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junikimm717BenBrock
junikimm717
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BenBrock
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implement tensors in binsparse (#21)
* dev environment * read tensor implemented * segfault debugging * tensor writer implemented TODO: you need to apparently set the format key. * tensor reader/writer successfully bootstrapped * testing framework for tensor read/write implemented * tests fixed * parse transposes too * json reading/writing adjusted for binsparse compliance * change to shared library * so it turns out that we need int32 indices * change everything to int32 * make ready for pr * Fix formatting * add cmakelists back in * Add Tensor tests to CI --------- Co-authored-by: Benjamin Brock <[email protected]>
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‎.github/workflows/ci.yml‎

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@@ -24,36 +24,35 @@ jobs:
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- name: Checks
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uses: pre-commit/[email protected]
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gcc:
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build:
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runs-on: 'ubuntu-latest'
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strategy:
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matrix:
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include:
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- cc: gcc-12
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cxx: g++-12
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- cc: clang
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cxx: clang++
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name: ${{ matrix.cc }}
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env:
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CXX: g++-12
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CC: gcc-12
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CC: ${{ matrix.cc }}
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CXX: ${{ matrix.cxx }}
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steps:
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- uses: actions/checkout@v4
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- name: CMake
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run: |
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sudo apt-get update
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sudo apt-get install libhdf5-dev $CXX $CC
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sudo apt-get install libhdf5-dev gcc-12 g++-12 clang
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cmake -B build
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- name: Build
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run: VERBOSE=true make -C build -j `nproc`
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- name: Test
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run: ctest --test-dir ./build/test/bash
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clang:
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runs-on: 'ubuntu-latest'
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env:
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CXX: clang++
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CC: clang
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steps:
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- uses: actions/checkout@v4
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- name: CMake
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run: |
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sudo apt-get update
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sudo apt-get install libhdf5-dev clang
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cmake -B build
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- name: Build
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run: VERBOSE=true make -C build -j `nproc`
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- name: Test
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- name: Matrix Tests
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run: ctest --test-dir ./build/test/bash
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- name: Install Julia
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run: curl -fsSL https://install.julialang.org | sh -s -- -y
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- name: Disable Julia precompilation
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run: julia -e 'using Pkg; Pkg.add(["PrecompileTools", "Preferences"]); using PrecompileTools, Preferences; set_preferences!(PrecompileTools, "precompile_workloads" => false; force=true)'
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- name: Install Julia Packages
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run: julia -e 'using Pkg; Pkg.add(["Finch", "HDF5"])'
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- name: Tensor Tests
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run: ctest --test-dir ./build/test/julia

‎.gitignore‎

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@@ -5,4 +5,6 @@
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scripts
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venv
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build*
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compile_flags.txt
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._*
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tensor_test_files

‎CMakeLists.txt‎

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@@ -46,11 +46,6 @@ target_include_directories(${PROJECT_NAME}
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$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
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${HDF5_INCLUDE_DIRS})
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if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
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add_subdirectory(examples)
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add_subdirectory(test)
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endif()
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# Installation rules - these are always needed when the library is built
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install(TARGETS binsparse
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EXPORT binsparse-targets
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"${CMAKE_CURRENT_BINARY_DIR}/binsparse-config.cmake"
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"${CMAKE_CURRENT_BINARY_DIR}/binsparse-config-version.cmake"
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DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/binsparse)
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if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
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add_subdirectory(examples)
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add_subdirectory(test)
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endif()

‎examples/CMakeLists.txt‎

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@@ -19,5 +19,6 @@ add_example(bsp-ls)
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add_example(benchmark_read)
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add_example(benchmark_read_parallel)
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add_example(benchmark_write)
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add_example(tensor_test)
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add_subdirectory(cpp)

‎examples/cpp/CMakeLists.txt‎

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@@ -15,5 +15,6 @@ add_example(mtx2bsp)
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add_example(bsp2mtx)
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add_example(check_equivalence)
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add_example(bsp-ls)
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add_example(tensor_test)
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add_example(benchmark_read)
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add_example(benchmark_write)

‎examples/cpp/tensor_test.cpp‎

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/*
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* SPDX-FileCopyrightText: 2024 Binsparse Developers
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*
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* SPDX-License-Identifier: BSD-3-Clause
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*/
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#include "../tensor_test.c"

‎examples/simple_read.c‎

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#include <binsparse/binsparse.h>
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int main(int argc, char** argv) {
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char* file_name = "test.hdf5";
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char* file_name = (char*) "test.hdf5";
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hid_t f = H5Fopen(file_name, H5F_ACC_RDWR, H5P_DEFAULT);
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‎examples/tensor_test.c‎

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/*
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* SPDX-FileCopyrightText: 2024 Binsparse Developers
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*
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* SPDX-License-Identifier: BSD-3-Clause
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*/
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#include <binsparse/read_tensor.h>
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#include <binsparse/tensor.h>
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#include <binsparse/write_tensor.h>
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int main(int argc, char** argv) {
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if (argc < 3) {
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fprintf(stderr,
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"usage: ./tensor_test [file_name.h5] [output_file_name.h5]\n");
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return 1;
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}
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char* file_name = argv[1];
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bsp_tensor_t tensor = bsp_read_tensor(argv[1], NULL);
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printf("rank: %d\n", tensor.rank);
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printf("dims:");
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for (int i = 0; i < tensor.rank; i++) {
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printf("%ld, ", tensor.dims[i]);
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}
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printf("\n");
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bsp_write_tensor(argv[2], tensor, NULL, NULL, 9);
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bsp_destroy_tensor_t(tensor);
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return 0;
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}

‎include/binsparse/read_tensor.h‎

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/*
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* SPDX-FileCopyrightText: 2024 Binsparse Developers
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*
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* SPDX-License-Identifier: BSD-3-Clause
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*/
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#pragma once
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#include <binsparse/tensor.h>
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#ifndef __cplusplus
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#include <stddef.h>
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#else
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#include <cstddef>
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#endif
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#ifdef __cplusplus
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extern "C" {
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#endif
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char* key_with_index(const char* key, size_t index);
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#ifdef BSP_USE_HDF5
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#include <hdf5.h>
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bsp_tensor_t bsp_read_tensor_from_group(hid_t f);
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#endif
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bsp_tensor_t bsp_read_tensor(const char* file_name, const char* group);
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#ifdef __cplusplus
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}
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#endif

‎include/binsparse/tensor.h‎

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/*
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* SPDX-FileCopyrightText: 2024 Binsparse Developers
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*
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* SPDX-License-Identifier: BSD-3-Clause
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*/
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#pragma once
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#include <binsparse/array.h>
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#include <binsparse/structure.h>
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typedef enum {
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BSP_TENSOR_SPARSE = 0,
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BSP_TENSOR_DENSE = 1,
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BSP_TENSOR_ELEMENT = 2,
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} bsp_level_kind_t;
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typedef struct {
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bsp_level_kind_t kind;
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// data here should be bsp_element_t*, bsp_sparse_t*, or bsp_dense_t*
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void* data;
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} bsp_level_t;
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// corresponds to BSP_TENSOR_ELEMENT
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typedef struct {
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bsp_array_t values;
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} bsp_element_t;
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// corresponds to BSP_TENSOR_SPARSE
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typedef struct {
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int rank;
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// pointers_to, while it will only ever point to one bsp_array_t, must be kept
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// as a pointer (rather than a struct) because there are cases where it MUST
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// be null.
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bsp_array_t* pointers_to;
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// indices is supposed to be an array of bsp_array_t's.
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bsp_array_t* indices;
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bsp_level_t* child;
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} bsp_sparse_t;
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// corresponds to BSP_TENSOR_DENSE
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typedef struct {
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int rank;
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bsp_level_t* child;
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} bsp_dense_t;
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typedef struct {
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int rank;
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size_t* dims;
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size_t* transpose;
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size_t nnz;
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bool is_iso;
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bsp_level_t* level;
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// don't think too much about this at the moment.
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bsp_structure_t structure;
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} bsp_tensor_t;
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static inline bsp_tensor_t bsp_construct_default_tensor_t() {
60+
bsp_tensor_t tensor;
61+
tensor.structure = BSP_GENERAL;
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tensor.is_iso = false;
63+
tensor.nnz = tensor.rank = 0;
64+
tensor.dims = NULL;
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tensor.transpose = NULL;
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tensor.level = NULL;
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return tensor;
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}
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static void bsp_destroy_level_t(bsp_level_t* level) {
72+
if (level == NULL)
73+
return;
74+
switch (level->kind) {
75+
case BSP_TENSOR_ELEMENT: {
76+
bsp_element_t* element = (bsp_element_t*) level->data;
77+
bsp_destroy_array_t(element->values);
78+
free(element);
79+
break;
80+
}
81+
case BSP_TENSOR_DENSE: {
82+
bsp_dense_t* dense = (bsp_dense_t*) level->data;
83+
bsp_destroy_level_t(dense->child);
84+
free(dense);
85+
break;
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}
87+
case BSP_TENSOR_SPARSE: {
88+
bsp_sparse_t* sparse = (bsp_sparse_t*) level->data;
89+
90+
if (sparse->pointers_to != NULL)
91+
bsp_destroy_array_t(*sparse->pointers_to);
92+
if (sparse->indices != NULL) {
93+
for (int i = 0; i < sparse->rank; i++) {
94+
bsp_destroy_array_t(sparse->indices[i]);
95+
}
96+
}
97+
bsp_destroy_level_t(sparse->child);
98+
free(sparse);
99+
break;
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}
101+
default:;
102+
}
103+
}
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105+
static bsp_array_t bsp_get_tensor_values(bsp_tensor_t tensor) {
106+
bsp_level_t* level = tensor.level;
107+
while (level != NULL) {
108+
switch (level->kind) {
109+
case BSP_TENSOR_ELEMENT: {
110+
bsp_element_t* element = (bsp_element_t*) level->data;
111+
return element->values;
112+
break;
113+
}
114+
case BSP_TENSOR_SPARSE: {
115+
bsp_sparse_t* sparse = (bsp_sparse_t*) level->data;
116+
level = sparse->child;
117+
break;
118+
}
119+
case BSP_TENSOR_DENSE: {
120+
bsp_dense_t* dense = (bsp_dense_t*) level->data;
121+
level = dense->child;
122+
break;
123+
}
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default:;
125+
}
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}
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// this should never happen!
128+
assert(false);
129+
}
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static inline void bsp_destroy_tensor_t(bsp_tensor_t tensor) {
132+
bsp_destroy_level_t(tensor.level);
133+
if (tensor.dims != NULL)
134+
free(tensor.dims);
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if (tensor.transpose != NULL)
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free(tensor.transpose);
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}

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