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test version with std::simd for Hamming u32*16
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@jean-pierreBoth
jean-pierreBoth committed Nov 20, 2021
1 parent 8802239 commit 1bc3c9a
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Showing 3 changed files with 189 additions and 12 deletions.
5 changes: 5 additions & 0 deletions Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -80,9 +80,14 @@ lazy_static = { version = "1.4"}
log = { version = "0.4"}
env_logger = { version = "0.8"}

packed_simd_2 = { version = "0.3", optional = true}

# for benchmark reading, so the lbrary do not depend on hdf5 nor ndarray
[dev-dependencies]
hdf5 = {version = "0.7"}
ndarray = {version = "0.14"}



[features]
packed_simd_f = [ "packed_simd_2"]
194 changes: 182 additions & 12 deletions src/dist.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@


use std::simd::{u32x16, u64x8, i32x16, i64x8};

use simdeez::avx2::*;
use simdeez::sse2::*;
use simdeez::*;
Expand Down Expand Up @@ -98,7 +100,7 @@ implementL1Distance!(u8);


unsafe fn distance_l1_f32<S: Simd> (va:&[f32], vb: &[f32]) -> f32 {
let mut dist = 0_f32;
let mut dist_simd = S::setzero_ps();
//
let nb_simd = va.len() / S::VF32_WIDTH;
let simd_length = nb_simd * S::VF32_WIDTH;
Expand All @@ -107,10 +109,11 @@ unsafe fn distance_l1_f32<S: Simd> (va:&[f32], vb: &[f32]) -> f32 {
let a = S::loadu_ps(&va[i]);
let b = S::loadu_ps(&vb[i]);
let delta = S::abs_ps(a-b);
dist += S::horizontal_add_ps(delta);
dist_simd += delta;
//
i += S::VF32_WIDTH;
}
let mut dist : f32 = S::horizontal_add_ps(dist_simd);
for i in simd_length..va.len() {
// log::debug!("distance_l1_f32, i {:?} len {:?} nb_simd {:?} VF32_WIDTH {:?}", i, va.len(), nb_simd, S::VF32_WIDTH);
dist += (va[i]- vb[i]).abs();
Expand Down Expand Up @@ -174,20 +177,21 @@ implementL2Distance!(u8);


unsafe fn distance_l2_f32<S: Simd> (va:&[f32], vb: &[f32]) -> f32 {
let mut dist = 0_f32;
//
let nb_simd = va.len() / S::VF32_WIDTH;
let simd_length = nb_simd * S::VF32_WIDTH;
let mut dist_simd = S::setzero_ps();
let mut i = 0;
while i < simd_length {
let a = S::loadu_ps(&va[i]);
let b = S::loadu_ps(&vb[i]);
let mut delta = a-b;
delta *= delta;
dist += S::horizontal_add_ps(delta);
dist_simd = dist_simd + delta;
//
i += S::VF32_WIDTH;
}
let mut dist = S::horizontal_add_ps(dist_simd);
for i in simd_length..va.len() {
dist += (va[i]- vb[i]) * (va[i]- vb[i]);
}
Expand Down Expand Up @@ -294,19 +298,20 @@ macro_rules! implementDotDistance(


unsafe fn distance_dot_f32<S: Simd> (va:&[f32], vb: &[f32]) -> f32 {
let mut dot = 0_f32;
//
let mut i = 0;
let mut dot_simd = S::setzero_ps();
let nb_simd = va.len() / S::VF32_WIDTH;
let simd_length = nb_simd * S::VF32_WIDTH;
while i < simd_length {
let a = S::loadu_ps(&va[i]);
let b = S::loadu_ps(&vb[i]);
let delta = a*b;
dot += S::horizontal_add_ps(delta);
dot_simd += delta;
//
i += S::VF32_WIDTH;
}
let mut dot = S::horizontal_add_ps(dot_simd);
for i in simd_length..va.len() {
dot += va[i]*vb[i];
}
Expand Down Expand Up @@ -393,7 +398,7 @@ implementHellingerDistance!(f64);


unsafe fn distance_hellinger_f32<S: Simd> (va:&[f32], vb: &[f32]) -> f32 {
let mut dist = 0_f32;
let mut dist_simd = S::setzero_ps();
//
let mut i = 0;
let nb_simd = va.len() / S::VF32_WIDTH;
Expand All @@ -403,10 +408,11 @@ unsafe fn distance_hellinger_f32<S: Simd> (va:&[f32], vb: &[f32]) -> f32 {
let b = S::loadu_ps(&vb[i]);
let prod = a * b;
let prod_s = S::sqrt_ps(prod);
dist += S::horizontal_add_ps(prod_s);
dist_simd += prod_s;
//
i += S::VF32_WIDTH;
}
let mut dist = S::horizontal_add_ps(dist_simd);
for i in simd_length..va.len() {
dist += va[i].sqrt() * vb[i].sqrt();
}
Expand Down Expand Up @@ -486,7 +492,7 @@ implementJeffreysDistance!(f64);


unsafe fn distance_jeffreys_f32<S: Simd> (va:&[f32], vb: &[f32]) -> f32 {
let mut dist = 0_f32;
let mut dist_simd = S::setzero_ps();
//
let mut i = 0;
let mut logslice = Vec::<f32>::with_capacity(S::VF32_WIDTH as usize);
Expand All @@ -501,11 +507,12 @@ unsafe fn distance_jeffreys_f32<S: Simd> (va:&[f32], vb: &[f32]) -> f32 {
logslice.push((va[i+j].max(M_MIN)/vb[i+j].max(M_MIN)).ln());
}
let prod_s = delta * S::loadu_ps(&logslice.as_slice()[0]);
dist += S::horizontal_add_ps(prod_s);
dist_simd += prod_s;
logslice.clear();
//
i += S::VF32_WIDTH;
}
let mut dist = S::horizontal_add_ps(dist_simd);
for i in simd_length..va.len() {
if vb[i] > 0. {
dist += (va[i] - vb[i]) * (va[i].max(M_MIN) / vb[i].max(M_MIN)).ln();
Expand Down Expand Up @@ -638,6 +645,59 @@ unsafe fn distance_hamming_i32<S: Simd> (va:&[i32], vb: &[i32]) -> f32 {



//#[cfg(packed_simd_f)]
fn distance_jaccard_u32_16_simd(va:&[u32], vb: &[u32]) -> f32 {
let mut dist_simd = i32x16::splat(0);
//
assert_eq!(va.len(), vb.len());
//
let nb_lanes = 16;
let nb_simd = va.len()/ nb_lanes;
let simd_length = nb_simd * nb_lanes;
//
for i in (0..simd_length).step_by(nb_lanes) {
let a = u32x16::from_slice(&va[i..]);
let b = u32x16::from_slice(&vb[i..]);
// recall a test return 0 if false -1 if true!
let delta = a.lanes_ne(b);
dist_simd = dist_simd - delta.to_int();
}
let mut dist = dist_simd.horizontal_sum();
// residual
for i in simd_length..va.len() {
dist = dist + if va[i] != vb[i] { 1 } else {0};
}
return dist as f32/ va.len() as f32;
} // end of distance_jaccard_u32_simd



fn distance_jaccard_u64_8_simd(va:&[u64], vb: &[u64]) -> f32 {
let mut dist_simd = i64x8::splat(0);
//
assert_eq!(va.len(), vb.len());
//
let nb_lanes = 8;
let nb_simd = va.len()/ nb_lanes;
let simd_length = nb_simd * nb_lanes;
//
for i in (0..simd_length).step_by(nb_lanes) {
let a = u64x8::from_slice(&va[i..]);
let b = u64x8::from_slice(&vb[i..]);
// recall a test return 0 if false -1 if true!
let delta = a.lanes_ne(b);
dist_simd = dist_simd - delta.to_int();
}
let mut dist = dist_simd.horizontal_sum();
// residual
for i in simd_length..va.len() {
dist = dist + if va[i] != vb[i] { 1 } else {0};
}
return dist as f32/ va.len() as f32;
} // end of distance_jaccard_u64_8_simd



impl Distance<i32> for DistHamming {
fn eval(&self, va:&[i32], vb: &[i32]) -> f32 {
//
Expand All @@ -652,11 +712,47 @@ impl Distance<i32> for DistHamming {
}
} // end implementation Distance<i32>



//#[cfg(packed_simd_f)]
impl Distance<u32> for DistHamming {
fn eval(&self, va:&[u32], vb: &[u32]) -> f32 {
//
if is_x86_feature_detected!("avx512f") {
return distance_jaccard_u32_16_simd(va,vb);
}
assert_eq!(va.len(), vb.len());
let dist : f32 = va.iter().zip(vb.iter()).filter(|t| t.0 != t.1).count() as f32;
dist / va.len() as f32
} // end of eval
} // end implementation Distance<u32>



impl Distance<u64> for DistHamming {
fn eval(&self, va:&[u64], vb: &[u64]) -> f32 {
//
if is_x86_feature_detected!("avx512f") {
return distance_jaccard_u64_8_simd(va,vb);
}
assert_eq!(va.len(), vb.len());
let dist : f32 = va.iter().zip(vb.iter()).filter(|t| t.0 != t.1).count() as f32;
dist / va.len() as f32
} // end of eval
} // end implementation Distance<u64>



// i32 is implmeented by simd
implementHammingDistance!(u8);
implementHammingDistance!(u16);
implementHammingDistance!(u32);
implementHammingDistance!(u64);

#[cfg(not(packed_simd_f))]
//implementHammingDistance!(u32);


//implementHammingDistance!(u64);

implementHammingDistance!(i16);


Expand Down Expand Up @@ -834,6 +930,14 @@ mod tests {
use super::*;
use crate::hnsw::*;

fn init_log() -> u64 {
let mut builder = env_logger::Builder::from_default_env();
let _ = builder.is_test(true).try_init();
println!("\n ************** initializing logger *****************\n");
return 1;
}


#[test]
fn test_access_to_dist_l1() {
let distl1 = DistL1;
Expand Down Expand Up @@ -864,6 +968,16 @@ fn have_avx2() {
}
}

#[test]
fn have_avx512f() {
if is_x86_feature_detected!("avx512f") {
println!("I have avx512f");
}
else {
println!(" ************ I DO NOT have avx512f ***************");
}
}

#[test]

fn have_sse2() {
Expand Down Expand Up @@ -1075,6 +1189,8 @@ fn test_jeffreys() {

#[test]
fn test_jensenshannon() {
init_log();
//
let length = 19;
let mut p_data : Vec<f32> = Vec::with_capacity(length);
let mut q_data : Vec<f32> = Vec::with_capacity(length);
Expand Down Expand Up @@ -1122,6 +1238,60 @@ fn test_simd_hamming_i32() {
}
} // end of test test_simd_jaccard_i32

// to run with cargo test --features packed_simd_f -- dist::tests::test_simd_hamming_u32
#[test]
fn test_simd_hamming_u32() {
init_log();
log::info!("testing test_simd_hamming_u32 with packed_simd_2");
//
let size_test = 500;
let imax = 3;
let mut rng = rand::thread_rng();
for i in 4..size_test {
// generer 2 va et vb s des vecteurs<i32> de taille i avec des valeurs entre -imax et + imax et controler les resultat
let between = Uniform::<u32>::from(0..imax);
let va : Vec<u32> = (0..i).into_iter().map( |_| between.sample(&mut rng)).collect();
let vb : Vec<u32> = (0..i).into_iter().map( |_| between.sample(&mut rng)).collect();
let simd_dist = distance_jaccard_u32_16_simd(&va, &vb);

let easy_dist : u32 = va.iter().zip(vb.iter()).map( |(a,b)| if a!=b { 1} else {0}).sum();
let easy_dist = easy_dist as f32 / va.len() as f32;
println!("test size {:?} simd exact = {:?} {:?}", i, simd_dist, easy_dist);
if (easy_dist - simd_dist).abs() > 1.0e-5 {
println!(" jsimd = {:?} , jexact = {:?}", simd_dist, easy_dist);
println!("va = {:?}" , va);
println!("vb = {:?}" , vb);
std::process::exit(1);
}
}
} // end of test_simd_hamming_u32


#[test]
fn test_simd_hamming_u64() {
init_log();
log::info!("testing test_simd_hamming_u32 with packed_simd_2");
//
let size_test = 500;
let imax = 3;
let mut rng = rand::thread_rng();
for i in 4..size_test {
// generer 2 va et vb s des vecteurs<i32> de taille i avec des valeurs entre -imax et + imax et controler les resultat
let between = Uniform::<u64>::from(0..imax);
let va : Vec<u64> = (0..i).into_iter().map( |_| between.sample(&mut rng)).collect();
let vb : Vec<u64> = (0..i).into_iter().map( |_| between.sample(&mut rng)).collect();
let simd_dist = distance_jaccard_u64_8_simd(&va, &vb);

let easy_dist : u64 = va.iter().zip(vb.iter()).map( |(a,b)| if a!=b { 1} else {0}).sum();
let easy_dist = easy_dist as f32 / va.len() as f32;
println!("test size {:?} simd exact = {:?} {:?}", i, simd_dist, easy_dist);
if (easy_dist - simd_dist).abs() > 1.0e-5 {
println!(" jsimd = {:?} , jexact = {:?}", simd_dist, easy_dist);
println!("va = {:?}" , va);
println!("vb = {:?}" , vb);
std::process::exit(1);
}
}
} // end of test_simd_hamming_u64

} // end of module tests
2 changes: 2 additions & 0 deletions src/lib.rs
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
#![feature(portable_simd)]

// for logging (debug mostly, switched at compile time in cargo.toml)
use env_logger::{Builder};
Expand All @@ -6,6 +7,7 @@ use env_logger::{Builder};
extern crate lazy_static;



pub mod hnsw;
pub mod dist;
pub mod hnswio;
Expand Down

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