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src xcl::read_binary_file updates to remove memory leaks Jul 26, 2019
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README.md
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README.md

Smithwaterman Genetic Sequencing Demo

This is an optimized implementation of the smithwaterman algorithm targeting exection on an SDAccel support FPGA acceleration card.

The main algorithm characteristics of this application are

  1. Compute MaxScore
  2. Systolic array implementation

SUPPORTED PLATFORMS

Platform Board Software Version
xilinx_u200_qdma Xilinx Alveo U200 SDx 2019.1
xilinx_u50_xdma Xilinx Alveo U50 SDx 2019.1
xilinx_u250_qdma Xilinx Alveo U250 SDx 2019.1
xilinx_u200_xdma Xilinx Alveo U200 SDx 2019.1
xilinx_u280_xdma Xilinx Alveo U280 SDx 2019.1
xilinx_u250_xdma Xilinx Alveo U250 SDx 2019.1

DESIGN FILES

Application code is located in the src directory. Accelerator binary files will be compiled to the xclbin directory. The xclbin directory is required by the Makefile and its contents will be filled during compilation. A listing of all the files in this example is shown below

src/genseq.cpp
src/intel/kseq.h
src/intel/sc_demo.c
src/intel/ssw.c
src/intel/ssw.h
src/main.cpp
src/matcharray.cpp
src/matcharray.h
src/opencl_sw_maxscore_basic.cpp
src/opencl_sw_maxscore_systolic.cpp
src/smithwaterman.cpp
src/smithwaterman.h
src/sw.h

COMMAND LINE ARGUMENTS

Once the environment has been configured, the application can be executed by

./smithwaterman <krnl_smithwaterman XCLBIN>
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