Accelerating Binary String Comparisons with a Scalable, Streaming-Based System Architecture Based on FPGAs

Pilz S, Porrmann F, Kaiser M, Hagemeyer J, Hogan JM, Rückert U. Accelerating Binary String Comparisons with a Scalable, Streaming-Based System Architecture Based on FPGAs. Algorithms. 2020;13(2): 47.This paper is concerned with Field Programmable Gate Arrays (FPGA)-based systems for energy-efficient high-throughput string comparison. Modern applications which involve comparisons across large data sets—such as large sequence sets in molecular biology—are by their nature computationally intensive. In this work, we present a scalable FPGA-based system architecture to accelerate the comparison of binary strings. The current architecture supports arbitrary lengths in the range 16 to 2048-bit, covering a wide range of possible applications. In our example application, we consider DNA sequences embedded in a binary vector space through Locality Sensitive Hashing (LSH) one of several possible encodings that enable us to avoid more costly character-based operations. Here the resulting encoding is a 512-bit binary signature with comparisons based on the Hamming distance. In this approach, most of the load arises from the calculation of the O ( m ∗ n ) Hamming distances between the signatures, where m is the number of queries and n is the number of signatures contained in the database. Signature generation only needs to be performed once, and we do not consider it further, focusing instead on accelerating the signature comparisons. The proposed FPGA-based architecture is optimized for high-throughput using hundreds of computing elements, arranged in a systolic array. These core computing elements can be adapted to support other string comparison algorithms with little effort, while the other infrastructure stays the same. On a Xilinx Virtex UltraScale+ FPGA (XCVU9P-2), a peak throughput of 75.4 billion comparisons per second—of 512-bit signatures—was achieved, using a design with 384 parallel processing elements and a clock frequency of 200 MHz. This makes our FPGA design 86 times faster than a highly optimized CPU implementation. Compared to a GPU design, executed on an NVIDIA GTX1060, it performs nearly five times faster

Accelerating Hamming Distance Comparisons for Locality Sensitive Hashing (LSH) using FPGAs

Kaiser M, Pilz S, Porrmann F, Hagemeyer J, Porrmann M. Accelerating Hamming Distance Comparisons for Locality Sensitive Hashing (LSH) using FPGAs. In: 12th CeBiTec Symposium - Big Data in Medicine and Biotechnology - Abstract Book. Vol 12. Bielefeld; 2018: 48-49

OLT(RE)2: an On-Line on-demand Testing approach for permanent Radiation Effects in REconfigurable systems

Reconfigurable systems gained great interest in a wide range of application fields, including aerospace, where electronic devices are exposed to a very harsh working environment. Commercial SRAM-based FPGA devices represent an extremely interesting hardware platform for this kind of systems since they combine low cost with the possibility to utilize state-of-the-art processing power as well as the flexibility of reconfigurable hardware. In this paper we present OLT(RE)2: an on-line on-demand approach to test permanent faults induced by radiation in reconfigurable systems used in space missions. The proposed approach relies on a test circuit and on custom place-and-route algorithms. OLT(RE)2 exploits partial dynamic reconfigurability offered by today’s SRAM-based FPGAs to place the test circuits at run-time. The goal of OLT(RE)2 is to test unprogrammed areas of the FPGA before using them, thus preventing functional modules of the reconfigurable system to be placed on areas with faulty resources. Experimental results have shown that (i) it is possible to generate, place and route the test circuits needed to detect on average more than 99 % of the physical wires and on average about 97 % of the programmable interconnection points of an arbitrary large region of the FPGA in a reasonable time and that (ii) it is possible to download and run the whole test suite on the target device without interfering with the normal functioning of the system

Energy Efficiency of Sequence Alignment Tools - Software and Hardware Perspectives

Kierzynka M, Kosmann L, vor dem Berge M, et al. Energy Efficiency of Sequence Alignment Tools - Software and Hardware Perspectives. Future Generation Computer Systems. 2016;67:455-465

A Reconfigurable Heterogeneous Microserver Architecture for Energy-efficient Computing

Kaiser M, Griessl R, Hagemeyer J, et al. A Reconfigurable Heterogeneous Microserver Architecture for Energy-efficient Computing. In: Third International Workshop on Heterogeneous High-performance Reconfigurable Computing (H2RC'17). Denver, CO; 2017

FPGA-accelerated Heterogeneous Hyperscale Server Architecture for Next-Generation Compute Clusters

Griessl R, Peykanu M, Hagemeyer J, et al. FPGA-accelerated Heterogeneous Hyperscale Server Architecture for Next-Generation Compute Clusters. Presented at the First International Workshop on Heterogeneous High-performance Reconfigurable Computing (H2RC‘15), held in conjunction with Supercomputing 2015, Austin Texas, USA

LEGaTO: first steps towards energy-efficient toolset for heterogeneous computing

LEGaTO is a three-year EU H2020 project which started in December 2017. The LEGaTO project will leverage task-based programming models to provide a software ecosystem for Made-in-Europe heterogeneous hardware composed of CPUs, GPUs, FPGAs and dataflow engines. The aim is to attain one order of magnitude energy savings from the edge to the converged cloud/HPC.Peer ReviewedPostprint (author's final draft

LEGaTO: towards energy-efficient, secure, fault-tolerant toolset for heterogeneous computing

LEGaTO is a three-year EU H2020 project which started in December 2017. The LEGaTO project will leverage task-based programming models to provide a software ecosystem for Made-in-Europe heterogeneous hardware composed of CPUs, GPUs, FPGAs and dataflow engines. The aim is to attain one order of magnitude energy savings from the edge to the converged cloud/HPC.Peer ReviewedPostprint (author's final draft

Hardware Virtualization Exploiting Dynamically Reconfigurable Architectures

Hagemeyer J, Koester M, Porrmann M. Hardware Virtualization Exploiting Dynamically Reconfigurable Architectures. In: 1. GI/ITG KuVS Fachgespräch Virtualisierung. Heinz Nixdorf Institut, Universität Paderborn; 2008

Managing the Risk of Self-Judging Security Exceptions Through Insurance: How Recent Mergers and Acquisitions Practice Copes with Investment Screening

In light of the limited possibility to seek legal recourse against screening of foreign investments on grounds of national security, can insurance provide an alternative avenue to compensate affected investors? The answer is: Yes, but with caveats. For investors, even if insurance does not provide an equivalent to full reparation, it can serve as a useful mitigant of the risk that contemplated investment transactions cannot be consummated as anticipated due to screening measures. For host States, insurance provides a useful mechanism by which they can facilitate compensation of investors without having to disclose information contrary to their essential security interests and thus a means by which host States can remain attractive to foreign direct investment in spite of investment screening