fix: gpu benhcmarks actually use gpu

Author: sstadick

benchmarking/bench_scripts/bench.py

@@ -318,7 +318,8 @@ def main(
     score_sizes: list[ScoreSize],
     parasail_instruction_sets: list[ParasailInstructionSet] = [],
     output_dir: Path,
-    devices: int = 1
+    devices: int = 1,
+    iterations: int = 3
 ):
 
     # score_sizes = ["byte", "word", "adaptive"]
@@ -342,7 +343,7 @@ def main(
                         score_size=score_size,
                         scoring_matrix="Blosum62",
                         output_file=str(output_dir / "ish-aligner-result.csv"),
-                        iterations=3,
+                        iterations=iterations,
                         algo=ish_algorithm,
                         devices=device + 1,
                     )

pixi.toml

@@ -168,11 +168,12 @@ bash -c '
   fi &&
   python benchmarking/bench_scripts/bench.py \
       --ish-binaries $(readlink -f ./ish-aligner-gpu) \
-      --ish-algorithm striped-semi-global \
+      --ish-algorithm basic-semi-global-gpu-parallel \
       --score-size word \
       --query-seqs-base-dir ./bench/data/parasail/data/ \
-      --ref-data bench/data/refdata/uniprot_sprot_10x.fasta \
+      --ref-data bench/data/refdata/uniprot_sprot_5x.fasta \
       --devices 4 \
+      --iterations 1 \
       --output-dir ./bench_results/gpu/ \
       > ./bench_results/gpu/benchmark_results.csv &&
   python benchmarking/bench_scripts/plot.py \