change fasta benchmark to Veedrac's implementation
This commit is contained in:
Andre Bogus
parent
8fe79bdfda
commit
960e85c8ea
@ -39,114 +39,332 @@
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// OF THE POSSIBILITY OF SUCH DAMAGE.
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use std::cmp::min;
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use std::env;
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use std::fs::File;
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use std::io::{self, BufWriter};
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use std::io::prelude::*;
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use std::io::{self, Write};
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use std::sync::{Arc, Mutex};
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use std::thread;
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const LINE_LENGTH: usize = 60;
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const IM: u32 = 139968;
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struct MyRandom {
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const LINE_LEN: usize = 60;
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const BLOCK_LINES: usize = 512;
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const BLOCK_THOROUGHPUT: usize = LINE_LEN * BLOCK_LINES;
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const BLOCK_LEN: usize = BLOCK_THOROUGHPUT + BLOCK_LINES;
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const STDIN_BUF: usize = (LINE_LEN + 1) * 1024;
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const ALU: &'static [u8] =
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b"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG\
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GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA\
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CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT\
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ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA\
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GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG\
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AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC\
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AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
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const IUB: &'static [(u8, f32)] =
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&[(b'a', 0.27), (b'c', 0.12), (b'g', 0.12),
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(b't', 0.27), (b'B', 0.02), (b'D', 0.02),
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(b'H', 0.02), (b'K', 0.02), (b'M', 0.02),
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(b'N', 0.02), (b'R', 0.02), (b'S', 0.02),
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(b'V', 0.02), (b'W', 0.02), (b'Y', 0.02)];
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const HOMOSAPIENS: &'static [(u8, f32)] =
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&[(b'a', 0.3029549426680),
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(b'c', 0.1979883004921),
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(b'g', 0.1975473066391),
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(b't', 0.3015094502008)];
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// We need a specific Rng,
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// so implement this manually
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const MODULUS: u32 = 139968;
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const MULTIPLIER: u32 = 3877;
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const ADDITIVE: u32 = 29573;
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// Why doesn't rust already have this?
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// Algorithm directly taken from Wikipedia
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fn powmod(mut base: u64, mut exponent: u32, modulus: u64) -> u64 {
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let mut ret = 1;
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base %= modulus;
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while exponent > 0 {
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if exponent & 1 == 1 {
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ret *= base;
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ret %= modulus;
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}
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exponent >>= 1;
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base *= base;
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base %= modulus;
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}
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ret
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}
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// Just a typical LCRNG
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pub struct Rng {
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last: u32
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}
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impl MyRandom {
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fn new() -> MyRandom { MyRandom { last: 42 } }
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fn normalize(p: f32) -> u32 {(p * IM as f32).floor() as u32}
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fn gen(&mut self) -> u32 {
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self.last = (self.last * 3877 + 29573) % IM;
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impl Rng {
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pub fn new() -> Rng {
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Rng { last: 42 }
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}
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pub fn max_value() -> u32 {
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MODULUS - 1
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}
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pub fn normalize(p: f32) -> u32 {
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(p * MODULUS as f32).floor() as u32
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}
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pub fn gen(&mut self) -> u32 {
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self.last = (self.last * MULTIPLIER + ADDITIVE) % MODULUS;
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self.last
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}
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}
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struct AAGen<'a> {
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rng: &'a mut MyRandom,
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data: Vec<(u32, u8)>
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}
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impl<'a> AAGen<'a> {
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fn new<'b>(rng: &'b mut MyRandom, aa: &[(char, f32)]) -> AAGen<'b> {
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let mut cum = 0.;
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let data = aa.iter()
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.map(|&(ch, p)| { cum += p; (MyRandom::normalize(cum), ch as u8) })
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.collect();
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AAGen { rng: rng, data: data }
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}
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}
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impl<'a> Iterator for AAGen<'a> {
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type Item = u8;
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// This allows us to fast-forward the RNG,
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// allowing us to run it in parallel.
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pub fn future(&self, n: u32) -> Rng {
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let a = MULTIPLIER as u64;
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let b = ADDITIVE as u64;
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let m = MODULUS as u64;
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fn next(&mut self) -> Option<u8> {
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let r = self.rng.gen();
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self.data.iter()
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.skip_while(|pc| pc.0 < r)
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.map(|&(_, c)| c)
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.next()
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// (a^n - 1) mod (a-1) m
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// x_k = ((a^n x_0 mod m) + --------------------- b) mod m
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// a - 1
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//
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// Since (a - 1) divides (a^n - 1) mod (a-1) m,
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// the subtraction does not overflow and thus can be non-modular.
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//
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let new_seed =
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(powmod(a, n, m) * self.last as u64) % m +
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(powmod(a, n, (a-1) * m) - 1) / (a-1) * b;
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Rng { last: (new_seed % m) as u32 }
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}
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}
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fn make_fasta<W: Write, I: Iterator<Item=u8>>(
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wr: &mut W, header: &str, mut it: I, mut n: usize)
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-> io::Result<()>
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{
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try!(wr.write(header.as_bytes()));
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let mut line = [0; LINE_LENGTH + 1];
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while n > 0 {
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let nb = min(LINE_LENGTH, n);
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for i in 0..nb {
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line[i] = it.next().unwrap();
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// This will end up keeping track of threads, like
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// in the other multithreaded Rust version, in
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// order to keep writes in order.
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//
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// This is stolen from another multithreaded Rust
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// implementation, although that implementation
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// was not able to parallelize the RNG itself.
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struct BlockSubmitter<W: io::Write> {
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writer: W,
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pub waiting_on: usize,
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}
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impl<W: io::Write> BlockSubmitter<W> {
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fn submit(&mut self, data: &[u8], block_num: usize) -> Option<io::Result<()>> {
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if block_num == self.waiting_on {
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self.waiting_on += 1;
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Some(self.submit_async(data))
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}
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else {
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None
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}
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n -= nb;
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line[nb] = '\n' as u8;
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try!(wr.write(&line[..nb+1]));
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}
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fn submit_async(&mut self, data: &[u8]) -> io::Result<()> {
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self.writer.write_all(data)
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}
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}
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// For repeating strings as output
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fn fasta_static<W: io::Write>(
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writer: &mut W,
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header: &[u8],
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data: &[u8],
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mut n: usize
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) -> io::Result<()>
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{
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// The aim here is to print a short(ish) string cyclically
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// with line breaks as appropriate.
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//
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// The secret technique is to repeat the string such that
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// any wanted line is a single offset in the string.
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//
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// This technique is stolen from the Haskell version.
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try!(writer.write_all(header));
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// Maximum offset is data.len(),
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// Maximum read len is LINE_LEN
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let stream = data.iter().cloned().cycle();
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let mut extended: Vec<u8> = stream.take(data.len() + LINE_LEN + 1).collect();
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let mut offset = 0;
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while n > 0 {
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let write_len = min(LINE_LEN, n);
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let end = offset + write_len;
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n -= write_len;
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let tmp = extended[end];
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extended[end] = b'\n';
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try!(writer.write_all(&extended[offset..end + 1]));
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extended[end] = tmp;
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offset = end;
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offset %= data.len();
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}
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Ok(())
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}
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fn run<W: Write>(writer: &mut W) -> io::Result<()> {
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let mut args = env::args();
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let n = if env::var_os("RUST_BENCH").is_some() {
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25000000
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} else if args.len() <= 1 {
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1000
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} else {
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args.nth(1).unwrap().parse().unwrap()
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};
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let rng = &mut MyRandom::new();
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let alu =
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"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG\
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GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA\
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CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT\
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ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA\
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GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG\
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AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC\
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AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
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let iub = &[('a', 0.27), ('c', 0.12), ('g', 0.12),
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('t', 0.27), ('B', 0.02), ('D', 0.02),
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('H', 0.02), ('K', 0.02), ('M', 0.02),
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('N', 0.02), ('R', 0.02), ('S', 0.02),
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('V', 0.02), ('W', 0.02), ('Y', 0.02)];
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let homosapiens = &[('a', 0.3029549426680),
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('c', 0.1979883004921),
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('g', 0.1975473066391),
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('t', 0.3015094502008)];
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// For RNG streams as output
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fn fasta<W: io::Write + Send + 'static>(
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submitter: &Arc<Mutex<BlockSubmitter<W>>>,
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header: &[u8],
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table: &[(u8, f32)],
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rng: &mut Rng,
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n: usize
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) -> io::Result<()>
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{
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// There's another secret technique in use here:
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// we generate a lookup table to cache search of the
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// aa buffer.
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//
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// The secret technique used is stolen from Haskell's
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// implementation, and is the main secret to the Haskell
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// implementation's speed.
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fn gen_lookup_table(aa: &[(u8, f32)]) -> Vec<u8> {
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let mut table = Vec::with_capacity(Rng::max_value() as usize + 1);
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try!(make_fasta(writer, ">ONE Homo sapiens alu\n",
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alu.as_bytes().iter().cycle().cloned(), n * 2));
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try!(make_fasta(writer, ">TWO IUB ambiguity codes\n",
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AAGen::new(rng, iub), n * 3));
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try!(make_fasta(writer, ">THREE Homo sapiens frequency\n",
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AAGen::new(rng, homosapiens), n * 5));
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let mut cumulative_prob = 0.0;
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let mut cumulative_norm = 0;
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writer.flush()
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for &(byte, prob) in aa {
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let last_norm = cumulative_norm;
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cumulative_prob += prob;
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cumulative_norm = min(Rng::max_value(), Rng::normalize(cumulative_prob)) + 1;
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table.extend((0..cumulative_norm - last_norm).map(|_| byte));
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}
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table
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}
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{
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try!(submitter.lock().unwrap().submit_async(header));
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}
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let lookup_table = Arc::new(gen_lookup_table(table));
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let thread_count = 4; // avoid external dependency
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let mut threads = Vec::new();
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for block_num in (0..thread_count) {
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let offset = BLOCK_THOROUGHPUT * block_num;
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let local_submitter = submitter.clone();
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let local_lookup_table = lookup_table.clone();
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let local_rng = rng.future(offset as u32);
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threads.push(thread::spawn(move || {
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gen_block(
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local_submitter,
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local_lookup_table,
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local_rng,
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n.saturating_sub(offset),
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block_num,
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thread_count
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)
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}));
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}
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for thread in threads {
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try!(thread.join().unwrap());
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}
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*rng = rng.future(n as u32);
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Ok(())
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}
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// A very optimized writer.
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// I have a feeling a simpler version wouldn't slow
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// things down too much, though, since the RNG
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// is the really heavy hitter.
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fn gen_block<W: io::Write>(
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submitter: Arc<Mutex<BlockSubmitter<W>>>,
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lookup_table: Arc<Vec<u8>>,
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mut rng: Rng,
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mut length: usize,
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mut block_num: usize,
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block_stride: usize,
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) -> io::Result<()>
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{
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// Include newlines in block
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length += length / LINE_LEN;
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let block: &mut [u8] = &mut [b'\n'; BLOCK_LEN];
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while length > 0 {
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{
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let gen_into = &mut block[..min(length, BLOCK_LEN)];
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// Write random numbers, skipping newlines
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for (i, byte) in gen_into.iter_mut().enumerate() {
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if (i + 1) % (LINE_LEN + 1) != 0 {
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*byte = lookup_table[rng.gen() as usize];
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}
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}
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}
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let write_out = {
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if length >= BLOCK_LEN { &mut *block }
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else if length % (LINE_LEN + 1) == 0 { &mut block[..length] }
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else { &mut block[..length + 1] }
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};
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*write_out.last_mut().unwrap() = b'\n';
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loop {
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match submitter.lock().unwrap().submit(write_out, block_num) {
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Some(result) => { try!(result); break; }
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None => std::thread::yield_now()
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}
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}
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block_num += block_stride;
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rng = rng.future((BLOCK_THOROUGHPUT * (block_stride - 1)) as u32);
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length = length.saturating_sub(BLOCK_LEN * (block_stride - 1));
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length = length.saturating_sub(BLOCK_LEN);
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}
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Ok(())
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}
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fn run<W: io::Write + Send + 'static>(writer: W) -> io::Result<()> {
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let n = std::env::args_os().nth(1)
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.and_then(|s| s.into_string().ok())
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.and_then(|n| n.parse().ok())
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.unwrap_or(1000);
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let rng = &mut Rng::new();
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// Use automatic buffering for the static version...
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let mut writer = io::BufWriter::with_capacity(STDIN_BUF, writer);
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try!(fasta_static(&mut writer, b">ONE Homo sapiens alu\n", ALU, n * 2));
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// ...but the dynamic version does its own buffering already
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let writer = try!(writer.into_inner());
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let submitter = Arc::new(Mutex::new(BlockSubmitter { writer: writer, waiting_on: 0 }));
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{ submitter.lock().unwrap().waiting_on = 0; }
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try!(fasta(&submitter, b">TWO IUB ambiguity codes\n", &IUB, rng, n * 3));
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{ submitter.lock().unwrap().waiting_on = 0; }
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try!(fasta(&submitter, b">THREE Homo sapiens frequency\n", &HOMOSAPIENS, rng, n * 5));
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Ok(())
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}
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fn main() {
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let res = if env::var_os("RUST_BENCH").is_some() {
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let mut file = BufWriter::new(File::create("./shootout-fasta.data").unwrap());
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run(&mut file)
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} else {
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run(&mut io::stdout())
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};
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res.unwrap()
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run(io::stdout()).unwrap()
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}
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