ENH: new function zip_sp_matmul_topn that can zip matrices zip_j A.do…

…t(B_j)

Function will return a zipped matrix Z in CSR format, zip_j C_j, where
Z = [sorted top n results > lower_bound for each row of C_j], where C_j = A.dot(B_j)
and where B has been split row-wise into sub-matrices B_j.

Function only allows for sorted variant of sp_matzip function;
unsorted variant (sorted based on insertion order) cannot be (made) equal to unsorted function on full matrices.
zip_sp_matmul_topn by default sorts by value.

And added python function to zip split matrices.
Plus added two unit tests to test functionality.

NB Skip unit test test_stack_zip_sp_matmul_topn for python 3.8 due to bug in scipy vstack function,
it does not support all data types.

Bump version to 1.0.1

CMakeLists.txt

@@ -42,6 +42,7 @@ set(SDTN_SRC_FILES
     ${SDTN_SRC_PREF}/extension.cpp
     ${SDTN_SRC_PREF}/sp_matmul_bindings.cpp
     ${SDTN_SRC_PREF}/sp_matmul_topn_bindings.cpp
+    ${SDTN_SRC_PREF}/zip_sp_matmul_topn_bindings.cpp
 )
 
 include(FindDependencies)

README.md

@@ -80,6 +80,47 @@ pip install sparse_dot_topn --no-binary sparse_dot_topn
 Building from source can enable architecture specific optimisations and is recommended for those that have a C++ compiler installed.
 See INSTALLATION.md for details.
 
+## Distributing the top-n multiplication of two large O(10M+) sparse matrices over a cluster
+
+The top-n multiplication of two large O(10M+) sparse matrices can be broken down into smaller chunks.
+For example, one may want to split sparse matrices into matrices with just 1M rows, and do the
+the (top-n) multiplication of all those matrix pairs.
+Reasons to do this are to reduce the memory footprint of each pair, and to employ available distributed computing power.
+
+The pairs can be distributed and calculated over a cluster (eg. we use a spark cluster).
+The resulting matrix-products are then zipped and stacked in order to reproduce the full matrix product.
+
+Here's an example how to do this, where we are matching 1000 rows in sparse matrix A against 600 rows in sparse matrix B,
+and both A and B are split into chunks.
+
+```python
+import numpy as np
+import scipy.sparse as sparse
+from sparse_dot_topn import sp_matmul_topn, zip_sp_matmul_topn
+
+# 1a. Example matching 1000 rows in sparse matrix A against 600 rows in sparse matrix B.
+A = sparse.random(1000, 2000, density=0.1, format="csr", dtype=np.float32, random_state=rng)
+B = sparse.random(600, 2000, density=0.1, format="csr", dtype=np.float32, random_state=rng)
+
+# 1b. Reference full matrix product with top-n
+C_ref = sp_matmul_topn(A, B.T, top_n=10, threshold=0.01, sort=True)
+
+# 2a. Split the sparse matrices. Here A is split into three parts, and B into five parts.
+As = [A[i*200:(i+1)*200] for i in range(5)]
+Bs = [B[:100], B[100:300], B[300:]]
+
+# 2b. Perform the top-n multiplication of all sub-matrix pairs, here in a double loop.
+# E.g. all sub-matrix pairs could be distributed over a cluster and multiplied there.
+Cs = [[sp_matmul_topn(Aj, Bi.T, top_n=10, threshold=0.01, sort=True) for Bi in Bs] for Aj in As]
+
+# 2c. top-n zipping of the C-matrices, done over the index of the B sub-matrices.
+Czip = [zip_sp_matmul_topn(top_n=10, C_mats=Cis) for Cis in Cs]
+
+# 2d. stacking over zipped C-matrices, done over the index of the A sub-matrices
+# The resulting matrix C equals C_ref.
+C = sparse.vstack(Czip, dtype=np.float32)
+```
+
 ## Migrating to v1.
 
 **sparse\_dot\_topn** v1 is a significant change from `v0.*` with a new bindings and API.
@@ -147,4 +188,5 @@ You can read about it in a [blog](https://medium.com/@ingwbaa/https-medium-com-i
 * [Stephane Collet](https://github.com/stephanecollot)
 * [Particular Miner](https://github.com/ParticularMiner) (no ING affiliation)
 * [Ralph Urlus](https://github.com/RUrlus)
+* [Max Baak](https://github.com/RUrlus)
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "sparse_dot_topn"
-version = "1.0.0"
+version = "1.0.1"
 description = "This package boosts a sparse matrix multiplication followed by selecting the top-n multiplication"
 readme = "README.md"
 requires-python = ">=3.8"
@@ -135,8 +135,8 @@ select = [
   "RSE",
   # flynt
   "FLY",
-  "CPY001"
 ]
+
 ignore = [
   "E501", # line length
   "PLR0913", # too many arguments

src/sparse_dot_topn/__init__.py

@@ -2,8 +2,16 @@
 import importlib.metadata
 
 __version__ = importlib.metadata.version("sparse_dot_topn")
-from sparse_dot_topn.api import awesome_cossim_topn, sp_matmul, sp_matmul_topn
+from sparse_dot_topn.api import awesome_cossim_topn, sp_matmul, sp_matmul_topn, zip_sp_matmul_topn
 from sparse_dot_topn.lib import _sparse_dot_topn_core as _core
 from sparse_dot_topn.lib._sparse_dot_topn_core import _has_openmp_support
 
-__all__ = ["awesome_cossim_topn", "sp_matmul", "sp_matmul_topn", "_core", "__version__", "_has_openmp_support"]
+__all__ = [
+    "awesome_cossim_topn",
+    "sp_matmul",
+    "sp_matmul_topn",
+    "zip_sp_matmul_topn",
+    "_core",
+    "__version__",
+    "_has_openmp_support",
+]

src/sparse_dot_topn/api.py

@@ -282,3 +282,60 @@ def sp_matmul_topn(
             msg = "sparse_dot_topn: extension was compiled without parallelisation (OpenMP) support, ignoring ``n_threads``"
             warnings.warn(msg, stacklevel=1)
     return csr_matrix(func(**kwargs), shape=(A_nrows, B_ncols))
+
+
+def zip_sp_matmul_topn(top_n: int, C_mats: list[csr_matrix]) -> csr_matrix:
+    """Compute zip-matrix C = zip_i C_i = zip_i A * B_i = A * B whilst only storing the `top_n` elements.
+
+    Combine the sub-matrices together and keep only the `top_n` elements per row.
+
+    Pre-calling this function, matrix B has been split row-wise into chunks B_i, and C_i = A * B_i have been calculated.
+    This function computes C = zip_i C_i, which is equivalent to A * B when only keeping the `top_n` elements.
+    It allows very large matrices to be split and multiplied with a limited memory footprint.
+
+    Args:
+        top_n: the number of results to retain; should be smaller or equal to top_n used to obtain C_mats.
+        C_mats: a list with each C_i sub-matrix, with format csr_matrix.
+
+    Returns:
+        C: zipped result matrix
+
+    Raises:
+        TypeError: when not all elements of `C_mats` is a csr_matrix or trivially convertable
+        ValueError: when not all elements of `C_mats` has the same number of rows
+    """
+    _nrows = []
+    ncols = []
+    data = []
+    indptr = []
+    indices = []
+    for C in C_mats:
+        # check correct type of each C
+        if isinstance(C, (coo_matrix, csc_matrix)):
+            C = C.tocsr(False)
+        elif not isinstance(C, csr_matrix):
+            msg = f"type of `C` must be one of `csr_matrix`, `csc_matrix` or `csr_matrix`, got `{type(C)}`"
+            raise TypeError(msg)
+
+        nrows, c_nc = C.shape
+        _nrows.append(nrows)
+        ncols.append(c_nc)
+        data.append(C.data)
+        indptr.append(C.indptr)
+        indices.append(C.indices)
+
+    if not np.all(np.diff(_nrows) == 0):
+        msg = "Each `C` in `C_mats` should have the same number of rows."
+        raise ValueError(msg)
+
+    return csr_matrix(
+        _core.zip_sp_matmul_topn(
+            top_n=top_n,
+            Z_max_nnz=nrows * top_n,
+            nrows=nrows,
+            B_ncols=np.asarray(ncols, int),
+            data=data,
+            indptr=indptr,
+            indices=indices,
+        )
+    )

src/sparse_dot_topn_core/include/sparse_dot_topn/maxheap.hpp

@@ -96,7 +96,7 @@ class MaxHeap {
     }
 
     /**
-     * \brief Sort the heap accoring to the insertion order.
+     * \brief Sort the heap according to the insertion order.
      *
      * \details Note that calling `insertion_sort` invalidates the heap.
      * Calls should be followed by a call to `reset`.
@@ -106,7 +106,7 @@ class MaxHeap {
     }
 
     /**
-     * \brief Sort the heap accoring to values.
+     * \brief Sort the heap according to values.
      *
      * \details Note that calling `value_sort` invalidates the heap.
      * Calls should be followed by a call to `reset`.

src/sparse_dot_topn_core/include/sparse_dot_topn/sp_matmul_topn.hpp

@@ -19,6 +19,7 @@
 
 #include <algorithm>
 #include <cstring>
+#include <limits>
 #include <memory>
 #include <numeric>
 #include <tuple>

src/sparse_dot_topn_core/include/sparse_dot_topn/zip_sp_matmul_topn.hpp

@@ -0,0 +1,117 @@
+/* Copyright (c) 2023 ING Analytics Wholesale Banking
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *	http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+#pragma once
+
+#include <limits>
+#include <vector>
+
+#include <sparse_dot_topn/common.hpp>
+#include <sparse_dot_topn/maxheap.hpp>
+
+namespace sdtn::core {
+
+/**
+ * \brief Zip and compute Z = zip_j C_j = zip_j A.dot(B_j) keeping only the
+ * top-n of the zipped results.
+ *
+ * \details This function will return a zipped matrix Z in CSR format, zip_j
+ * C_j, where Z = [sorted top n results > lower_bound for each row of C_j],
+ * where C_j = A.dot(B_j) and where B has been split row-wise into sub-matrices
+ * B_j. Note that `C_j` must be `CSR` format where the nonzero elements of the
+ * `i`th row are located in ``data[indptr[i]:indptr[i+1]]``. The column indices
+ * for row `i` are stored in
+ * ``indices[indptr[i]:indptr[i+1]]``.
+ *
+ * \tparam eT   element type of the matrices
+ * \tparam idxT integer type of the index arrays, must be at least 32 bit int
+ * \param[in] top_n the top n values to store
+ * \param[in] nrowsA the number of rows in A
+ * \param[in] ncolsB_vec the number of columns in each B_i sub-matrix
+ * \param[in] C_data_vec vector of the nonzero elements of each C_data_j
+ *     sub-matrix
+ * \param[in] C_indptr_vec vector of arrays containing the row indices for
+ *     `C_data_j` sub-matrices
+ * \param[in] C_indices_vec vector of arrays containing the column indices
+       for the C_j sub-matrices
+ * \param[out] Z_data the nonzero elements of zipped Z matrix
+ * \param[out] Z_indptr array containing the row indices for zipped `Z_data`
+ * \param[out] Z_indices array containing the zipped column indices
+ */
+template <typename eT, typename idxT, iffInt<idxT> = true>
+inline void zip_sp_matmul_topn(
+    const idxT top_n,
+    const idxT nrows,
+    const idxT* B_ncols,
+    const std::vector<const eT*>& C_data,
+    const std::vector<const idxT*>& C_indptrs,
+    const std::vector<const idxT*>& C_indices,
+    eT* __restrict Z_data,
+    idxT* __restrict Z_indptr,
+    idxT* __restrict Z_indices
+) {
+    idxT nnz = 0;
+    Z_indptr[0] = 0;
+    eT* Z_data_head = Z_data;
+    idxT* Z_indices_head = Z_indices;
+    const int n_mat = C_data.size();
+
+    // threshold is already consistent between matrices, so accept every line.
+    auto max_heap = MaxHeap<eT, idxT>(top_n, std::numeric_limits<eT>::min());
+
+    // offset the index when concatenating the C sub-matrices (split by row)
+    std::vector<idxT> offset(n_mat, idxT(0));
+    for (int i = 0; i < n_mat - 1; ++i) {
+        for (int j = i; j < n_mat - 1; ++j) {
+            offset[j + 1] += B_ncols[i];
+        }
+    }
+
+    // concatenate the results of each row, apply top_n and add those results to
+    // the C matrix
+    for (idxT i = 0; i < nrows; ++i) {
+        eT min = max_heap.reset();
+
+        // keep topn of stacked lines for each row insert in reverse order,
+        // similar to the reverse linked list in sp_matmul_topn
+        for (int j = n_mat - 1; j >= 0; --j) {
+            const idxT* C_indptr_j = C_indptrs[j];
+            const idxT* C_indices_j = C_indices[j];
+            for (idxT k = C_indptr_j[i]; k < C_indptr_j[i + 1]; ++k) {
+                eT val = (C_data[j])[k];
+                if (val > min) {
+                    min = max_heap.push_pop(offset[j] + C_indices_j[k], val);
+                }
+            }
+        }
+
+        // sort the heap s.t. the first value is the largest
+        max_heap.value_sort();
+
+        // fill the zipped sparse matrix Z
+        int n_set = max_heap.get_n_set();
+        for (int ii = 0; ii < n_set; ++ii) {
+            *Z_indices_head = max_heap.heap[ii].idx;
+            *Z_data_head = max_heap.heap[ii].val;
+            Z_indices_head++;
+            Z_data_head++;
+        }
+        nnz += n_set;
+        Z_indptr[i + 1] = nnz;
+    }
+}
+
+}  // namespace sdtn::core

src/sparse_dot_topn_core/include/sparse_dot_topn/zip_sp_matmul_topn_bindings.hpp

@@ -0,0 +1,88 @@
+/* Copyright (c) 2023 ING Analytics Wholesale Banking
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *	http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+#pragma once
+
+#include <nanobind/nanobind.h>
+#include <nanobind/ndarray.h>
+#include <nanobind/stl/vector.h>
+
+#include <memory>
+#include <numeric>
+#include <vector>
+
+#include <sparse_dot_topn/common.hpp>
+#include <sparse_dot_topn/maxheap.hpp>
+#include <sparse_dot_topn/zip_sp_matmul_topn.hpp>
+
+namespace sdtn {
+namespace nb = nanobind;
+
+namespace api {
+
+template <typename eT, typename idxT, core::iffInt<idxT> = true>
+inline nb::tuple zip_sp_matmul_topn(
+    const int top_n,
+    const idxT Z_max_nnz,
+    const idxT nrows,
+    const nb_vec<idxT>& B_ncols,
+    const std::vector<nb_vec<eT>>& data,
+    const std::vector<nb_vec<idxT>>& indptr,
+    const std::vector<nb_vec<idxT>>& indices
+) {
+    const int n_mats = B_ncols.size();
+    std::vector<const eT*> data_ptrs;
+    data_ptrs.reserve(n_mats);
+    std::vector<const idxT*> indptr_ptrs;
+    indptr_ptrs.reserve(n_mats);
+    std::vector<const idxT*> indices_ptrs;
+    indices_ptrs.reserve(n_mats);
+
+    for (int i = 0; i < n_mats; ++i) {
+        data_ptrs.push_back(data[i].data());
+        indptr_ptrs.push_back(indptr[i].data());
+        indices_ptrs.push_back(indices[i].data());
+    }
+
+    auto Z_indptr = std::unique_ptr<idxT[]>(new idxT[nrows + 1]);
+    auto Z_indices = std::unique_ptr<idxT>(new idxT[Z_max_nnz]);
+    auto Z_data = std::unique_ptr<eT>(new eT[Z_max_nnz]);
+
+    core::zip_sp_matmul_topn<eT, idxT>(
+        top_n,
+        nrows,
+        B_ncols.data(),
+        data_ptrs,
+        indptr_ptrs,
+        indices_ptrs,
+        Z_data.get(),
+        Z_indptr.get(),
+        Z_indices.get()
+    );
+
+    return nb::make_tuple(
+        to_nbvec<eT>(Z_data.release(), Z_max_nnz),
+        to_nbvec<idxT>(Z_indices.release(), Z_max_nnz),
+        to_nbvec<idxT>(Z_indptr.release(), nrows + 1)
+    );
+}
+}  //  namespace api
+
+namespace bindings {
+void bind_zip_sp_matmul_topn(nb::module_& m);
+}
+
+}  // namespace sdtn