mu94-csl / genasm_hls

GenASM Framework on FPGA using HLS

ECE 5775 Final Project.

This project uses SDSoC v2018.2 or v2019.1, and targets the ZCU104 board.

Instructions to build

Initialize your SDx/SDSoC environment.

CSim and HLS synthesis (SDSoC stuff pragma'd out) can be run inside src directory using the Makefile.

For deployment on the board, the hardware needs to be built inside hw_build_* using make. This should result in a sd_card directory containing BOOT.BIN, a Linux image, and the GenASM shared library. For the host software, run make inside sw_build to build an elf application. Copy these files, and the src/data folder, on to an SD card and insert into board to boot.

Example Builds

Already built files have been provided for ZCU104, inside the example_builds folder, using SDSoC v2018.2.

Copy the contents of the baseline/optimized subdirectory to an SD card, and insert into board to boot from it.

On the board, do

export LD_LIBRARY_PATH=/mnt/
cd /mnt
./host.elf <mode>

where <mode> should be replaced by 1/2 for processing the sample short/long reads dataset.

Notes

The GenASM software has been modified to support only a maximum of 64 pattern length at a time. The divide-and-conquer approach must be used for longer strings.

References

D. S. Cali et al., "GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis," 2020 53rd Annual IEEE/ACM International Symposium on Microarchitecture (MICRO), 2020, pp. 951-966, doi: 10.1109/MICRO50266.2020.00081.