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PanSashkoPanSashko
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Merge branch 'hanabi1224:main' into zig
2 parents a593325 + 77f6bd5 commit 743ac2c

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‎bench/algorithm/fasta/6.rs

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// Ported from 1.zig
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use std::io::{self, BufWriter, StdoutLock, Write};
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const MAX_LINE_LENGTH: usize = 60;
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const IM: u32 = 139968;
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const IA: u32 = 3877;
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const IC: u32 = 29573;
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struct AminoAcid {
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l: u8,
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p: f64,
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}
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struct Random {
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seed: u32,
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}
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impl Random {
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fn new() -> Self {
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Self { seed: 42 }
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}
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fn next(&mut self) -> f64 {
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self.seed = (self.seed * IA + IC) % IM;
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(IM as f64 * self.seed as f64) / IM as f64
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}
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}
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impl Iterator for Random {
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type Item = f64;
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fn next(&mut self) -> Option<Self::Item> {
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Some(self.next())
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}
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}
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fn repeat_and_wrap(
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out: &mut BufWriter<StdoutLock<'static>>,
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sequence: &[u8],
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count: usize,
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) -> io::Result<()> {
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let n = sequence.len();
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let padded_sequence = (0..(n + MAX_LINE_LENGTH))
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.map(|i| sequence[i % n])
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.collect::<Vec<_>>();
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let mut off = 0;
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let mut idx = 0;
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while idx < count {
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let rem = count - idx;
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let line_length = MAX_LINE_LENGTH.min(rem);
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out.write_all(&padded_sequence[off..off + line_length])?;
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out.write_all(&[b'\n'])?;
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off += line_length;
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if off > n {
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off -= n;
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}
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idx += line_length;
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}
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Ok(())
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}
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fn generate_and_wrap(
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random: &mut Random,
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out: &mut BufWriter<StdoutLock<'static>>,
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nucleotides: &[AminoAcid],
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count: usize,
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) -> io::Result<()> {
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let mut cum_prob = 0.0;
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let cum_prob_total = nucleotides
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.iter()
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.map(|&AminoAcid { l: _, p }| {
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cum_prob += p;
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cum_prob * IM as f64
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})
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.collect::<Vec<_>>();
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let mut line = [0u8; MAX_LINE_LENGTH + 1];
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line[MAX_LINE_LENGTH] = b'\n';
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let mut idx = 0;
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while idx < count {
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let rem = count - idx;
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let line_length = MAX_LINE_LENGTH.min(rem);
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line[..line_length]
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.iter_mut()
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.zip(&mut *random)
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.for_each(|(col, r)| {
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let c = cum_prob_total
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.iter()
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.fold(0, |acc, &n| acc + (n <= r) as usize);
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*col = nucleotides[c].l;
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});
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line[line_length] = b'\n';
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out.write_all(&line[..line_length + 1])?;
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idx += line_length;
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}
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Ok(())
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}
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pub fn main() -> io::Result<()> {
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let stdout = io::stdout();
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let mut stdout = io::BufWriter::new(stdout.lock());
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let n = std::env::args_os()
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.nth(1)
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.and_then(|s| s.as_os_str().to_str().and_then(|s| s.parse().ok()))
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.unwrap_or(1000);
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let homo_sapiens_alu =
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b"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTC\
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AGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCG\
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TGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGG\
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AGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
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stdout.write_all(b">ONE Homo sapiens alu\n".as_slice())?;
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repeat_and_wrap(&mut stdout, &homo_sapiens_alu[..], 2 * n)?;
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let mut random = Random::new();
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let iub_nucleotide_info = &[
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AminoAcid { l: b'a', p: 0.27 },
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AminoAcid { l: b'c', p: 0.12 },
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AminoAcid { l: b'g', p: 0.12 },
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AminoAcid { l: b't', p: 0.27 },
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AminoAcid { l: b'B', p: 0.02 },
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AminoAcid { l: b'D', p: 0.02 },
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AminoAcid { l: b'H', p: 0.02 },
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AminoAcid { l: b'K', p: 0.02 },
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AminoAcid { l: b'M', p: 0.02 },
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AminoAcid { l: b'N', p: 0.02 },
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AminoAcid { l: b'R', p: 0.02 },
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AminoAcid { l: b'S', p: 0.02 },
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AminoAcid { l: b'V', p: 0.02 },
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AminoAcid { l: b'W', p: 0.02 },
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AminoAcid { l: b'Y', p: 0.02 },
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];
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stdout.write_all(b">TWO IUB ambiguity codes\n".as_slice())?;
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generate_and_wrap(&mut random, &mut stdout, iub_nucleotide_info, 3 * n)?;
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let homo_sapien_nucleotide_info = &[
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AminoAcid {
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l: b'a',
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p: 0.3029549426680,
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},
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AminoAcid {
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l: b'c',
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p: 0.1979883004921,
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},
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AminoAcid {
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l: b'g',
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p: 0.1975473066391,
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},
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AminoAcid {
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l: b't',
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p: 0.3015094502008,
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},
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];
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stdout.write_all(b">THREE Homo sapiens frequency\n".as_slice())?;
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generate_and_wrap(&mut random, &mut stdout, homo_sapien_nucleotide_info, 5 * n)?;
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Ok(())
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}

‎bench/algorithm/nbody/3.zig

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const std = @import("std");
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const math = std.math;
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const solar_mass = 4.0 * math.pi * math.pi;
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const year = 365.24;
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const vec3 = @Vector(3, f64);
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fn scale(v: anytype, f: f64) @TypeOf(v) {
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return v * @as(@TypeOf(v), @splat(f));
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}
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fn lengthSq(v: vec3) f64 {
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return @reduce(.Add, v * v);
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}
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fn length(v: vec3) f64 {
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return @sqrt(lengthSq(v));
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}
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const Body = struct {
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pos: vec3,
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vel: vec3,
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mass: f64,
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};
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fn offsetMomentum(bodies: []Body) void {
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@setFloatMode(.optimized);
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var pos: vec3 = @splat(0);
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for (bodies[1..]) |b| pos += scale(@as(vec3, b.vel), b.mass);
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bodies[0].vel = -scale(pos, 1.0 / solar_mass);
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}
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fn allPairs(comptime n: usize) [n * (n - 1)/2][2]u32 {
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var res: [n * (n - 1)/2][2]u32 = undefined;
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var k: usize = 0;
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for (0..n - 1) |i| for (i + 1..n) |j| {
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res[k] = .{@intCast(i), @intCast(j)};
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k += 1;
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};
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return res;
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}
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fn advance(comptime n: usize, bodies: *[n]Body, dt: f64) void {
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@setFloatMode(.optimized);
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const pairs = comptime allPairs(n);
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var dp: [pairs.len]vec3 = undefined;
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var distSq: @Vector(pairs.len, f64) = undefined;
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inline for (pairs, 0..) |p, i| {
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const d = bodies[p[0]].pos - bodies[p[1]].pos;
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dp[i] = d;
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distSq[i] = lengthSq(dp[i]);
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}
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const mag = @as(@Vector(pairs.len, f64), @splat(dt)) / (distSq * @sqrt(distSq));
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inline for (pairs, 0..) |p, i| {
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bodies[p[0]].vel -= scale(dp[i], bodies[p[1]].mass * mag[i]);
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bodies[p[1]].vel += scale(dp[i], bodies[p[0]].mass * mag[i]);
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}
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inline for (bodies) |*body| body.pos += scale(body.vel, dt);
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}
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fn energy(bodies: []const Body) f64 {
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@setFloatMode(.optimized);
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var e: f64 = 0.0;
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for (bodies, 0..) |bi, i| {
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e += 0.5 * lengthSq(bi.vel) * bi.mass;
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for (bodies[i + 1 ..]) |bj| {
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e -= bi.mass * bj.mass / length(bi.pos - bj.pos);
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}
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}
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return e;
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}
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var solar_bodies = [_]Body{
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// Sun
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Body{
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.pos = @splat(0),
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.vel = @splat(0),
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.mass = solar_mass,
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},
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// Jupiter
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Body{
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.pos = .{ 4.84143144246472090, -1.16032004402742839, -0.103622044471123109 },
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.vel = scale(vec3{ 1.66007664274403694e-03, 7.69901118419740425e-03, -6.90460016972063023e-05 }, year),
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.mass = 9.54791938424326609e-04 * solar_mass,
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},
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// Saturn
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Body{
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.pos = .{ 8.34336671824457987, 4.12479856412430479, -0.403523417114321381 },
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.vel = scale(vec3{ -2.76742510726862411e-03, 4.99852801234917238e-03, 2.30417297573763929e-05 }, year),
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.mass = 2.85885980666130812e-04 * solar_mass,
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},
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// Uranus
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Body{
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.pos = .{ 12.8943695621391310, -15.1111514016986312, -0.223307578892655734 },
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.vel = scale(vec3{ 2.96460137564761618e-03, 2.37847173959480950e-03, -2.96589568540237556e-05 }, year),
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.mass = 4.36624404335156298e-05 * solar_mass,
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},
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// Neptune
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Body{
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.pos = .{ 15.3796971148509165, -25.9193146099879641, 0.179258772950371181 },
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.vel = scale(vec3{ 2.68067772490389322e-03, 1.62824170038242295e-03, -9.51592254519715870e-05 }, year),
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.mass = 5.15138902046611451e-05 * solar_mass,
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},
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};
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pub fn main() !void {
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const steps = try getSteps();
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offsetMomentum(&solar_bodies);
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const initial_energy = energy(&solar_bodies);
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for (0..steps) |_| advance(solar_bodies.len, &solar_bodies, 0.01);
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const final_energy = energy(&solar_bodies);
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const stdout = std.io.getStdOut().writer();
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try stdout.print("{d:.9}\n{d:.9}\n", .{ initial_energy, final_energy });
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}
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fn getSteps() !usize {
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var arg_it = std.process.args();
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_ = arg_it.skip();
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const arg = arg_it.next() orelse return 1000;
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return try std.fmt.parseInt(usize, arg, 10);
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}

‎bench/bench_rust.yaml

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- 1c.rs
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- 5-m.rs
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- 5c-m.rs
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- 6.rs
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- name: knucleotide
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source:
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- 8.rs

‎bench/bench_zig.yaml

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source:
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- 1.zig
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- 2.zig
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- 3.zig
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- name: spectral-norm
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source:
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- 1.zig

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