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Super-parallel comparison method and system

An algorithm and row data technology, applied in natural language, genetic engineering, information technology and biological engineering, image recognition, and biological sequence alignment sub-fields of protein engineering. Compliant with biometric equivalence issues

Active Publication Date: 2020-01-03
丁贤根
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0012] Although TCAM can achieve single-cycle comparison of tens of millions of data, its original intention is for the routing table of the router, which is seriously different from the comparison requirements of biological data, natural language data, and image data, and does not meet the requirements of biological comparison. right request

Method used

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  • Super-parallel comparison method and system

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specific Embodiment 1

[0189] Specific embodiment one: Biological sequence ultra-parallel comparison server

[0190] 1. Description of the module structure diagram

[0191] Such as Figure 5 It is an embodiment of the biological sequence super-parallel alignment server of the present invention. In the figure, two comparison units are used, among which the comparison unit 1 is larger, the entry width is 256 bytes, the depth is 1M entry rows, and 1 million entry rows are compared at a time in a single cycle; the comparison unit 2 is smaller, the entry width is 64 bytes, the depth is 16, and 16 entry lines are compared at a time in a single cycle. If it is a SAM file for biological sequences, the alignment can be done in Byte units. At this time, the following method is used: figure 2 The logical definition of the byte-based alignment unit shown, and Figure 4 Alignment array of and Figure 5 It is also a logical definition based on a byte-based comparison array; otherwise, it is a logical defini...

specific Embodiment 2

[0354] Specific embodiment two: PCIE card type overspeed comparison system

[0355] Such as Figure 6 As shown, this embodiment is another application of the present invention—the PCIE card type overspeed comparison system. What is the same as the previous embodiment will not be repeated here, and only the difference is emphasized here.

[0356] 1. Use TCAM chip or FPGA to design PCIE card type super speed comparison system. The system includes: comparator array, management module, shift controller, reconfigurable logic, memory and table entry mapping, and PCIE interface.

[0357] 2. This system needs to be inserted into the PCIE slot of the PC to run, and it does not have the ability to run independently.

[0358] 3. The system includes a comparison unit, which uses the built-in CPU and program design of the TCAM chip as the management module of the system.

[0359] 4. The management module of this system designs a management interface for the host PC.

[0360] 5. The en...

specific Embodiment 3

[0361] Specific embodiment three: general data overspeed comparison system

[0362] Such as Figure 6 As shown, this embodiment is another application of the present invention—a general data overspeed comparison system. What is the same as the previous embodiment will not be repeated here, and only the difference is emphasized here.

[0363] 1, Figure 4 The alignment array is defined using bit-alignment-based logic, such as figure 1 shown.

[0364] Therefore, for the step S109, the logic defines that the position is a bit, and the comparison is a bit-by-bit comparison in units of bits.

[0365] 2. For the comparison of image data, the width of the table item is suitable for the image size. For example, based on the 4K RGB three primary color video image format, when each picture is 3840*2160 pixels, the width of the table item is determined to be 3840*3* 24bits=270Kbits, the entry depth is 2160*3*24bits=151875bits=152Kbits, and the depth of the entry can also be increase...

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Abstract

A single-period super-parallel comparison method is designed by adopting an FPGA (Field Programmable Gate Array), a programmable logic or TCAM (Ternary Content Addressable Memory) chip, so that simultaneous bit-by-bit comparison of a keyword item and a plurality of table item rows is realized in a single logic period, and a matched table item row address, similarities and differences point statistical data and position information are output. The algorithm supports table item reconfiguration, dissimilar site processing, filter filtering, table item mapping, one-dimensional array, two-dimensional data and multi-dimensional data comparison; the system comprises a comparator array, reconfigurable logic, a dissimilar site processor, a mapping memory, a filter and a communication interface. Anindependent comparison server and an independent PCIE acceleration card can be formed. According to the method, when comparison is carried out on 10M table item rows, the speed is increased by more than 109 orders of magnitudes compared with the Von's computer comparison algorithm of the fastest CPU at present.

Description

technical field [0001] The invention relates to the fields of information technology and bioengineering, in particular to the fields of gene engineering, biological sequence alignment in protein engineering, and the fields of natural language and image recognition. Background technique [0002] Biological sequence comparison, natural language processing and image comparison are emerging disciplines. After searching and researching, the inventor found that almost all of the existing comparison technologies are Fung’s computer comparison algorithms. Some attempts to use GPU parallel algorithms, Its limitations are too large, and it cannot really achieve high-speed parallel comparison of specific data. [0003] TCAM (Ternary Content Addressable Memory, tri-state content addressable memory), it uses bit comparison technology, so that after a huge number of memories are arranged, they can be compared with a specific memory at the same time in a single cycle, and output the first ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F16/903
CPCG06F16/90339G06F16/90344
Inventor 丁远彤丁贤根
Owner 丁贤根
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