NDLI: NCBI BLASTP on the convey HC1-EX (CARN, Vol. 41, Issue. 5)

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Volume 41, Issue 5, December 2013

Accelerating sequential Monte Carlo method for real-time air traffic management

Internet nuggets

Accelerating sequential Monte Carlo method for real-time air traffic management

Internet nuggets

Disk arrays with multiple RAID levels

NCBI BLASTP on the convey HC1-EX

Disk arrays with multiple RAID levels

NCBI BLASTP on the convey HC1-EX

Design and simulation of MAC unit using combinational circuit and adder

Efficient custom computing of fully-streamed lattice boltzmann method on tightly-coupled FPGA cluster

Design and simulation of MAC unit using combinational circuit and adder

Efficient custom computing of fully-streamed lattice boltzmann method on tightly-coupled FPGA cluster

A hybrid CPU-FPGA system for high throughput (10Gb/s) streaming document classification

A hybrid CPU-FPGA system for high throughput (10Gb/s) streaming document classification

Customisable pipelined engine for intensity evaluation in multivariate hawkes point processes

Customisable pipelined engine for intensity evaluation in multivariate hawkes point processes

Accelerating finite difference time domain simulations with reconfigurable dataflow computers

Accelerating finite difference time domain simulations with reconfigurable dataflow computers

A reconfigurable Java accelerator with software compatibility for embedded systems

A reconfigurable Java accelerator with software compatibility for embedded systems

Reconfigurable and hardwired ORB engine on FPGA by Java-to-HDL synthesizer for realtime application

Reconfigurable and hardwired ORB engine on FPGA by Java-to-HDL synthesizer for realtime application

Fixed-point trigonometric functions on FPGAs

Fixed-point trigonometric functions on FPGAs

Performance evaluation of 3-D stacked 32-bit parallel multipliers

Performance evaluation of 3-D stacked 32-bit parallel multipliers

The Ultrasmall soft processor

The Ultrasmall soft processor

Customisable architectures for the set covering problem

Customisable architectures for the set covering problem

A run-time reconfigurable system for adaptive high performance efficient computing

A run-time reconfigurable system for adaptive high performance efficient computing

Volume 41, Issue 5, December 2013

Volume 41, Issue 4, September 2013

Volume 41, Issue 3, June 2013

Volume 41, Issue 2, May 2013

Volume 41, Issue 1, March 2013

NCBI BLASTP on the convey HC1-EX (CARN, Vol. 41, Issue. 5)

Content Provider	ACM Digital Library
Author	Herbordt, Martin C. Mahram, Atabak
Abstract	The BLAST sequence alignment program is a central application in bioinformatics. The de facto standard version, NCBI BLAST, uses complex heuristics which make it challenging to simultaneously achieve both high performance and exact agreement. In previous work, a system that used novel FPGA-based filters reduced the input database by over 99.97% without loss of sensitivity. In the present work we report experiences in getting from a prototype to a potential product for the Convey HC1-EX. There are several issues. The first is the efforts made to maintain timing for a highly complex configuration as it is optimized by including additional filter stages. This requires implementation and optimization of new interface logic as well as floor-planning. The second is the system-level tradeoffs necessary to maintain correctness. The issue here is preventing low frequency events, which necessarily cannot be mapped to the FPGA, from diluting the performance benefits without sacrificing sensitivity. We present results for various usage scenarios and find a factor of nearly 5x speed-up over a fully parallel implementation of the reference code on a contemporaneous CPU. We believe that the resulting system is the leading accelerated NCBI BLAST. The significance of this work is that, while such in-depth work is necessary to achieve highperformance for complex systems, these issues are rarely described nin the academic literature.
Starting Page	41
Ending Page	46
Page Count	6
File Format	PDF
ISSN	01635964
DOI	10.1145/2641361.2641368
Journal	ACM SIGARCH Computer Architecture News (CARN)
Volume Number	41
Issue Number	5
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	1981-04-01
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Content Type	Text
Resource Type	Article

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