Xilinx SMEM Genomics¶
Smithwaterman demo resides in L2/tests/smem directory.
Xilinx SMEM Algorithm is FPGA based implementation of standard SMEM. Xilinx implementation of SMEM application is aimed for achieving high throughput. This Xilinx Smithwaterman application is developed and tested on Xilinx Alveo U250.
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 |
|---|---|---|---|---|---|
| SMEM | 46K | 5K | 60K | 70 | 70 |
Performance Data¶
Table below presents kernel throughput achieved for a single compute unit.
| Topic | Results |
|---|---|
| Average DRAM Bandwidth | 2 GB/s |
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 U250)
Executable Usage¶
To execute single file for genomics :
./build/xil_smem ./build/xclbin_<xsa_name>_<TARGET mode>/<smem.xclbin> <file_name>- Note: Default arguments are set in Makefile