NCBI BLAST accelerated on the Mitrion Virtual Processor
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1 NCBI BLAST accelerated on the Mitrion Virtual Processor
2 FPGAs How a circuit is formed on an FPGA Configurable computing element (LUT) A look-up table for a simple Boolean operation Configurable interconnect element Configured to connect any LUT with any other LUT (2)
3 Circuit design vs Programming The difference between using VHDL and C is much more than syntax Circuit design works in the physical world of real electronics Like building a bridge Continual judgments about cost and safety Software programming works in the abstract world of pure logic Like mathematics Purely logical description of problem (3)
4 Executing software To achieve the abstract world of software, a device that physically embodies a model of execution is required The device operates in the real world Its operations form the pure abstract world of software This is the essence of a computer processor (4)
5 The Mitrion Platform 1) The Mitrion Virtual Processor (MVP) A configurable processor design for a fine-grain massively parallel, soft-core processor times faster than traditional CPUs 2) The Mitrion-C programming language An intrinsically parallel C-family language 3) The Mitrion Software Development Kit Compiler Debugger/Simulator Processor configurator IDE (5)
6 What the MVP gives you No hardware design considerations or judgments about physical electronics Real, fully abstract, software programming No clock, the MVP is designed to run at 100MHz The MVP keeps track of data and send it to the right place at the right time No timing considerations whatsoever No gates, drive-high, drive-low, ground, combinatorial paths, flip-flops, clocks, PLLs, DCMs, latches, etc, etc (6)
7 What you need to do You must write a parallel program You have to give sufficient parallelism to feed the compute units in parallel If you have 20 data parallel processing units, you need 20 independent data elements If you have 20 pipelined processing units, you need 20 independent data elements Mitrion-C is designed to help you achieve this (7)
8 The Mitrion Platform (8)
9 NCBI BLAST accelerated on the MVP
10 Mitrion-Accelerated NCBI BLAST Built on the NCBI blastall application Identical interface and output options BLASTN algorithm is accelerated: Critical parts ported Runs on the Mitrion Virtual Processor in FPGA hardware (10)
11 NCBI BLAST accelerated on the MVP Mitrion BLAST is open-source, released under GPL Requires at least MVP on Virtex4-LX200 Not a Black Box fully open-source: Anyone can add to it, change it, add secret sauce Total Mitrion-C code is less than 1300 lines Free to download on Sourceforge Newly released! 60x performance increase vs standard NCBI BLAST run on Opteron 2.8 (11)
12 NCBI BLAST accelerated on the MVP Current main limitations All being worked on BLAST-N only BLAST-P in development Currently limited to less than ~100K queries (unlimited database sizes) Gapped extension not run on MVP Small percentage of run-time for most queries Only 11-length kernels (12)
13 Basic architecture of NCBI BLAST Build a hash-table of all WMERs (11- basepair sequences) in query Produce all possible WMERs from database Remove the produced WMERs that do not exist in query Do ungapped extension of WMER hits Do gapped extension of WMER hits (13)
14 Changes in the port to the MVP Minimal changes Strong concern regarding repeatability of results with standard NCBI BLAST Changes to parallelize code, but done in a safe way Works as a pre-filter Inserted before the standard filters of NCBI BLAST, the full standard BLAST is run afterwards (but just on the hits that passed) Removes a bit fewer than optimal number of hits (14)
15 Mitrion BLASTN Performance (15)
16 The Mitrion-C Open Bio Project Open source development of key Bioinformatics applications for the Mitrion Virtual Processor at Sourceforge.net: Currently BLAST, others to come (16)
17 Contact Information Mitrionics AB Ideon Science Park SE Lund (17)
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