trnsparse 0.1.1__py3-none-any.whl

trnsparse/__init__.py

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+"""
+trnsparse — Sparse matrix operations for AWS Trainium via NKI.
+
+CSR/COO formats, SpMV, SpMM, and integral screening for
+sparse scientific computing. Part of the trnsci scientific computing suite.
+"""
+
+__version__ = "0.1.0"
+
+from .formats import CSRMatrix, COOMatrix, from_dense, from_scipy, eye_sparse
+from .ops import (spmv, spmm, spmv_symmetric, sparse_add, sparse_scale,
+                  sparse_transpose, nnz_per_row)
+from .screening import schwarz_bounds, screen_quartets, density_screen, sparsity_stats
+from .nki import HAS_NKI, set_backend, get_backend
+
+__all__ = [
+    "CSRMatrix", "COOMatrix", "from_dense", "from_scipy", "eye_sparse",
+    "spmv", "spmm", "spmv_symmetric", "sparse_add", "sparse_scale",
+    "sparse_transpose", "nnz_per_row",
+    "schwarz_bounds", "screen_quartets", "density_screen", "sparsity_stats",
+    "HAS_NKI", "set_backend", "get_backend",
+]

trnsparse/formats.py

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+"""
+Sparse matrix formats for Trainium.
+
+CSR (Compressed Sparse Row) and COO (Coordinate) formats with
+conversion routines. CSR is the primary compute format; COO is
+the natural construction format.
+
+For quantum chemistry: the two-electron integral tensor (μν|λσ) is
+extremely sparse after Schwarz screening — typically >99% zero for
+large molecules. Storing and operating on it in dense format is
+the difference between O(N⁴) and O(N²) effective cost.
+"""
+
+from __future__ import annotations
+
+import torch
+from typing import Optional, Tuple
+from dataclasses import dataclass
+
+
+@dataclass
+class CSRMatrix:
+    """Compressed Sparse Row format.
+
+    For an m×n matrix with nnz non-zeros:
+        values: (nnz,) — non-zero values
+        col_indices: (nnz,) — column index for each value
+        row_ptrs: (m+1,) — row_ptrs[i]:row_ptrs[i+1] span row i's entries
+        shape: (m, n)
+    """
+    values: torch.Tensor
+    col_indices: torch.Tensor
+    row_ptrs: torch.Tensor
+    shape: Tuple[int, int]
+
+    @property
+    def nnz(self) -> int:
+        return self.values.shape[0]
+
+    @property
+    def dtype(self) -> torch.dtype:
+        return self.values.dtype
+
+    @property
+    def density(self) -> float:
+        return self.nnz / (self.shape[0] * self.shape[1])
+
+    def to_dense(self) -> torch.Tensor:
+        """Convert to dense tensor."""
+        m, n = self.shape
+        dense = torch.zeros(m, n, dtype=self.dtype)
+        for i in range(m):
+            start, end = self.row_ptrs[i].item(), self.row_ptrs[i + 1].item()
+            cols = self.col_indices[start:end]
+            vals = self.values[start:end]
+            dense[i, cols] = vals
+        return dense
+
+    def to_coo(self) -> COOMatrix:
+        """Convert to COO format."""
+        rows = []
+        for i in range(self.shape[0]):
+            start, end = self.row_ptrs[i].item(), self.row_ptrs[i + 1].item()
+            rows.extend([i] * (end - start))
+        return COOMatrix(
+            values=self.values.clone(),
+            row_indices=torch.tensor(rows, dtype=torch.long),
+            col_indices=self.col_indices.clone(),
+            shape=self.shape,
+        )
+
+    def __repr__(self) -> str:
+        return f"CSRMatrix(shape={self.shape}, nnz={self.nnz}, density={self.density:.4f})"
+
+
+@dataclass
+class COOMatrix:
+    """Coordinate (triplet) format.
+
+    values: (nnz,) — non-zero values
+    row_indices: (nnz,) — row index for each value
+    col_indices: (nnz,) — column index for each value
+    shape: (m, n)
+    """
+    values: torch.Tensor
+    row_indices: torch.Tensor
+    col_indices: torch.Tensor
+    shape: Tuple[int, int]
+
+    @property
+    def nnz(self) -> int:
+        return self.values.shape[0]
+
+    @property
+    def dtype(self) -> torch.dtype:
+        return self.values.dtype
+
+    @property
+    def density(self) -> float:
+        return self.nnz / (self.shape[0] * self.shape[1])
+
+    def to_dense(self) -> torch.Tensor:
+        m, n = self.shape
+        dense = torch.zeros(m, n, dtype=self.dtype)
+        dense[self.row_indices, self.col_indices] = self.values
+        return dense
+
+    def to_csr(self) -> CSRMatrix:
+        """Convert to CSR format."""
+        m, n = self.shape
+        # Sort by row then column
+        sort_idx = torch.argsort(self.row_indices * n + self.col_indices)
+        sorted_rows = self.row_indices[sort_idx]
+        sorted_cols = self.col_indices[sort_idx]
+        sorted_vals = self.values[sort_idx]
+
+        # Build row pointers
+        row_ptrs = torch.zeros(m + 1, dtype=torch.long)
+        for r in sorted_rows:
+            row_ptrs[r + 1] += 1
+        row_ptrs = torch.cumsum(row_ptrs, dim=0)
+
+        return CSRMatrix(
+            values=sorted_vals,
+            col_indices=sorted_cols,
+            row_ptrs=row_ptrs,
+            shape=self.shape,
+        )
+
+    def __repr__(self) -> str:
+        return f"COOMatrix(shape={self.shape}, nnz={self.nnz}, density={self.density:.4f})"
+
+
+# --- Construction helpers ---
+
+def from_dense(A: torch.Tensor, threshold: float = 0.0) -> CSRMatrix:
+    """Convert dense matrix to CSR, dropping values with |v| <= threshold."""
+    m, n = A.shape
+    mask = torch.abs(A) > threshold
+    rows, cols = torch.where(mask)
+    vals = A[mask]
+
+    # Build CSR
+    coo = COOMatrix(values=vals, row_indices=rows, col_indices=cols, shape=(m, n))
+    return coo.to_csr()
+
+
+def from_scipy(sp_matrix) -> CSRMatrix:
+    """Convert scipy.sparse matrix to CSRMatrix."""
+    import scipy.sparse as sp
+    csr = sp.csr_matrix(sp_matrix)
+    return CSRMatrix(
+        values=torch.tensor(csr.data, dtype=torch.float32),
+        col_indices=torch.tensor(csr.indices, dtype=torch.long),
+        row_ptrs=torch.tensor(csr.indptr, dtype=torch.long),
+        shape=csr.shape,
+    )
+
+
+def eye_sparse(n: int, dtype: torch.dtype = torch.float32) -> CSRMatrix:
+    """Sparse identity matrix."""
+    return CSRMatrix(
+        values=torch.ones(n, dtype=dtype),
+        col_indices=torch.arange(n, dtype=torch.long),
+        row_ptrs=torch.arange(n + 1, dtype=torch.long),
+        shape=(n, n),
+    )

trnsparse/nki/__init__.py

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+"""NKI dispatch for sparse operations."""
+from .dispatch import HAS_NKI, set_backend, get_backend
+__all__ = ["HAS_NKI", "set_backend", "get_backend"]

trnsparse/nki/dispatch.py

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+"""
+NKI dispatch for sparse operations.
+
+SpMM is the primary NKI target: gather non-zero column indices into
+dense tiles, run matmul on Tensor Engine, scatter results.
+
+The gather/scatter pattern uses the DMA engine for indirect memory
+access, while the matmul runs on the systolic array. This is the
+same pattern used in sparse attention implementations.
+"""
+
+from __future__ import annotations
+
+try:
+    import neuronxcc.nki as nki
+    import neuronxcc.nki.language as nl
+    HAS_NKI = True
+except ImportError:
+    HAS_NKI = False
+
+_backend = "auto"
+
+
+def set_backend(backend: str):
+    global _backend
+    assert backend in ("auto", "pytorch", "nki")
+    if backend == "nki" and not HAS_NKI:
+        raise RuntimeError("NKI backend requires neuronxcc")
+    _backend = backend
+
+
+def get_backend() -> str:
+    return _backend
+
+
+def _use_nki() -> bool:
+    if _backend == "nki":
+        return True
+    if _backend == "pytorch":
+        return False
+    return HAS_NKI

trnsparse/ops.py

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+"""
+Sparse matrix operations for Trainium.
+
+SpMV (sparse × dense vector), SpMM (sparse × dense matrix),
+sparse addition, and sparse scaling.
+
+For quantum chemistry:
+- SpMV: Fock matrix × MO vector in iterative eigensolvers (CG/Davidson)
+- SpMM: Sparse integral tensor × dense MO coefficient matrix
+- Sparse add: Accumulating screened integral contributions
+
+On Trainium, SpMV/SpMM map to gather-matmul patterns on the Tensor Engine:
+gather non-zero rows/cols into dense tiles, matmul, scatter back.
+"""
+
+from __future__ import annotations
+
+import torch
+from typing import Optional
+
+from .formats import CSRMatrix, COOMatrix
+
+
+def spmv(A: CSRMatrix, x: torch.Tensor, alpha: float = 1.0,
+         y: Optional[torch.Tensor] = None, beta: float = 0.0) -> torch.Tensor:
+    """Sparse matrix × dense vector: y = alpha * A @ x + beta * y
+
+    CSR row-wise dot products — each row's non-zeros dot with
+    corresponding entries of x.
+    """
+    m, n = A.shape
+    assert x.shape[0] == n, f"Dimension mismatch: A is {A.shape}, x is {x.shape}"
+
+    result = torch.zeros(m, dtype=A.dtype)
+    for i in range(m):
+        start = A.row_ptrs[i].item()
+        end = A.row_ptrs[i + 1].item()
+        if start < end:
+            cols = A.col_indices[start:end]
+            vals = A.values[start:end]
+            result[i] = torch.dot(vals, x[cols])
+
+    result = alpha * result
+    if y is not None and beta != 0.0:
+        result = result + beta * y
+    return result
+
+
+def spmm(A: CSRMatrix, B: torch.Tensor, alpha: float = 1.0,
+         C: Optional[torch.Tensor] = None, beta: float = 0.0) -> torch.Tensor:
+    """Sparse matrix × dense matrix: C = alpha * A @ B + beta * C
+
+    Each row of A selects and weights rows of B.
+    On NKI: gather selected B rows into dense tile, matmul, scatter.
+    """
+    m, n = A.shape
+    k = B.shape[1]
+    assert B.shape[0] == n, f"Dimension mismatch: A is {A.shape}, B is {B.shape}"
+
+    result = torch.zeros(m, k, dtype=A.dtype)
+    for i in range(m):
+        start = A.row_ptrs[i].item()
+        end = A.row_ptrs[i + 1].item()
+        if start < end:
+            cols = A.col_indices[start:end]
+            vals = A.values[start:end]
+            # vals (nnz_row,) × B[cols] (nnz_row, k) → (k,)
+            result[i] = vals @ B[cols]
+
+    result = alpha * result
+    if C is not None and beta != 0.0:
+        result = result + beta * C
+    return result
+
+
+def spmv_symmetric(A: CSRMatrix, x: torch.Tensor, alpha: float = 1.0,
+                   uplo: str = "upper") -> torch.Tensor:
+    """Symmetric sparse matrix × vector using only stored triangle.
+
+    For symmetric matrices (like the overlap matrix S or density P),
+    only half the non-zeros need to be stored. This computes A @ x
+    using only the upper or lower triangle entries.
+    """
+    m, n = A.shape
+    assert m == n, "Matrix must be square for symmetric SpMV"
+    result = torch.zeros(m, dtype=A.dtype)
+
+    for i in range(m):
+        start = A.row_ptrs[i].item()
+        end = A.row_ptrs[i + 1].item()
+        for idx in range(start, end):
+            j = A.col_indices[idx].item()
+            v = A.values[idx].item()
+            result[i] += v * x[j]
+            if i != j:
+                result[j] += v * x[i]  # Symmetric contribution
+
+    return alpha * result
+
+
+def sparse_add(A: CSRMatrix, B: CSRMatrix, alpha: float = 1.0, beta: float = 1.0) -> CSRMatrix:
+    """Sparse matrix addition: C = alpha * A + beta * B
+
+    Result may have more non-zeros than either input (union of patterns).
+    """
+    assert A.shape == B.shape, f"Shape mismatch: {A.shape} vs {B.shape}"
+    # Simple implementation via dense (fine for moderate sizes)
+    dense = alpha * A.to_dense() + beta * B.to_dense()
+    from .formats import from_dense
+    return from_dense(dense, threshold=0.0)
+
+
+def sparse_scale(A: CSRMatrix, alpha: float) -> CSRMatrix:
+    """Scale sparse matrix: B = alpha * A"""
+    return CSRMatrix(
+        values=alpha * A.values,
+        col_indices=A.col_indices.clone(),
+        row_ptrs=A.row_ptrs.clone(),
+        shape=A.shape,
+    )
+
+
+def sparse_transpose(A: CSRMatrix) -> CSRMatrix:
+    """Transpose sparse matrix (CSR → CSR of A^T)."""
+    coo = A.to_coo()
+    transposed = COOMatrix(
+        values=coo.values,
+        row_indices=coo.col_indices,
+        col_indices=coo.row_indices,
+        shape=(A.shape[1], A.shape[0]),
+    )
+    return transposed.to_csr()
+
+
+def nnz_per_row(A: CSRMatrix) -> torch.Tensor:
+    """Number of non-zeros per row."""
+    return A.row_ptrs[1:] - A.row_ptrs[:-1]

trnsparse/screening.py

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+"""
+Integral screening utilities for sparse quantum chemistry.
+
+Schwarz screening: |(μν|λσ)| ≤ √(μν|μν) √(λσ|λσ)
+Density screening: |P_λσ (μν|λσ)| ≤ |P_λσ| Q_μν Q_λσ
+
+These bounds determine which shell quartets contribute significantly
+to the Fock matrix, turning O(N⁴) integral evaluation into O(N²) for
+large molecules. The sparsity pattern feeds into trnsparse CSR matrices.
+"""
+
+from __future__ import annotations
+
+import torch
+from typing import Tuple
+
+from .formats import CSRMatrix, from_dense
+
+
+def schwarz_bounds(diagonal_integrals: torch.Tensor) -> torch.Tensor:
+    """Compute Schwarz upper bounds Q_μν = √(μν|μν).
+
+    Args:
+        diagonal_integrals: (nshells, nshells) diagonal ERI values (μν|μν)
+
+    Returns:
+        Q: (nshells, nshells) Schwarz bounds
+    """
+    return torch.sqrt(torch.abs(diagonal_integrals))
+
+
+def screen_quartets(
+    Q: torch.Tensor,
+    threshold: float = 1e-10,
+) -> torch.Tensor:
+    """Screen shell quartets using Schwarz inequality.
+
+    Returns a boolean mask (nshells, nshells) for significant shell pairs.
+    A quartet (μν|λσ) is significant if Q_μν * Q_λσ > threshold.
+    """
+    # Significant pairs: Q_μν > √threshold (since Q_μν * Q_λσ > threshold)
+    pair_threshold = threshold ** 0.5
+    return Q > pair_threshold
+
+
+def density_screen(
+    Q: torch.Tensor,
+    P: torch.Tensor,
+    threshold: float = 1e-10,
+) -> torch.Tensor:
+    """Density-weighted screening.
+
+    A quartet contributes if |P_λσ| * Q_μν * Q_λσ > threshold.
+    Returns significant (μν) mask given density P and bounds Q.
+
+    Args:
+        Q: (n, n) Schwarz bounds
+        P: (n, n) density matrix
+        threshold: screening threshold
+
+    Returns:
+        mask: (n, n) boolean — True for significant shell pairs
+    """
+    # Max |P_λσ * Q_λσ| over λσ gives the bound for each μν
+    PQ = torch.abs(P) * Q
+    max_PQ = PQ.max()  # Conservative: use global max
+    return Q * max_PQ > threshold
+
+
+def sparsity_stats(Q: torch.Tensor, threshold: float = 1e-10) -> dict:
+    """Report sparsity statistics for a set of Schwarz bounds.
+
+    Returns dict with total quartets, significant quartets, sparsity fraction.
+    """
+    n = Q.shape[0]
+    mask = screen_quartets(Q, threshold)
+    n_sig_pairs = mask.sum().item()
+    n_total_pairs = n * n
+    n_total_quartets = n_total_pairs * n_total_pairs
+    n_sig_quartets = n_sig_pairs * n_sig_pairs  # Upper bound
+
+    return {
+        "n_shells": n,
+        "total_pairs": n_total_pairs,
+        "significant_pairs": n_sig_pairs,
+        "pair_sparsity": 1.0 - n_sig_pairs / n_total_pairs,
+        "total_quartets": n_total_quartets,
+        "significant_quartets_upper": n_sig_quartets,
+        "quartet_sparsity_lower": 1.0 - n_sig_quartets / n_total_quartets,
+    }

trnsparse-0.1.1.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: trnsparse
+Version: 0.1.1
+Summary: Sparse matrix operations for AWS Trainium via NKI
+Author-email: Scott Friedman <3011922+scttfrdmn@users.noreply.github.com>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/trnsci/trnsparse
+Project-URL: Repository, https://github.com/trnsci/trnsparse
+Project-URL: Issues, https://github.com/trnsci/trnsparse/issues
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torch>=2.1
+Requires-Dist: numpy>=1.24
+Provides-Extra: neuron
+Requires-Dist: neuronxcc>=2.24; extra == "neuron"
+Requires-Dist: torch-neuronx>=2.9; extra == "neuron"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-benchmark>=4.0; extra == "dev"
+Requires-Dist: scipy>=1.11; extra == "dev"
+Dynamic: license-file
+
+# trnsparse
+
+[![CI](https://github.com/trnsci/trnsparse/actions/workflows/ci.yml/badge.svg)](https://github.com/trnsci/trnsparse/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/trnsparse)](https://pypi.org/project/trnsparse/)
+[![Python](https://img.shields.io/pypi/pyversions/trnsparse)](https://pypi.org/project/trnsparse/)
+[![License](https://img.shields.io/github/license/trnsci/trnsparse)](LICENSE)
+[![Docs](https://img.shields.io/badge/docs-mkdocs-blue)](https://trnsci.github.io/trnsparse/)
+
+Sparse matrix operations for AWS Trainium via NKI.
+
+CSR/COO formats, SpMV, SpMM, and integral screening for sparse scientific computing on Trainium. Part of the trnsci scientific computing suite ([github.com/trnsci](https://github.com/trnsci)).
+
+## Install
+
+```bash
+pip install trnsparse
+```
+
+## Usage
+
+```python
+import torch
+import trnsparse
+
+# Dense → sparse
+A = torch.randn(100, 100)
+A[torch.abs(A) < 1.0] = 0.0
+csr = trnsparse.from_dense(A)
+
+# SpMV: y = A @ x
+y = trnsparse.spmv(csr, x, alpha=2.0)
+
+# SpMM: C = A @ B
+C = trnsparse.spmm(csr, B)
+
+# Integral screening
+Q = trnsparse.schwarz_bounds(diagonal_integrals)
+mask = trnsparse.screen_quartets(Q, threshold=1e-10)
+stats = trnsparse.sparsity_stats(Q)
+```
+
+## Operations
+
+| Operation | Description |
+|-----------|-------------|
+| `spmv` | Sparse × dense vector |
+| `spmm` | Sparse × dense matrix |
+| `spmv_symmetric` | Symmetric SpMV (half storage) |
+| `sparse_add` | C = αA + βB |
+| `sparse_scale` | B = αA |
+| `sparse_transpose` | A^T |
+| `schwarz_bounds` | Schwarz screening bounds |
+| `screen_quartets` | Shell quartet significance mask |
+| `density_screen` | Density-weighted screening |
+
+## License
+
+Apache 2.0 — Copyright 2026 Scott Friedman

trnsparse-0.1.1.dist-info/RECORD

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+trnsparse-0.1.1.dist-info/RECORD,,

trnsparse-0.1.1.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

trnsparse-0.1.1.dist-info/licenses/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   Copyright 2026 Scott Friedman
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
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trnsparse-0.1.1.dist-info/top_level.txt

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+trnsparse