Protein alignment HW/SW optimizations

Biosequence alignment recently received an amazing support from both commodity and dedicated hardware platforms. The limitless requirements of this application motivate the search for improved implementations to boost processing time and capabilities. We propose an unprecedented hardware improvement to the classic Smith-Waterman (S-W) algorithm based on a twofold approach: i) an on-the-fly gap-open/gap-extension selection that reduces the hardware implementation complexity; ii) a pre-selection filter that uses reduced amino-acid alphabets to screen out not-significant sequences and to shorten the S-Witerations on huge reference databases.We demonstrated the improvements w.r.t. a classic approach both from the point of view of algorithm efficiency and of HW performance (FPGA and ASIC post-synthesis analysis)

On-the-fly memory compression for multibody algorithms.

Memory and bandwidth demands challenge developers of particle-based codes that have to scale on new architectures, as the growth of concurrency outperforms improvements in memory access facilities, as the memory per core tends to stagnate, and as communication networks cannot increase bandwidth arbitrary. We propose to analyse each particle of such a code to find out whether a hierarchical data representation storing data with reduced precision caps the memory demands without exceeding given error bounds. For admissible candidates, we perform this compression and thus reduce the pressure on the memory subsystem, lower the total memory footprint and reduce the data to be exchanged via MPI. Notably, our analysis and transformation changes the data compression dynamically, i.e. the choice of data format follows the solution characteristics, and it does not require us to alter the core simulation code

Planetary impact experimentation

An understanding of impact processes in low- and microgravity environments would be advanced significantly by the construction and use of an impact facility on the Space Station. It is proposed that initial studies begin as soon as possible in ground-based impact laboratories, on the NASA KC-135 Reduced-Gravity Aircraft, and in existing drop towers. The resulting experience and information base could then be applied toward an experiment package designed for use on Shuttle orbiters to support pilot studies in orbital environments. These experiments, as well as the first efforts made on the IOC Space Station, should involve the impact of various free-floating targets; such studies would yield a substantial scientific return while providing valuable experience and engineering information for use in refining the design of the dedicated Space Station Impact Facility. The dedicated facility should be designed to support impact experimentation, including but not limited to cratering, asteroid and ring-particle dynamics, and accretional processes

Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts

Genetic sequence alignment has always been a computational challenge in bioinformatics. Depending on the problem size, software-based aligners can take multiple CPU-days to process the sequence data, creating a bottleneck point in bioinformatic analysis flow. Reconfigurable accelerator can achieve high performance for such computation by providing massive parallelism, but at the expense of programming flexibility and thus has not been commensurately used by practitioners. Therefore, this paper aims to provide a thorough survey of the proposed accelerators by giving a qualitative categorization based on their algorithms and speedup. A comprehensive comparison between work is also presented so as to guide selection for biologist, and to provide insight on future research direction for FPGA scientists

An Energy Feedback System for the MIT/Bates Linear Accelerator

We report the development and implementation of an energy feedback system for the MIT/Bates Linear Accelerator Center. General requirements of the system are described, as are the specific requirements, features, and components of the system unique to its implementation at the Bates Laboratory. We demonstrate that with the system in operation, energy fluctuations correlated with the 60 Hz line voltage and with drifts of thermal origin are reduced by an order of magnitude

Design and Evaluation of a BLAST Ungapped Extension Accelerator, Master\u27s Thesis

The amount of biosequence data being produced each year is growing exponentially. Extracting useful information from this massive amount of data is becoming an increasingly difficult task. This thesis focuses on accelerating the most widely-used software tool for analyzing genomic data, BLAST. This thesis presents Mercury BLAST, a novel method for accelerating searches through massive DNA databases. Mercury BLAST takes a streaming approach to the BLAST computation by offloading the performance-critical sections onto reconfigurable hardware. This hardware is then used in combination with the processor of the host system to deliver BLAST results in a fraction of the time of the general-purpose processor alone. Mercury BLAST makes use of new algorithms combined with reconfigurable hardware to accelerate BLAST-like similarity search. An evaluation of this method for use in real BLAST-like searches is presented along with a characterization of the quality of results associated with using these new algorithms in specialized hardware. The primary focus of this thesis is the design of the ungapped extension stage of Mercury BLAST. The architecture of the ungapped extension stage is described along with the context of this stage within the Mercury BLAST system. The design is compact and performs over 20× faster than that of the standard software ungapped extension, yielding close to 50× speedup over the complete software BLAST application. The quality of Mercury BLAST results is essentially equivalent to the standard BLAST results

Measurement of the proton electric to magnetic form factor ratio from \vec ^1H(\vec e, e'p)

We report the first precision measurement of the proton electric to magnetic form factor ratio from spin-dependent elastic scattering of longitudinally polarized electrons from a polarized hydrogen internal gas target. The measurement was performed at the MIT-Bates South Hall Ring over a range of four-momentum transfer squared $Q^2$ from 0.15 to 0.65 (GeV/c)$^2$. Significantly improved results on the proton electric and magnetic form factors are obtained in combination with previous cross-section data on elastic electron-proton scattering in the same $Q^2$ region.Comment: 4 pages, 2 figures, submitted to PR

Reliability History and Improvements to the ANL 50 MEV H- Accelerator

The H- Accelerator consists of a 750 keV Cockcroft Walton preaccelerator and an Alvarez type 50 MeV linac. The accelerator has been in operation since 1961. Since 1981, it has been used as the injector for the Intense Pulsed Neutron Source (IPNS), a national user facility for neutron scattering. The linac delivers about 3.5x1012 H- ions per pulse, 30 times per second (30 Hz), for multi-turn injection to a 450 MeV Rapid Cycling Synchrotron (RCS). IPNS presently operates about 4,000 hours per year, and operating when scheduled is critical to meeting the needs of the user community. For many years the IPNS injector/RCS has achieved an average reliability of 95%, helped in large part by the preaccelerator/linac which has averaged nearly 99%. To maintain and improve system reliability, records need to show what each subsystem contributes to the total down time. The history of source and linac subsystem reliability, and improvements that have been made to improve reliability, will be described. Plans to maintain or enhance this reliability for at least another ten years of operation, will also be discussed.Comment: 3 pages, 1 figur

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