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lophat-0.1.0/Cargo.toml

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+[package]
+name = "lophat"
+version = "0.1.0"
+edition = "2021"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+[lib]
+name = "lophat"
+crate-type = ["cdylib"]
+
+[dependencies]
+crossbeam = "0.8.2"
+pinboard = "2.1.0"
+pyo3 = "0.18.1"
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lophat-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2023 Thomas Chaplin
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

lophat-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: lophat
+Version: 0.1.0
+Classifier: Programming Language :: Rust
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+License-File: LICENSE
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+
+<div align="center">
+
+<h1>LoPHAT</h1>
+
+<b>Lo</b>ckfree <b>P</b>ersistent <b>H</b>omology <b>A</b>lgorithm <b>T</b>oolbox
+
+</div>
+
+## Overview
+
+LoPHAT is a Rust library implementing the lockfree algorithm for computing persistent homology (PH), introduced in [[1]](#1).
+Python bindings are provided via PyO3, with an interface familiar to those who have used PHAT [[2]](#2).
+
+The primary goal of this library is to make the algorithm accessible to those wishing to compute PH of ___arbitrary filtered chain complexes___.
+In particular, LoPHAT is **not** specialised to compute PH of common filtrations or even filtered simplicial complexes.
+As such, you should expect LoPHAT to under-perform as compared to [giotto-ph [3]](#3) or [oineus  [4]](#4), both of which use the algorithm of [[1]](#1).
+
+The only changes from the algorithm described in [[1]](#1) are:
+* We use the `pinboard` library for memory managment of the matrices.
+* We store the $j^{th}$ column of $R$ and $V$ alongside each other in memory, allowing a full $R=DV$ decomposition (rather than just computing pairings).
+* Rather than split the matrix into chunks, we use a work-stealing paradigm, via the `rayon` library.
+
+> **Warning**
+> LoPHAT is currently in alpha.
+> The implementation is not optimised, the API is not fixed and no tests have been written.
+> Use at your own risk.
+
+## Usage
+
+## References
+
+<a id="1">[1]</a> Morozov, Dmitriy, and Arnur Nigmetov.
+"Towards lockfree persistent homology."
+Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures. 2020.
+
+<a id="2">[2]</a> Bauer, Ulrich, et al.
+"Phat–persistent homology algorithms toolbox." Journal of symbolic computation 78 (2017): 76-90.
+[Bitbucket](https://bitbucket.org/phat-code/phat/src/master/)
+
+<a id="3">[3]</a> Pérez, Julián Burella, et al.
+"giotto-ph: A python library for high-performance computation of persistent homology of Vietoris-Rips filtrations."
+arXiv preprint [arXiv:2107.05412](https://arxiv.org/abs/2107.05412) (2021).
+[GitHub](https://github.com/giotto-ai/giotto-ph)
+
+<a id="4">[4]</a> Nigmetov, Arnur, Morozov, Dmitriy, and USDOE.
+Oineus v1.0. Computer software.
+[https://www.osti.gov//servlets/purl/1774764](https://www.osti.gov//servlets/purl/1774764). USDOE. 1 Apr. 2021.
+Web. [doi:10.11578/dc.20210407.1](https://doi.org/10.11578/dc.20210407.1). [GitHub](https://github.com/anigmetov/oineus)
+

lophat-0.1.0/README.md

@@ -0,0 +1,48 @@
+<div align="center">
+
+<h1>LoPHAT</h1>
+
+<b>Lo</b>ckfree <b>P</b>ersistent <b>H</b>omology <b>A</b>lgorithm <b>T</b>oolbox
+
+</div>
+
+## Overview
+
+LoPHAT is a Rust library implementing the lockfree algorithm for computing persistent homology (PH), introduced in [[1]](#1).
+Python bindings are provided via PyO3, with an interface familiar to those who have used PHAT [[2]](#2).
+
+The primary goal of this library is to make the algorithm accessible to those wishing to compute PH of ___arbitrary filtered chain complexes___.
+In particular, LoPHAT is **not** specialised to compute PH of common filtrations or even filtered simplicial complexes.
+As such, you should expect LoPHAT to under-perform as compared to [giotto-ph [3]](#3) or [oineus  [4]](#4), both of which use the algorithm of [[1]](#1).
+
+The only changes from the algorithm described in [[1]](#1) are:
+* We use the `pinboard` library for memory managment of the matrices.
+* We store the $j^{th}$ column of $R$ and $V$ alongside each other in memory, allowing a full $R=DV$ decomposition (rather than just computing pairings).
+* Rather than split the matrix into chunks, we use a work-stealing paradigm, via the `rayon` library.
+
+> **Warning**
+> LoPHAT is currently in alpha.
+> The implementation is not optimised, the API is not fixed and no tests have been written.
+> Use at your own risk.
+
+## Usage
+
+## References
+
+<a id="1">[1]</a> Morozov, Dmitriy, and Arnur Nigmetov.
+"Towards lockfree persistent homology."
+Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures. 2020.
+
+<a id="2">[2]</a> Bauer, Ulrich, et al.
+"Phat–persistent homology algorithms toolbox." Journal of symbolic computation 78 (2017): 76-90.
+[Bitbucket](https://bitbucket.org/phat-code/phat/src/master/)
+
+<a id="3">[3]</a> Pérez, Julián Burella, et al.
+"giotto-ph: A python library for high-performance computation of persistent homology of Vietoris-Rips filtrations."
+arXiv preprint [arXiv:2107.05412](https://arxiv.org/abs/2107.05412) (2021).
+[GitHub](https://github.com/giotto-ai/giotto-ph)
+
+<a id="4">[4]</a> Nigmetov, Arnur, Morozov, Dmitriy, and USDOE.
+Oineus v1.0. Computer software.
+[https://www.osti.gov//servlets/purl/1774764](https://www.osti.gov//servlets/purl/1774764). USDOE. 1 Apr. 2021.
+Web. [doi:10.11578/dc.20210407.1](https://doi.org/10.11578/dc.20210407.1). [GitHub](https://github.com/anigmetov/oineus)

lophat-0.1.0/pyproject.toml

@@ -0,0 +1,16 @@
+[build-system]
+requires = ["maturin>=0.14,<0.15"]
+build-backend = "maturin"
+
+[project]
+name = "lophat"
+requires-python = ">=3.7"
+classifiers = [
+    "Programming Language :: Rust",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+]
+
+
+[tool.maturin]
+features = ["pyo3/extension-module"]

lophat-0.1.0/src/column.rs

@@ -0,0 +1,55 @@
+use std::cmp::Ordering;
+
+pub trait Column: Sync + Clone + Send + Default {
+    fn pivot(&self) -> Option<usize>;
+    fn add_col(&mut self, other: &Self);
+    fn add_entry(&mut self, entry: usize);
+}
+
+#[derive(Debug, Default, Clone)]
+pub struct VecColumn {
+    pub internal: Vec<usize>,
+}
+
+impl VecColumn {
+    // Returns the index where we should try to insert next entry
+    fn add_entry_starting_at(&mut self, entry: usize, starting_idx: usize) -> usize {
+        let mut working_idx = starting_idx;
+        while let Some(value_at_idx) = self.internal.iter().nth(working_idx) {
+            match value_at_idx.cmp(&entry) {
+                Ordering::Less => {
+                    working_idx += 1;
+                    continue;
+                }
+                Ordering::Equal => {
+                    self.internal.remove(working_idx);
+                    return working_idx;
+                }
+                Ordering::Greater => {
+                    self.internal.insert(working_idx, entry);
+                    return working_idx + 1;
+                }
+            }
+        }
+        // Bigger than all idxs in col - add to end
+        self.internal.push(entry);
+        return self.internal.len() - 1;
+    }
+}
+
+impl Column for VecColumn {
+    fn pivot(&self) -> Option<usize> {
+        self.internal.iter().last().copied()
+    }
+
+    fn add_entry(&mut self, entry: usize) {
+        self.add_entry_starting_at(entry, 0);
+    }
+
+    fn add_col(&mut self, other: &Self) {
+        let mut working_idx = 0;
+        for entry in other.internal.iter() {
+            working_idx = self.add_entry_starting_at(*entry, working_idx);
+        }
+    }
+}

lophat-0.1.0/src/decomposition.rs

@@ -0,0 +1,71 @@
+use crate::Column;
+use pyo3::prelude::*;
+use std::collections::{HashMap, HashSet};
+
+#[pyclass]
+#[derive(Default, Debug, Clone)]
+pub struct PersistenceDiagram {
+    #[pyo3(get)]
+    unpaired: HashSet<usize>,
+    #[pyo3(get)]
+    paired: Vec<(usize, usize)>,
+}
+
+#[derive(Debug, Default)]
+pub struct RVDecomposition<C: Column> {
+    pub r: Vec<C>,
+    pub v: Vec<C>,
+}
+
+fn col_idx_with_same_low<C: Column>(col: &C, low_inverse: &HashMap<usize, usize>) -> Option<usize> {
+    let pivot = col.pivot()?;
+    low_inverse.get(&pivot).copied()
+}
+
+impl<C: Column> RVDecomposition<C> {
+    // Receives column, reduces it with left-to-right addition from R
+    // Adds reduction to self
+    pub fn reduce_column(&mut self, mut column: C, low_inverse: &mut HashMap<usize, usize>) {
+        // v_col tracks how the final reduced column is built up
+        // Currently column contains 1 lot of the latest column in D
+        let mut v_col = C::default();
+        v_col.add_entry(self.r.len());
+        // Reduce the column, keeping track of how we do this in V
+        while let Some(col_idx) = col_idx_with_same_low(&column, &low_inverse) {
+            column.add_col(&self.r[col_idx]);
+            v_col.add_col(&self.v[col_idx]);
+        }
+        // Update low inverse
+        let final_pivot = column.pivot();
+        if let Some(final_pivot) = final_pivot {
+            // This column has a lowest 1 and is being inserted at the end of R
+            low_inverse.insert(final_pivot, self.r.len());
+        }
+        // Push to decomposition
+        self.r.push(column);
+        self.v.push(v_col);
+    }
+
+    pub fn diagram(&self) -> PersistenceDiagram {
+        let mut diagram = PersistenceDiagram::default();
+        for (idx, col) in self.r.iter().enumerate() {
+            if let Some(lowest_idx) = col.pivot() {
+                // Negative column
+                diagram.unpaired.remove(&lowest_idx);
+                diagram.paired.push((lowest_idx, idx))
+            } else {
+                // Positive column
+                diagram.unpaired.insert(idx);
+            }
+        }
+        diagram
+    }
+}
+
+pub fn rv_decompose<C: Column>(matrix: impl Iterator<Item = C>) -> RVDecomposition<C> {
+    let mut low_inverse = HashMap::new();
+    matrix.fold(RVDecomposition::default(), |mut accum, next_col| {
+        accum.reduce_column(next_col, &mut low_inverse);
+        accum
+    })
+}

lophat-0.1.0/src/lib.rs

@@ -0,0 +1,43 @@
+use column::VecColumn;
+use pyo3::prelude::*;
+use pyo3::types::PyIterator;
+
+mod column;
+mod decomposition;
+mod lock_free;
+
+pub use column::Column;
+pub use decomposition::{rv_decompose, PersistenceDiagram, RVDecomposition};
+pub use lock_free::rv_decompose_lock_free;
+
+#[pyfunction]
+fn compute_pairings_serial(matrix: &PyIterator) -> PersistenceDiagram {
+    rv_decompose(matrix.map(|col| {
+        VecColumn {
+            internal: col
+                .and_then(PyAny::extract::<Vec<usize>>)
+                .expect("Column is a list of unsigned integers"),
+        }
+    }))
+    .diagram()
+}
+
+#[pyfunction]
+fn compute_pairings(matrix: &PyIterator) -> PersistenceDiagram {
+    rv_decompose_lock_free(matrix.map(|col| {
+        VecColumn {
+            internal: col
+                .and_then(PyAny::extract::<Vec<usize>>)
+                .expect("Column is a list of unsigned integers"),
+        }
+    }))
+    .diagram()
+}
+
+/// A Python module implemented in Rust.
+#[pymodule]
+fn lophat(_py: Python, m: &PyModule) -> PyResult<()> {
+    m.add_function(wrap_pyfunction!(compute_pairings, m)?)?;
+    m.add_function(wrap_pyfunction!(compute_pairings_serial, m)?)?;
+    Ok(())
+}

lophat-0.1.0/src/lock_free.rs

@@ -0,0 +1,98 @@
+use std::fmt::Debug;
+
+use crate::Column;
+use crate::RVDecomposition;
+
+use crossbeam::atomic::AtomicCell;
+use pinboard::NonEmptyPinboard;
+use rayon::prelude::*;
+
+// Implements do while loop lines 6-9
+fn get_col_with_pivot<C: Column>(
+    l: usize,
+    matrix: &Vec<NonEmptyPinboard<(C, C)>>,
+    pivots: &Vec<AtomicCell<Option<usize>>>,
+) -> Option<(usize, (C, C))> {
+    loop {
+        let piv = pivots[l].load();
+        if let Some(piv) = piv {
+            let cols = matrix[piv].read();
+            if cols.0.pivot() != Some(l) {
+                // Got a column but it now has the wrong pivot; loop again.
+                continue;
+            };
+            // Get column with correct pivot, return to caller.
+            return Some((piv, cols));
+        } else {
+            // There is not yet a column with this pivot, inform caller.
+            return None;
+        }
+    }
+}
+
+fn reduce_column<C: Column>(
+    j: usize,
+    matrix: &Vec<NonEmptyPinboard<(C, C)>>,
+    pivots: &Vec<AtomicCell<Option<usize>>>,
+) {
+    let mut working_j = j;
+    'outer: loop {
+        let mut curr_column = matrix[working_j].read();
+        while let Some(l) = (&curr_column).0.pivot() {
+            let piv_with_column_opt = get_col_with_pivot(l, &matrix, &pivots);
+            if let Some((piv, piv_column)) = piv_with_column_opt {
+                // Lines 17-24
+                if piv < working_j {
+                    curr_column.0.add_col(&piv_column.0);
+                    curr_column.1.add_col(&piv_column.1);
+                } else if piv > working_j {
+                    matrix[working_j].set(curr_column);
+                    if pivots[l]
+                        .compare_exchange(Some(piv), Some(working_j))
+                        .is_ok()
+                    {
+                        working_j = piv;
+                    }
+                    continue 'outer;
+                } else {
+                    panic!()
+                }
+            } else {
+                // piv = -1 case
+                matrix[working_j].set(curr_column);
+                if pivots[l].compare_exchange(None, Some(working_j)).is_ok() {
+                    return;
+                } else {
+                    continue 'outer;
+                }
+            }
+        }
+        // Lines 25-27 (curr_column = 0 clause)
+        if (&curr_column.0).pivot().is_none() {
+            matrix[working_j].set(curr_column);
+            return;
+        }
+    }
+}
+
+pub fn rv_decompose_lock_free<C: Column + Debug + 'static>(
+    matrix: impl Iterator<Item = C>,
+) -> RVDecomposition<C> {
+    let matrix: Vec<_> = matrix
+        .enumerate()
+        .map(|(idx, r_col)| {
+            let mut v_col = C::default();
+            v_col.add_entry(idx);
+            NonEmptyPinboard::new((r_col, v_col))
+        })
+        .collect();
+    let pivots: Vec<_> = (0..matrix.len()).map(|_| AtomicCell::new(None)).collect();
+    // Reduce matrix
+    // TODO: Can we advice rayon to split work in chunks?
+    (0..matrix.len())
+        .into_par_iter()
+        .for_each(|j| reduce_column(j, &matrix, &pivots));
+    // Wrap into RV decomposition
+    let (r, v) = matrix.into_iter().map(|pinboard| pinboard.read()).unzip();
+    RVDecomposition { r, v }
+}