parallel_processor/memory_fs/
mod.rs

1use rustc_hash::FxHashMap;
2use std::fs::File;
3
4use std::path::{Path, PathBuf};
5
6use std::sync::Arc;
7
8use crate::memory_fs::file::flush::*;
9
10use parking_lot::Mutex;
11
12use crate::memory_data_size::MemoryDataSize;
13use crate::memory_fs::allocator::CHUNKS_ALLOCATOR;
14use crate::memory_fs::file::internal::{MemoryFileInternal, SWAPPABLE_FILES};
15
16pub const O_DIRECT: i32 = 0x4000;
17
18#[macro_use]
19pub mod allocator;
20pub mod file;
21pub mod flushable_buffer;
22pub(crate) mod stats;
23
24static FILES_FLUSH_HASH_MAP: Mutex<Option<FxHashMap<PathBuf, Vec<Arc<(PathBuf, Mutex<File>)>>>>> =
25    Mutex::new(None);
26
27pub struct MemoryFs;
28
29#[derive(Copy, Clone, Debug)]
30pub enum RemoveFileMode {
31    Keep,
32    Remove { remove_fs: bool },
33}
34
35impl MemoryFs {
36    pub fn init(
37        memory_size: MemoryDataSize,
38        flush_queue_size: usize,
39        threads_count: usize,
40        min_chunks_count: usize,
41    ) {
42        let chunk_size = (memory_size / (min_chunks_count as f64)).as_bytes();
43
44        let mut suggested_chunk_size_log = 1;
45
46        while (1 << (suggested_chunk_size_log + 1)) <= chunk_size {
47            suggested_chunk_size_log += 1;
48        }
49
50        CHUNKS_ALLOCATOR.initialize(memory_size, suggested_chunk_size_log, min_chunks_count);
51        *FILES_FLUSH_HASH_MAP.lock() = Some(FxHashMap::with_capacity_and_hasher(
52            8192,
53            Default::default(),
54        ));
55        GlobalFlush::init(flush_queue_size, threads_count);
56    }
57
58    pub fn remove_file(file: impl AsRef<Path>, remove_mode: RemoveFileMode) -> Result<(), ()> {
59        match remove_mode {
60            RemoveFileMode::Keep => {
61                // Do nothing
62                Ok(())
63            }
64            RemoveFileMode::Remove { remove_fs } => {
65                if MemoryFileInternal::delete(file, remove_fs) {
66                    Ok(())
67                } else {
68                    Err(())
69                }
70            }
71        }
72    }
73
74    pub fn get_file_size(file: impl AsRef<Path>) -> Option<usize> {
75        MemoryFileInternal::retrieve_reference(&file)
76            .map(|f| f.read().len())
77            .or_else(|| std::fs::metadata(&file).map(|m| m.len() as usize).ok())
78    }
79
80    pub fn ensure_flushed(file: impl AsRef<Path>) {
81        FILES_FLUSH_HASH_MAP
82            .lock()
83            .as_mut()
84            .unwrap()
85            .remove(&file.as_ref().to_path_buf());
86    }
87
88    pub fn remove_directory(dir: impl AsRef<Path>, remove_fs: bool) -> bool {
89        MemoryFileInternal::delete_directory(dir, remove_fs)
90    }
91
92    pub fn flush_all_to_disk() {
93        GlobalFlush::flush_to_disk();
94    }
95
96    pub fn free_memory() {
97        CHUNKS_ALLOCATOR.giveback_free_memory()
98    }
99
100    pub fn terminate() {
101        GlobalFlush::terminate();
102        CHUNKS_ALLOCATOR.deinitialize();
103    }
104
105    pub fn get_stats() -> stats::MemoryFsStats {
106        stats::get_stats()
107    }
108
109    pub fn stats_reset() {
110        stats::reset();
111    }
112
113    pub fn reduce_pressure() -> bool {
114        // crate::log_info!("Reducing pressure!");
115        let (current, max_size) = GlobalFlush::global_queue_occupation();
116        if current * 3 < max_size {
117            let mut map_lock = SWAPPABLE_FILES.lock();
118            if let Some(file) = map_lock.get_next() {
119                drop(map_lock);
120                let mut file = file.write();
121                file.change_to_disk_only();
122                file.flush_chunks(usize::MAX);
123                return true;
124            }
125        }
126
127        return !GlobalFlush::is_queue_empty();
128    }
129}
130
131#[cfg(test)]
132mod tests {
133    use crate::memory_data_size::MemoryDataSize;
134    use crate::memory_fs::file::flush::GlobalFlush;
135    use crate::memory_fs::file::internal::MemoryFileMode;
136    use crate::memory_fs::file::reader::FileReader;
137    use crate::memory_fs::file::writer::FileWriter;
138    use crate::memory_fs::MemoryFs;
139    use rayon::prelude::*;
140    use std::io::{Read, Seek, SeekFrom, Write};
141
142    #[test]
143    #[ignore]
144    pub fn memory_fs_test() {
145        MemoryFs::init(MemoryDataSize::from_mebioctets(100 * 1024), 1024, 3, 0);
146        let data = (0..3337).map(|x| (x % 256) as u8).collect::<Vec<u8>>();
147
148        (0..400).into_par_iter().for_each(|i: u32| {
149            crate::log_info!("Writing file {}", i);
150            let mut file = FileWriter::create(
151                format!("/home/andrea/genome-assembly/test1234/{}.tmp", i),
152                MemoryFileMode::PreferMemory { swap_priority: 3 },
153            );
154            for _ in 0..(1024 * 64) {
155                file.write(data.as_slice()).unwrap();
156            }
157            drop(file);
158            let mut file2 = FileReader::open(
159                format!("/home/andrea/genome-assembly/test1234/{}.tmp", i),
160                None,
161            )
162            .unwrap();
163
164            file2.seek(SeekFrom::Start(17 + 3337 * 12374)).unwrap();
165            let mut buffer = [0; 4];
166            file2.read_exact(&mut buffer).unwrap();
167            assert_eq!(&buffer, &data[17..21]);
168        });
169
170        GlobalFlush::flush_to_disk();
171
172        (0..400).into_par_iter().for_each(|i: u32| {
173            crate::log_info!("Reading file {}", i);
174            let mut datar = vec![0; 3337];
175            let mut file = FileReader::open(
176                format!("/home/andrea/genome-assembly/test1234/{}.tmp", i),
177                None,
178            )
179            .unwrap();
180            for _ in 0..(1024 * 64) {
181                file.read_exact(datar.as_mut_slice()).unwrap();
182                assert_eq!(datar, data);
183            }
184            assert_eq!(file.read(datar.as_mut_slice()).unwrap(), 0);
185            crate::log_info!("Read file {}", i);
186        });
187
188        MemoryFs::terminate();
189    }
190}
parallel_processor/memory_fs/mod.rs

parallel_processor/memory_fs/
mod.rs
