FPGA acceleration of sequence analysis tools in bioinformatics

Thesis (Ph.D.)--Boston UniversityWith advances in biotechnology and computing power, biological data are being produced at an exceptional rate. The purpose of this study is to analyze the application of FPGAs to accelerate high impact production biosequence analysis tools. Compared with other alternatives, FPGAs offer huge compute power, lower power consumption, and reasonable flexibility. BLAST has become the de facto standard in bioinformatic approximate string matching and so its acceleration is of fundamental importance. It is a complex highly-optimized system, consisting of tens of thousands of lines of code and a large number of heuristics. Our idea is to emulate the main phases of its algorithm on FPGA. Utilizing our FPGA engine, we quickly reduce the size of the database to a small fraction, and then use the original code to process the query. Using a standard FPGA-based system, we achieved 12x speedup over a highly optimized multithread reference code. Multiple Sequence Alignment (MSA)--the extension of pairwise Sequence Alignment to multiple Sequences--is critical to solve many biological problems. Previous attempts to accelerate Clustal-W, the most commonly used MSA code, have directly mapped a portion of the code to the FPGA. We use a new approach: we apply prefiltering of the kind commonly used in BLAST to perform the initial all-pairs alignments. This results in a speedup of from 8Ox to 190x over the CPU code (8 cores). The quality is comparable to the original according to a commonly used benchmark suite evaluated with respect to multiple distance metrics. The challenge in FPGA-based acceleration is finding a suitable application mapping. Unfortunately many software heuristics do not fall into this category and so other methods must be applied. One is restructuring: an entirely new algorithm is applied. Another is to analyze application utilization and develop accuracy/performance tradeoffs. Using our prefiltering approach and novel FPGA programming models we have achieved significant speedup over reference programs. We have applied approximation, seeding, and filtering to this end. The bulk of this study is to introduce the pros and cons of these acceleration models for biosequence analysis tools

FPGA acceleration of DNA sequence alignment: design analysis and optimization

Existing FPGA accelerators for short read mapping often fail to utilize the complete biological information in sequencing data for simple hardware design, leading to missed or incorrect alignment. In this work, we propose a runtime reconfigurable alignment pipeline that considers all information in sequencing data for the biologically accurate acceleration of short read mapping. We focus our efforts on accelerating two string matching techniques: FM-index and the Smith-Waterman algorithm with the affine-gap model which are commonly used in short read mapping. We further optimize the FPGA hardware using a design analyzer and merger to improve alignment performance. The contributions of this work are as follows. 1. We accelerate the exact-match and mismatch alignment by leveraging the FM-index technique. We optimize memory access by compressing the data structure and interleaving the access with multiple short reads. The FM-index hardware also considers complete information in the read data to maximize accuracy. 2. We propose a seed-and-extend model to accelerate alignment with indels. The FM-index hardware is extended to support the seeding stage while a Smith-Waterman implementation with the affine-gap model is developed on FPGA for the extension stage. This model can improve the efficiency of indel alignment with comparable accuracy versus state-of-the-art software. 3. We present an approach for merging multiple FPGA designs into a single hardware design, so that multiple place-and-route tasks can be replaced by a single task to speed up functional evaluation of designs. We first experiment with this approach to demonstrate its feasibility for different designs. Then we apply this approach to optimize one of the proposed FPGA aligners for better alignment performance.Open Acces

Mapping applications onto FPGA-centric clusters

High Performance Computing (HPC) is becoming increasingly important throughout science and engineering as ever more complex problems must be solved through computational simulations. In these large computational applications, the latency of communication between processing nodes is often the key factor that limits performance. An emerging alternative computer architecture that addresses the latency problem is the FPGA-centric cluster (FCC); in these systems, the devices (FPGAs) are directly interconnected and thus many layers of hardware and software are avoided. The result can be scalability not currently achievable with other technologies. In FCCs, FPGAs serve multiple functions: accelerator, network interface card (NIC), and router. Moreover, because FPGAs are configurable, there is substantial opportunity to tailor the router hardware to the application; previous work has demonstrated that such application-aware configuration can effect a substantial improvement in hardware efficiency. One constraint of FCCs is that it is convenient for their interconnect to be static, direct, and have a two or three dimensional mesh topology. Thus, applications that are naturally of a different dimensionality (have a different logical topology) from that of the FCC must be remapped to obtain optimal performance. In this thesis we study various aspects of the mapping problem for FCCs. There are two major research thrusts. The first is finding the optimal mapping of logical to physical topology. This problem has received substantial attention by both the theory community, where topology mapping is referred to as graph embedding, and by the High Performance Computing (HPC) community, where it is a question of process placement. We explore the implications of the different mapping strategies on communication behavior in FCCs, especially on resulting load imbalance. The second major research thrust is built around the hypothesis that applications that need to be remapped (due to differing logical and physical topologies) will have different optimal router configurations from those applications that do not. For example, due to remapping, some virtual or physical communication links may have little occupancy; therefore fewer resources should be allocated to them. Critical here is the creation of a new set of parameterized hardware features that can be configured to best handle load imbalances caused by remapping. These two thrusts form a codesign loop: certain mapping algorithms may be differentially optimal due to application-aware router reconfiguration that accounts for this mapping. This thesis has four parts. The first part introduces the background and previous work related to communication in general and, in particular, how it is implemented in FCCs. We build on previous work on application-aware router configuration. The second part introduces topology mapping mechanisms including those derived from graph embeddings and a greedy algorithm commonly used in HPC. In the third part, topology mappings are evaluated for performance and imbalance; we note that different mapping strategies lead to different imbalances both in the overall network and in each node. The final part introduces reconfigure router design that allocates resources based on different imbalance situations caused by different mapping behaviors

Towards hardware as a reconfigurable, elastic, and specialized service

As modern Data Center workloads become increasingly complex, constrained, and critical, mainstream CPU-centric computing has had ever more difficulty in keeping pace. Future data centers are moving towards a more fluid and heterogeneous model, with computation and communication no longer localized to commodity CPUs and routers. Next generation data-centric Data Centers will compute everywhere, whether data is stationary (e.g. in memory) or on the move (e.g. in network). While deploying FPGAs in NICS, as co-processors, in the router, and in Bump-in-the-Wire configurations is a step towards implementing the data-centric model, it is only part of the overall solution. The other part is actually leveraging this reconfigurable hardware. For this to happen, two problems must be addressed: code generation and deployment generation. By code generation we mean transforming abstract representations of an algorithm into equivalent hardware. Deployment generation refers to the runtime support needed to facilitate the execution of this hardware on an FPGA. Efforts at creating supporting tools in these two areas have thus far provided limited benefits. This is because the efforts are limited in one or more of the following ways: They i) do not provide fundamental solutions to a number of challenges, which makes them useful only to a limited group of (mostly) hardware developers, ii) are constrained in their scope, or iii) are ad hoc, i.e., specific to a single usage context, FPGA vendor, or Data Center configuration. Moreover, efforts in these areas have largely been mutually exclusive, which results in incompatibility across development layers; this requires wrappers to be designed to make interfaces compatible. As a result there is significant complexity and effort required to code and deploy efficient custom hardware for FPGAs; effort that may be orders-of-magnitude greater than for analogous software environments. The goal of this dissertation is to create a framework that enables reconfigurable logic in Data Centers to be targeted with the same level of effort as for a single CPU core. The underlying mechanism to this is a framework, which we refer to as Hardware as a Reconfigurable, Elastic and Specialized Service, or HaaRNESS. In this dissertation, we address two of the core challenges of HaaRNESS: reducing the complexity of code generation by constraining High Level Synthesis (HLS) toolflows, and replacing ad hoc models of deployment generation by generalizing and formalizing what is needed for a hardware Operating System. These parts are unified by the back-end of HLS toolflows which link generated compute pipelines with the operating system, and provide appropriate APIs, wrappers, and software runtimes. The contributions of this dissertation are the following: i) an empirically guided set of systematic transformations for generating high quality HLS code; ii) a framework for instrumenting HLS compiler to identify and remove optimization blockers; iii) a framework for RTL simulation and IP generation of HLS kernels for rapid turnaround; and iv) a framework for generalization and formalization of hardware operating systems to address the {\it ad hoc}'ness of existing deployment generation and ensure uniform structure and APIs