[query] Benchmark configurations

hail-is · Dec 17, 2024 · d38592f · d38592f
1 parent b6f3b19
commit d38592f
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diff --git a/hail/python/benchmark/hail/benchmark_benchmark_analysis.py b/hail/python/benchmark/hail/benchmark_benchmark_analysis.py
@@ -7,7 +7,7 @@
 from benchmark.tools.statistics import analyze_benchmarks
 
 
-@pytest.mark.benchmark()
+@pytest.mark.benchmark(mds=1.2, instances=10, iterations=5, burn_in_iterations=10)
 def benchmark_analyze_benchmarks(local_tmpdir, onethreetwo, onethreethree):
     inputs = (onethreetwo, onethreethree)
     inputs = ((v, Path(tempfile.mktemp(dir=local_tmpdir))) for v in inputs)

diff --git a/hail/python/benchmark/hail/benchmark_combiner.py b/hail/python/benchmark/hail/benchmark_combiner.py
@@ -24,30 +24,30 @@ def benchmark_compile_2k_merge(empty_gvcf, tmp_path):
     hl.vds.write_variant_datasets(combined, str(tmp_path / 'combiner-multi-write'), overwrite=True)
 
 
-@pytest.mark.benchmark()
+@pytest.mark.benchmark(mds=1.1, instances=10, iterations=10, burn_in_iterations=10)
 @pytest.mark.xtimeout(270)
 def benchmark_python_only_10k_transform(empty_gvcf):
     for vcf in [import_vcf(empty_gvcf)] * 10_000:
         transform_gvcf(vcf, [])
 
 
-@pytest.mark.benchmark()
+@pytest.mark.benchmark(mds=1.1, instances=10, iterations=10, burn_in_iterations=20)
 def benchmark_python_only_10k_combine(empty_gvcf):
     vcf = import_vcf(empty_gvcf)
     mt = transform_gvcf(vcf, [])
     for mts in chunk(COMBINE_GVCF_MAX, [mt] * 10_000):
         combine_variant_datasets(mts)
 
 
-@pytest.mark.benchmark()
+@pytest.mark.benchmark(mds=1.1, instances=20, iterations=10, burn_in_iterations=10)
 def benchmark_import_and_transform_gvcf(single_gvcf):
     mt = import_vcf(single_gvcf)
     vds = transform_gvcf(mt, [])
     vds.reference_data._force_count_rows()
     vds.variant_data._force_count_rows()
 
 
-@pytest.mark.benchmark()
+@pytest.mark.benchmark(mds=1.2, instances=10, iterations=15, burn_in_iterations=8)
 def benchmark_import_gvcf_force_count(single_gvcf):
     mt = import_vcf(single_gvcf)
     mt._force_count_rows()
@@ -62,7 +62,7 @@ def tmp_and_output_paths(tmp_path):
     return (tmp, output)
 
 
-@pytest.mark.benchmark()
+@pytest.mark.benchmark(mds=1.1, instances=10, iterations=5, burn_in_iterations=10)
 @pytest.mark.xtimeout(180)
 def benchmark_vds_combiner_chr22(chr22_gvcfs, tmp_and_output_paths):
     parts = hl.eval([hl.parse_locus_interval('chr22:start-end', reference_genome='GRCh38')])

diff --git a/hail/python/benchmark/hail/benchmark_linalg.py b/hail/python/benchmark/hail/benchmark_linalg.py
@@ -12,32 +12,32 @@ def benchmark_block_matrix_nested_multiply(tmp_path):
     bm.write(str(tmp_path / 'result.mt'), overwrite=True)
 
 
-@pytest.mark.benchmark()
+@pytest.mark.benchmark(mds=1.2, instances=10, iterations=5, burn_in_iterations=5)
 def benchmark_make_ndarray():
     ht = hl.utils.range_table(200_000)
     ht = ht.annotate(x=hl.nd.array(hl.range(ht.idx)))
     ht._force_count()
 
 
-@pytest.mark.benchmark()
+@pytest.mark.benchmark(mds=1.2, instances=10, iterations=20, burn_in_iterations=10)
 def benchmark_ndarray_addition():
     arr = hl.nd.ones((1024, 1024))
     hl.eval(arr + arr)
 
 
-@pytest.mark.benchmark()
+@pytest.mark.benchmark(mds=1.2, instances=20, iterations=5, burn_in_iterations=10)
 def benchmark_ndarray_matmul_int64():
     arr = hl.nd.arange(1024 * 1024).map(hl.int64).reshape((1024, 1024))
     hl.eval(arr @ arr)
 
 
-@pytest.mark.benchmark()
+@pytest.mark.benchmark(mds=1.1, instances=20, iterations=15, burn_in_iterations=6)
 def benchmark_ndarray_matmul_float64():
     arr = hl.nd.arange(1024 * 1024).map(hl.float64).reshape((1024, 1024))
     hl.eval(arr @ arr)
 
 
-@pytest.mark.benchmark()
+@pytest.mark.benchmark(mds=1.2, instances=10, iterations=5, burn_in_iterations=10)
 @pytest.mark.xtimeout(200)
 def benchmark_blockmatrix_write_from_entry_expr_range_mt(tmp_path):
     mt = hl.utils.range_matrix_table(40_000, 40_000, n_partitions=4)
@@ -55,13 +55,14 @@ def benchmark_blockmatrix_write_from_entry_expr_range_mt_standardize(tmp_path):
     )
 
 
-@pytest.mark.benchmark()
+@pytest.mark.benchmark(mds=1.1, instances=5, iterations=8, burn_in_iterations=10)
+@pytest.mark.xtimeout(200)
 def benchmark_sum_table_of_ndarrays():
     ht = hl.utils.range_table(400).annotate(nd=hl.nd.ones((4096, 4096)))
     ht.aggregate(hl.agg.ndarray_sum(ht.nd))
 
 
-@pytest.mark.benchmark()
+@pytest.mark.benchmark(mds=1.1, instances=10, iterations=5, burn_in_iterations=4)
 @pytest.mark.xtimeout(250)
 def benchmark_block_matrix_to_matrix_table_row_major():
     mt = hl.utils.range_matrix_table(20_000, 20_000, n_partitions=4)