancement solutions for on-chip memory structures including L1 cache, L2 cache and directory memory. Our proposed solutions greatly improve yield with negligible area and performance overhead. Furthermore, we develop a decoupled yield model of compute cores and L2 caches in CMPs, which show that there will be many more L2 caches than compute cores in a chip. We propose efficient utilization techniques for excess caches. Evaluation results show that excess caches significantly improve overall performance of CMPs

Adaptive Prefetching and Cache Partitioning for Multicore Processors

El acceso a la memoria principal en los procesadores actuales supone un importante cuello de botella para las prestaciones, dado que los diferentes núcleos compiten por el limitado ancho de banda de memoria, agravando la brecha entre las prestaciones del procesador y las de la memoria principal. Distintas técnicas atacan este problema, siendo las más relevantes el uso de jerarquías de caché multinivel y la prebúsqueda. Las cachés jerárquicas aprovechan la localidad temporal y espacial que en general presentan los programas en el acceso a los datos, para mitigar las enormes latencias de acceso a memoria principal. Para limitar el número de accesos a la memoria DRAM, fuera del chip, los procesadores actuales cuentan con grandes cachés de último nivel (LLC). Para mejorar su utilización y reducir costes, estas cachés suelen compartirse entre todos los núcleos del procesador. Este enfoque mejora significativamente el rendimiento de la mayoría de las aplicaciones en comparación con el uso de cachés privados más pequeños. Compartir la caché, sin embargo, presenta una problema importante: la interferencia entre aplicaciones. La prebúsqueda, por otro lado, trae bloques de datos a las cachés antes de que el procesador los solicite, ocultando la latencia de memoria principal. Desafortunadamente, dado que la prebúsqueda es una técnica especulativa, si no tiene éxito puede contaminar la caché con bloques que no se usarán. Además, las prebúsquedas interfieren con los accesos a memoria normales, tanto los del núcleo que emite las prebúsquedas como los de los demás. Esta tesis se centra en reducir la interferencia entre aplicaciones, tanto en las caché compartidas como en el acceso a la memoria principal. Para reducir la interferencia entre aplicaciones en el acceso a la memoria principal, el mecanismo propuesto en esta disertación regula la agresividad de cada prebuscador, activando o desactivando selectivamente algunos de ellos, dependiendo de su rendimiento individual y de los requisitos de ancho de banda de memoria principal de los otros núcleos. Con respecto a la interferencia en cachés compartidos, esta tesis propone dos técnicas de particionado para la LLC, las cuales otorgan más espacio de caché a las aplicaciones que progresan más lentamente debido a la interferencia entre aplicaciones. La primera propuesta de particionado de caché requiere hardware específico no disponible en procesadores comerciales, por lo que se ha evaluado utilizando un entorno de simulación. La segunda propuesta de particionado de caché presenta una familia de políticas que superan las limitaciones en el número de particiones y en el número de vías de caché disponibles mediante la agrupación de aplicaciones en clústeres y la superposición de particiones de caché, por lo que varias aplicaciones comparten las mismas vías. Dado que se ha implementado utilizando los mecanismos para el particionado de la LLC que presentan algunos procesadores Intel modernos, esta propuesta ha sido evaluada en una máquina real. Los resultados experimentales muestran que el mecanismo de prebúsqueda selectiva propuesto en esta tesis reduce el número de solicitudes de memoria principal en un 20%, cosa que se traduce en mejoras en la equidad del sistema, el rendimiento y el consumo de energía. Por otro lado, con respecto a los esquemas de partición propuestos, en comparación con un sistema sin particiones, ambas propuestas reducen la iniquidad del sistema en un promedio de más del 25%, independientemente de la cantidad de aplicaciones en ejecución, y esta reducción en la injusticia no afecta negativamente al rendimiento.Accessing main memory represents a major performance bottleneck in current processors, since the different cores compete among them for the limited offchip bandwidth, aggravating even more the so called memory wall. Several techniques have been applied to deal with the core-memory performance gap, with the most preeminent ones being prefetching and hierarchical caching. Hierarchical caches leverage the temporal and spacial locality of the accessed data, mitigating the huge main memory access latencies. To limit the number of accesses to the off-chip DRAM memory, current processors feature large Last Level Caches. These caches are shared between all the cores to improve the utilization of the cache space and reduce cost. This approach significantly improves the performance of most applications compared to using smaller private caches. Cache sharing, however, presents an important shortcoming: the interference between applications. Prefetching, on the other hand, brings data blocks to the caches before they are requested, hiding the main memory latency. Unfortunately, since prefetching is a speculative technique, inaccurate prefetches may pollute the cache with blocks that will not be used. In addition, the prefetches interfere with the regular memory requests, both the ones from the application running on the core that issued the prefetches and the others. This thesis focuses on reducing the inter-application interference, both in the shared cache and in the access to the main memory. To reduce the interapplication interference in the access to main memory, the proposed approach regulates the aggressiveness of each core prefetcher, and selectively activates or deactivates some of them, depending on their individual performance and the main memory bandwidth requirements of the other cores. With respect to interference in shared caches, this thesis proposes two LLC partitioning techniques that give more cache space to the applications that have their progress diminished due inter-application interferences. The first cache partitioning proposal requires dedicated hardware not available in commercial processors, so it has been evaluated using a simulation framework. The second proposal dealing with cache partitioning presents a family of partitioning policies that overcome the limitations in the number of partitions and the number of available ways by grouping applications and overlapping cache partitions, so multiple applications share the same ways. Since it has been implemented using the cache partitioning features of modern Intel processors it has been evaluated in a real machine. Experimental results show that the proposed selective prefetching mechanism reduces the number of main memory requests by 20%, which translates to improvements in unfairness, performance, and energy consumption. On the other hand, regarding the proposed partitioning schemes, compared to a system with no partitioning, both reduce unfairness more than 25% on average, regardless of the number of applications running in the multicore, and this reduction in unfairness does not negatively affect the performance.L'accés a la memòria principal en els processadors actuals suposa un important coll d'ampolla per a les prestacions, ja que els diferents nuclis competeixen pel limitat ample de banda de memòria, agreujant la bretxa entre les prestacions del processador i les de la memòria principal. Diferents tècniques ataquen aquest problema, sent les més rellevants l'ús de jerarquies de memòria cau multinivell i la prebusca. Les memòries cau jeràrquiques aprofiten la localitat temporal i espacial que en general presenten els programes en l'accés a les dades per mitigar les enormes latències d'accés a memòria principal. Per limitar el nombre d'accessos a la memòria DRAM, fora del xip, els processadors actuals compten amb grans caus d'últim nivell (LLC). Per millorar la seva utilització i reduir costos, aquestes memòries cau solen compartir-se entre tots els nuclis del processador. Aquest enfocament millora significativament el rendiment de la majoria de les aplicacions en comparació amb l'ús de caus privades més menudes. Compartir la memòria cau, no obstant, presenta una problema important: la interferencia entre aplicacions. La prebusca, per altra banda, porta blocs de dades a les memòries cau abans que el processador els sol·licite, ocultant la latència de memòria principal. Desafortunadament, donat que la prebusca és una técnica especulativa, si no té èxit pot contaminar la memòria cau amb blocs que no fan falta. A més, les prebusques interfereixen amb els accessos normals a memòria, tant els del nucli que emet les prebusques com els dels altres. Aquesta tesi es centra en reduir la interferència entre aplicacions, tant en les cau compartides com en l'accés a la memòria principal. Per reduir la interferència entre aplicacions en l'accés a la memòria principal, el mecanismo proposat en aquesta dissertació regula l'agressivitat de cada prebuscador, activant o desactivant selectivament alguns d'ells, en funció del seu rendiment individual i dels requisits d'ample de banda de memòria principal dels altres nuclis. Pel que fa a la interferència en caus compartides, aquesta tesi proposa dues tècniques de particionat per a la LLC, les quals atorguen més espai de memòria cau a les aplicacions que progressen més lentament a causa de la interferència entre aplicacions. La primera proposta per al particionat de memòria cau requereix hardware específic no disponible en processadors comercials, per la qual cosa s'ha avaluat utilitzant un entorn de simulació. La segona proposta de particionat per a memòries cau presenta una família de polítiques que superen les limitacions en el nombre de particions i en el nombre de vies de memòria cau disponibles mitjan¿ cant l'agrupació d'aplicacions en clústers i la superposició de particions de memòria cau, de manera que diverses aplicacions comparteixen les mateixes vies. Atès que s'ha implementat utilitzant els mecanismes per al particionat de la LLC que ofereixen alguns processadors Intel moderns, aquesta proposta s'ha avaluat en una màquina real. Els resultats experimentals mostren que el mecanisme de prebusca selectiva proposat en aquesta tesi redueix el nombre de sol·licituds a la memòria principal en un 20%, cosa que es tradueix en millores en l'equitat del sistema, el rendiment i el consum d'energia. Per altra banda, pel que fa als esquemes de particiónat proposats, en comparació amb un sistema sense particions, ambdues propostes redueixen la iniquitat del sistema en més d'un 25% de mitjana, independentment de la quantitat d'aplicacions en execució, i aquesta reducció en la iniquitat no afecta negativament el rendiment.Selfa Oliver, V. (2018). Adaptive Prefetching and Cache Partitioning for Multicore Processors [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/112423TESI

Dynamic Processor Reconfiguration for Power, Performance and Reliability Management

Technology advancements allowed more transistors to be packed in a smaller area, while the improved performance helped in achieving higher clock frequencies. This, unfortunately led to a power density problem, forcing processor industry to lower the clock frequency and integrate multiple cores on the same die. Depending on core characteristics, the multiple cores in the die could be symmetric or asymmetric. Asymmetric multi-core processors (AMPs) have been proposed as an alternative to symmetric multi-cores to improve power efficiency. AMPs comprise of cores that implement the same ISA, but differ in performance and power characteristics due to varying sizes of micro-architectural resources. As the computational bottleneck of a workload shifts from one resource to another during its course of execution, reassigning it to another core (where it runs more efficiently), can improve the overall power efficiency. Thus achieving high power efficiency in AMPs requires (i) a diverse set of cores that are optimized for various program phases, (ii) runtime analysis to determine the best core to run on, and (iii) low overhead of re-assigning a thread to a different core type. Decisions to swap threads between AMPs are made at coarse grain granularity of millions of instructions, to mitigate the impact of thread migration overhead. But the computational needs of the program rapidly change during the course of its execution. The best core configuration for an application such that, both power consumption and performance are optimized, changes over time rapidly at fine granularity of thousands of instructions. This dissertation explores ways to design core micro-architecture such that high power efficiency could be achieved, if switching overhead could be lowered, enabling fine grain switching. To take advantage of power saving opportunities at fine grain granularity, this thesis explores reconfigurable/morphable architectures where core resources are reconfigured on demand to suit the needs of the executing application. At first, we explore reconfigurable architectures consisting of two kinds of cores: out-of-order (OOO) big cores and in-order (InO) small cores. The big cores provide higher performance while the small cores are more power efficient. In this proposed architecture, OOO core reconfigures into InO core at run time. Our proposed online management scheme decides to switch between these core types such that we obtain significant power benefits without impacting performance. We also observe that, resource requirements of applications can be quite diverse and consequently, resource bottlenecks or excesses can vary considerably. Thus, reconfiguration between just two core modes may not fully exploit power and performance improvement opportunities. We therefore, explore reconfigurable architectures consisting of diverse core types that not limited to big and little cores. A single core can reconfigure into multiple core modes where each mode has unique power and performance characteristics. Workload performance on a particular core mode depends on a large set of processor resources. Some workloads are highly memory intensive, some exhibit large instruction dependency, some experience high rates of branch mis-prediction, while other workloads exhibit large exploitable instruction level parallelism. A diverse set of core modes is needed, that could address shifting resource needs during various program phases of an application. Different trade-offs in power and performance could be achieved by reducing or expanding the size of various resource. Trade-offs for each core mode are also affected by operating voltage and frequency. We therefore, propose joint core resource resizing with dynamic voltage and frequency scaling (DVFS), which is important for applications whose performance is sensitive to changes in frequency. Thus, at fine granularity, the core should adapt to varying instruction window sizes, execution bandwidth and frequency to meet the demands of the workload at run-time to improve power efficiency. Many current processors employ DVFS aggressively to improve power efficiency and maximize performance. This dissertation studies the tradeoff in power efficiency in using fine grain DVFS and reconfigurable architectures mentioned above.We also explore another important problem due to continued scaling of devices which results in higher vulnerability to soft-errors. We consider dynamic core reconfiguration from the perspectives of both power efficiency and vulnerability to soft-errors. An online management scheme is proposed such that core reconfiguration upon a thread switch not only improves power efficiency but also does not increase the vulnerability to soft errors. In summary, we propose in this thesis several solutions for improving power efficiency by integrating heterogeneity within the core. We also address how popular power reduction techniques like DVFS are comparable to our approach. Finally, we address reliability challenges along with improving power efficiency