4 research outputs found
High performance bioinformatics and computational biology on general-purpose graphics processing units
Bioinformatics and Computational Biology (BCB) is a relatively new
multidisciplinary field which brings together many aspects of the fields of
biology, computer science, statistics, and engineering. Bioinformatics extracts
useful information from biological data and makes these more intuitive and
understandable by applying principles of information sciences, while
computational biology harnesses computational approaches and technologies
to answer biological questions conveniently. Recent years have seen an
explosion of the size of biological data at a rate which outpaces the rate of
increases in the computational power of mainstream computer technologies,
namely general purpose processors (GPPs). The aim of this thesis is to explore
the use of off-the-shelf Graphics Processing Unit (GPU) technology in the high
performance and efficient implementation of BCB applications in order to meet
the demands of biological data increases at affordable cost.
The thesis presents detailed design and implementations of GPU solutions for
a number of BCB algorithms in two widely used BCB applications, namely
biological sequence alignment and phylogenetic analysis. Biological sequence
alignment can be used to determine the potential information about a newly
discovered biological sequence from other well-known sequences through
similarity comparison. On the other hand, phylogenetic analysis is concerned
with the investigation of the evolution and relationships among organisms,
and has many uses in the fields of system biology and comparative genomics.
In molecular-based phylogenetic analysis, the relationship between species is
estimated by inferring the common history of their genes and then
phylogenetic trees are constructed to illustrate evolutionary relationships
among genes and organisms. However, both biological sequence alignment
and phylogenetic analysis are computationally expensive applications as their computing and memory requirements grow polynomially or even worse with
the size of sequence databases.
The thesis firstly presents a multi-threaded parallel design of the Smith-
Waterman (SW) algorithm alongside an implementation on NVIDIA GPUs. A
novel technique is put forward to solve the restriction on the length of the
query sequence in previous GPU-based implementations of the SW algorithm.
Based on this implementation, the difference between two main task
parallelization approaches (Inter-task and Intra-task parallelization) is
presented. The resulting GPU implementation matches the speed of existing
GPU implementations while providing more flexibility, i.e. flexible length of
sequences in real world applications. It also outperforms an equivalent GPPbased
implementation by 15x-20x. After this, the thesis presents the first
reported multi-threaded design and GPU implementation of the Gapped
BLAST with Two-Hit method algorithm, which is widely used for aligning
biological sequences heuristically. This achieved up to 3x speed-up
improvements compared to the most optimised GPP implementations.
The thesis then presents a multi-threaded design and GPU implementation of
a Neighbor-Joining (NJ)-based method for phylogenetic tree construction and
multiple sequence alignment (MSA). This achieves 8x-20x speed up compared
to an equivalent GPP implementation based on the widely used ClustalW
software. The NJ method however only gives one possible tree which strongly
depends on the evolutionary model used. A more advanced method uses
maximum likelihood (ML) for scoring phylogenies with Markov Chain Monte
Carlo (MCMC)-based Bayesian inference. The latter was the subject of another
multi-threaded design and GPU implementation presented in this thesis,
which achieved 4x-8x speed up compared to an equivalent GPP
implementation based on the widely used MrBayes software.
Finally, the thesis presents a general evaluation of the designs and
implementations achieved in this work as a step towards the evaluation of
GPU technology in BCB computing, in the context of other computer technologies including GPPs and Field Programmable Gate Arrays (FPGA)
technology
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
Contributions to the efficient use of general purpose coprocessors: kernel density estimation as case study
142 p.The high performance computing landscape is shifting from assemblies of homogeneous nodes towards heterogeneous systems, in which nodes consist of a combination of traditional out-of-order execution cores and accelerator devices. Accelerators provide greater theoretical performance compared to traditional multi-core CPUs, but exploiting their computing power remains as a challenging task.This dissertation discusses the issues that arise when trying to efficiently use general purpose accelerators. As a contribution to aid in this task, we present a thorough survey of performance modeling techniques and tools for general purpose coprocessors. Then we use as case study the statistical technique Kernel Density Estimation (KDE). KDE is a memory bound application that poses several challenges for its adaptation to the accelerator-based model. We present a novel algorithm for the computation of KDE that reduces considerably its computational complexity, called S-KDE. Furthermore, we have carried out two parallel implementations of S-KDE, one for multi and many-core processors, and another one for accelerators. The latter has been implemented in OpenCL in order to make it portable across a wide range of devices. We have evaluated the performance of each implementation of S-KDE in a variety of architectures, trying to highlight the bottlenecks and the limits that the code reaches in each device. Finally, we present an application of our S-KDE algorithm in the field of climatology: a novel methodology for the evaluation of environmental models