-
-
Notifications
You must be signed in to change notification settings - Fork 693
/
Copy pathdense.rs
278 lines (245 loc) · 8.84 KB
/
dense.rs
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
use std::io::{self, Write};
use common::BinarySerializable;
use crate::column_index::optional_index::{SelectCursor, Set, SetCodec, ELEMENTS_PER_BLOCK};
#[inline(always)]
fn get_bit_at(input: u64, n: u16) -> bool {
input & (1 << n) != 0
}
#[inline]
fn set_bit_at(input: &mut u64, n: u16) {
*input |= 1 << n;
}
/// For the `DenseCodec`, `data` which contains the encoded blocks.
/// Each block consists of [u8; 12]. The first 8 bytes is a bitvec for 64 elements.
/// The last 4 bytes are the offset, the number of set bits so far.
///
/// When translating the original index to a dense index, the correct block can be computed
/// directly `orig_idx/64`. Inside the block the position is `orig_idx%64`.
///
/// When translating a dense index to the original index, we can use the offset to find the correct
/// block. Direct computation is not possible, but we can employ a linear or binary search.
const ELEMENTS_PER_MINI_BLOCK: u16 = 64;
const MINI_BLOCK_BITVEC_NUM_BYTES: usize = 8;
const MINI_BLOCK_OFFSET_NUM_BYTES: usize = 2;
pub const MINI_BLOCK_NUM_BYTES: usize = MINI_BLOCK_BITVEC_NUM_BYTES + MINI_BLOCK_OFFSET_NUM_BYTES;
/// Number of bytes in a dense block.
pub const DENSE_BLOCK_NUM_BYTES: u32 =
(ELEMENTS_PER_BLOCK / ELEMENTS_PER_MINI_BLOCK as u32) * MINI_BLOCK_NUM_BYTES as u32;
pub struct DenseBlockCodec;
impl SetCodec for DenseBlockCodec {
type Item = u16;
type Reader<'a> = DenseBlock<'a>;
fn serialize(els: impl Iterator<Item = u16>, wrt: impl io::Write) -> io::Result<()> {
serialize_dense_codec(els, wrt)
}
#[inline]
fn open(data: &[u8]) -> Self::Reader<'_> {
assert_eq!(data.len(), DENSE_BLOCK_NUM_BYTES as usize);
DenseBlock(data)
}
}
/// Interpreting the bitvec as a set of integer within 0..=63
/// and given an element, returns the number of elements in the
/// set lesser than the element.
///
/// # Panics
///
/// May panic or return a wrong result if el <= 64.
#[inline(always)]
fn rank_u64(bitvec: u64, el: u16) -> u16 {
debug_assert!(el < 64);
let mask = (1u64 << el) - 1;
let masked_bitvec = bitvec & mask;
masked_bitvec.count_ones() as u16
}
#[inline(always)]
fn select_u64(mut bitvec: u64, rank: u16) -> u16 {
for _ in 0..rank {
bitvec &= bitvec - 1;
}
bitvec.trailing_zeros() as u16
}
// TODO test the following solution on Intel... on Ryzen Zen <3 it is a catastrophy.
// #[target_feature(enable = "bmi2")]
// unsafe fn select_bitvec_unsafe(bitvec: u64, rank: u16) -> u16 {
// let pdep = _pdep_u64(1u64 << rank, bitvec);
// pdep.trailing_zeros() as u16
// }
#[derive(Clone, Copy, Debug)]
struct DenseMiniBlock {
bitvec: u64,
rank: u16,
}
impl DenseMiniBlock {
fn from_bytes(data: [u8; MINI_BLOCK_NUM_BYTES]) -> Self {
let bitvec = u64::from_le_bytes(data[..MINI_BLOCK_BITVEC_NUM_BYTES].try_into().unwrap());
let rank = u16::from_le_bytes(data[MINI_BLOCK_BITVEC_NUM_BYTES..].try_into().unwrap());
Self { bitvec, rank }
}
fn to_bytes(self) -> [u8; MINI_BLOCK_NUM_BYTES] {
let mut bytes = [0u8; MINI_BLOCK_NUM_BYTES];
bytes[..MINI_BLOCK_BITVEC_NUM_BYTES].copy_from_slice(&self.bitvec.to_le_bytes());
bytes[MINI_BLOCK_BITVEC_NUM_BYTES..].copy_from_slice(&self.rank.to_le_bytes());
bytes
}
}
#[derive(Copy, Clone)]
pub struct DenseBlock<'a>(&'a [u8]);
pub struct DenseBlockSelectCursor<'a> {
block_id: u16,
dense_block: DenseBlock<'a>,
}
impl SelectCursor<u16> for DenseBlockSelectCursor<'_> {
#[inline]
fn select(&mut self, rank: u16) -> u16 {
self.block_id = self
.dense_block
.find_miniblock_containing_rank(rank, self.block_id)
.unwrap();
let index_block = self.dense_block.mini_block(self.block_id);
let in_block_rank = rank - index_block.rank;
self.block_id * ELEMENTS_PER_MINI_BLOCK + select_u64(index_block.bitvec, in_block_rank)
}
}
impl<'a> Set<u16> for DenseBlock<'a> {
type SelectCursor<'b>
= DenseBlockSelectCursor<'a>
where Self: 'b;
#[inline(always)]
fn contains(&self, el: u16) -> bool {
let mini_block_id = el / ELEMENTS_PER_MINI_BLOCK;
let bitvec = self.mini_block(mini_block_id).bitvec;
let pos_in_bitvec = el % ELEMENTS_PER_MINI_BLOCK;
get_bit_at(bitvec, pos_in_bitvec)
}
#[inline(always)]
fn rank_if_exists(&self, el: u16) -> Option<u16> {
let block_pos = el / ELEMENTS_PER_MINI_BLOCK;
let index_block = self.mini_block(block_pos);
let pos_in_block_bit_vec = el % ELEMENTS_PER_MINI_BLOCK;
let ones_in_block = rank_u64(index_block.bitvec, pos_in_block_bit_vec);
let rank = index_block.rank + ones_in_block;
if get_bit_at(index_block.bitvec, pos_in_block_bit_vec) {
Some(rank)
} else {
None
}
}
#[inline(always)]
fn rank(&self, el: u16) -> u16 {
let block_pos = el / ELEMENTS_PER_MINI_BLOCK;
let index_block = self.mini_block(block_pos);
let pos_in_block_bit_vec = el % ELEMENTS_PER_MINI_BLOCK;
let ones_in_block = rank_u64(index_block.bitvec, pos_in_block_bit_vec);
index_block.rank + ones_in_block
}
#[inline(always)]
fn select(&self, rank: u16) -> u16 {
let block_id = self.find_miniblock_containing_rank(rank, 0).unwrap();
let index_block = self.mini_block(block_id);
let in_block_rank = rank - index_block.rank;
block_id * ELEMENTS_PER_MINI_BLOCK + select_u64(index_block.bitvec, in_block_rank)
}
#[inline(always)]
fn select_cursor(&self) -> Self::SelectCursor<'_> {
DenseBlockSelectCursor {
block_id: 0,
dense_block: *self,
}
}
}
impl DenseBlock<'_> {
#[inline]
fn mini_block(&self, mini_block_id: u16) -> DenseMiniBlock {
let data_start_pos = mini_block_id as usize * MINI_BLOCK_NUM_BYTES;
DenseMiniBlock::from_bytes(
self.0[data_start_pos..data_start_pos + MINI_BLOCK_NUM_BYTES]
.try_into()
.unwrap(),
)
}
#[inline]
fn iter_miniblocks(
&self,
from_block_id: u16,
) -> impl Iterator<Item = (u16, DenseMiniBlock)> + '_ {
self.0
.chunks_exact(MINI_BLOCK_NUM_BYTES)
.enumerate()
.skip(from_block_id as usize)
.map(|(block_id, bytes)| {
let mini_block = DenseMiniBlock::from_bytes(bytes.try_into().unwrap());
(block_id as u16, mini_block)
})
}
/// Finds the block position containing the dense_idx.
///
/// # Correctness
/// dense_idx needs to be smaller than the number of values in the index
///
/// The last offset number is equal to the number of values in the index.
#[inline]
fn find_miniblock_containing_rank(&self, rank: u16, from_block_id: u16) -> Option<u16> {
self.iter_miniblocks(from_block_id)
.take_while(|(_, block)| block.rank <= rank)
.map(|(block_id, _)| block_id)
.last()
}
}
/// Iterator over all values, true if set, otherwise false
pub fn serialize_dense_codec(
els: impl Iterator<Item = u16>,
mut output: impl Write,
) -> io::Result<()> {
let mut non_null_rows_before: u16 = 0u16;
let mut block = 0u64;
let mut current_block_id = 0u16;
for el in els {
let block_id = el / ELEMENTS_PER_MINI_BLOCK;
let in_offset = el % ELEMENTS_PER_MINI_BLOCK;
while block_id > current_block_id {
let dense_mini_block = DenseMiniBlock {
bitvec: block,
rank: non_null_rows_before,
};
output.write_all(&dense_mini_block.to_bytes())?;
non_null_rows_before += block.count_ones() as u16;
block = 0u64;
current_block_id += 1u16;
}
set_bit_at(&mut block, in_offset);
}
while current_block_id <= u16::MAX / ELEMENTS_PER_MINI_BLOCK {
block.serialize(&mut output)?;
non_null_rows_before.serialize(&mut output)?;
// This will overflow to 0 exactly if all bits are set.
// This is however not problem as we won't use this last value.
non_null_rows_before = non_null_rows_before.wrapping_add(block.count_ones() as u16);
block = 0u64;
current_block_id += 1u16;
}
Ok(())
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn test_select_bitvec() {
assert_eq!(select_u64(1u64, 0), 0);
assert_eq!(select_u64(2u64, 0), 1);
assert_eq!(select_u64(4u64, 0), 2);
assert_eq!(select_u64(8u64, 0), 3);
assert_eq!(select_u64(1 | 8u64, 0), 0);
assert_eq!(select_u64(1 | 8u64, 1), 3);
}
#[test]
fn test_count_ones() {
for i in 0..=63 {
assert_eq!(rank_u64(u64::MAX, i), i);
}
}
#[test]
fn test_dense() {
assert_eq!(DENSE_BLOCK_NUM_BYTES, 10_240);
}
}