commit 2d59b72f91ec5fb72a69fc0b09ad5fba24807239
parent 191fb44e1be803e1161752d75660aefc57a5d124
Author: Walther Chen <walther.chen@gmail.com>
Date: Fri, 1 Nov 2024 11:17:37 -0400
lower page size for arenas in neighbor
Memory usage does go down when lowering page size in neighbor arenas
(although making it too small is not good either)
First is from before arena swapping. Second is arena swapping and page
size at 1024.
bioinformatics on main [+1] > poop "./ba1j input.txt" "./ba1j-mem input.txt"
Benchmark 1 (99 runs): ./ba1j input.txt
measurement mean ± σ min … max outliers delta
wall_time 50.5ms ± 2.81ms 45.8ms … 59.7ms 1 ( 1%) 0%
peak_rss 22.4MB ± 52.8KB 22.3MB … 22.5MB 0 ( 0%) 0%
cpu_cycles 110M ± 2.82M 105M … 120M 4 ( 4%) 0%
instructions 223M ± 3.92 223M … 223M 1 ( 1%) 0%
cache_references 1.53M ± 15.0K 1.49M … 1.60M 6 ( 6%) 0%
cache_misses 660K ± 48.6K 580K … 764K 0 ( 0%) 0%
branch_misses 140K ± 2.12K 135K … 145K 2 ( 2%) 0%
Benchmark 2 (147 runs): ./ba1j-mem input.txt
measurement mean ± σ min … max outliers delta
wall_time 34.0ms ± 2.64ms 30.5ms … 46.0ms 3 ( 2%) ⚡- 32.7% ± 1.4%
peak_rss 19.1MB ± 52.8KB 19.1MB … 19.2MB 0 ( 0%) ⚡- 14.6% ± 0.1%
cpu_cycles 68.7M ± 3.86M 65.5M … 100M 7 ( 5%) ⚡- 37.5% ± 0.8%
instructions 128M ± 2.34 128M … 128M 4 ( 3%) ⚡- 42.3% ± 0.0%
cache_references 1.07M ± 13.9K 1.04M … 1.17M 8 ( 5%) ⚡- 30.5% ± 0.2%
cache_misses 359K ± 51.1K 297K … 598K 4 ( 3%) ⚡- 45.7% ± 1.9%
branch_misses 133K ± 2.06K 130K … 140K 4 ( 3%) ⚡- 4.8% ± 0.4%
Diffstat:
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/util.c3 b/util.c3
@@ -209,8 +209,8 @@ fn String[] neighbors(String pattern, int d, Allocator alloc = allocator::heap()
if (pattern.len == 0) return {};
DynamicArenaAllocator neighborhood_arena;
DynamicArenaAllocator suffix_neighborhood_arena;
- neighborhood_arena.init(4096, allocator::temp());
- suffix_neighborhood_arena.init(4096, allocator::temp());
+ neighborhood_arena.init(1024, allocator::temp());
+ suffix_neighborhood_arena.init(1024, allocator::temp());
List(<String>) neighborhood;
List(<String>) suffix_neighborhood;
neighborhood.new_init_with_array({"A", "C", "G", "T"}, &neighborhood_arena);
