Xilinx Smithwaterman Genomics¶
Smithwaterman demo resides in L2/demos/smithwaterman directory.
Xilinx Smithwaterman Algorithm is FPGA based implementation of standard Smithwaterman. Xilinx implementation of Smithwaterman application is aimed for achieving high throughput. This Xilinx Smithwaterman application is developed and tested on Xilinx Alveo U200.
Results¶
Resource Utilization¶
Table below presents resource utilization of Xilinx Smithwaterman Genomics kernels. The final Fmax achieved is 300MHz
| Flow | LUT | LUTMem | REG | BRAM | URAM |
|---|---|---|---|---|---|
| Smithwaterman | 172K | 11K | 136K | 2 | 0 |
Performance Data¶
Table below presents kernel throughput achieved for a single compute unit.
| Topic | Results |
|---|---|
| Genomics Throughput | 267GCUPS |
Note: Overall throughput can still be increased with multiple compute units.
Software & Hardware¶
Software: Xilinx Vitis 2021.2
Hardware: xilinx_u200_xdma_201830_2 (Xilinx Alveo U200)
Executable Usage¶
To execute single file for genomics :
./build/xil_sw -xbin ./build/xclbin_<xsa_name>_<TARGET mode>/<krnl_smithwaterman.xclbin>To validate single file (genomics) :
./build/xil_sw -xbin ./build/xclbin_<xsa_name>_<TARGET mode>/<krnl_smithwaterman.xclbin>- Note: Default arguments are set in Makefile