change fasta benchmark to Veedrac's implementation

This commit is contained in:
Andre Bogus 2015-09-24 11:29:15 +02:00
parent 8fe79bdfda
commit 960e85c8ea

View File

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