Update to add SPDX identifiers (#13)

* Add SPDX statement to files.

.clang-format

@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2024 Binsparse Developers
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
 ---
 BasedOnStyle: LLVM
 PointerAlignment: Left

.github/workflows/ci.yml

@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2024 Binsparse Developers
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
 name: "CI"
 
 on:

.gitignore

@@ -0,0 +1,8 @@
+# SPDX-FileCopyrightText: 2024 Binsparse Developers
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+scripts
+venv
+build
+._*

.pre-commit-config.yaml

@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2024 Binsparse Developers
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
 repos:
 
 - repo: https://github.com/pre-commit/mirrors-clang-format
@@ -12,3 +16,8 @@ repos:
     - id: end-of-file-fixer
     - id: mixed-line-ending
     - id: check-added-large-files
+
+- repo: https://github.com/fsfe/reuse-tool
+  rev: v2.1.0
+  hooks:
+  - id: reuse

CMakeLists.txt

@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2024 Binsparse Developers
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
 cmake_minimum_required(VERSION 3.5)
 project(binsparse-rc)
 

README.md

@@ -1,3 +1,9 @@
+<!--
+SPDX-FileCopyrightText: 2024 Binsparse Developers
+
+SPDX-License-Identifier: BSD-3-Clause
+-->
+
 # Binsparse C Reference Implementation
 
 This library is a reference implementation of the [binsparse Binary Sparse Format Specification](https://github.com/GraphBLAS/binsparse-specification) written using C.

examples/CMakeLists.txt

@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2024 Binsparse Developers
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
 function(add_example example_name)
   add_executable(${example_name} ${example_name}.c)
   target_link_libraries(${example_name} binsparse-rc)
@@ -10,6 +14,7 @@ add_example(simple_write)
 add_example(mtx2bsp)
 add_example(bsp2mtx)
 add_example(check_equivalence)
+add_example(check_equivalence_parallel)
 add_example(bsp-ls)
 add_example(benchmark_read)
 add_example(benchmark_read_parallel)

examples/benchmark_read.c

@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2024 Binsparse Developers
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 #include <stdlib.h>
 #include <time.h>

examples/benchmark_read_parallel.c

@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2024 Binsparse Developers
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 #include <stdlib.h>
 #include <time.h>
@@ -61,8 +67,9 @@ int main(int argc, char** argv) {
   char* file_name = argv[1];
 
   printf("Opening %s\n", file_name);
+  fflush(stdout);
 
-  const int num_trials = 2;
+  const int num_trials = 10;
 
   int num_threads = 6;
 
@@ -71,11 +78,10 @@ int main(int argc, char** argv) {
   size_t nbytes = 0;
 
   // To flush the filesystem cache before each trial, change to `true`.
-  bool cold_cache = true;
+  bool cold_cache = false;
 
   // If running warm cache experiments, read once to warm cache.
-  if (!cold_cache && false) {
-    printf("Warm cache read...\n");
+  if (!cold_cache) {
     bsp_matrix_t mat = bsp_read_matrix_parallel(file_name, NULL, num_threads);
     bsp_destroy_matrix_t(mat);
   }
@@ -84,6 +90,7 @@ int main(int argc, char** argv) {
     if (cold_cache) {
       flush_cache();
     }
+    fflush(stdout);
     double begin = gettime();
     bsp_matrix_t mat = bsp_read_matrix_parallel(file_name, NULL, num_threads);
     double end = gettime();
@@ -95,6 +102,7 @@ int main(int argc, char** argv) {
     double gbytes = ((double) nbytes) / 1024 / 1024 / 1024;
     double gbytes_s = gbytes / durations[i];
     printf("FORPARSER: %s,%lf,%lf\n", file_name, durations[i], gbytes_s);
+    fflush(stdout);
   }
 
   printf("[");

examples/benchmark_write.c

@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2024 Binsparse Developers
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 #include <stdlib.h>
 #include <time.h>

examples/bsp-ls.c

@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2024 Binsparse Developers
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 
 herr_t visit_group(hid_t loc_id, const char* name, const H5L_info_t* linfo,

examples/bsp2mtx.c

@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2024 Binsparse Developers
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 #include <stdio.h>
 

examples/check_equivalence.c

@@ -1,3 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2024 Binsparse Developers
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 
 int check_array_equivalence(bsp_array_t array1, bsp_array_t array2) {

examples/check_equivalence_parallel.c

@@ -0,0 +1,217 @@
+/*
+ * SPDX-FileCopyrightText: 2024 Binsparse Developers
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
+#include <binsparse/binsparse.h>
+
+int check_array_equivalence(bsp_array_t array1, bsp_array_t array2) {
+  if (array1.size != array2.size) {
+    fprintf(stderr, "Array sizes do not match. %zu != %zu\n", array1.size,
+            array2.size);
+    return 1;
+  }
+
+  if (array1.size == 0) {
+    return 0;
+  }
+
+  bsp_matrix_market_type_t mm_type1 = BSP_MM_REAL;
+
+  if ((array1.type >= BSP_UINT8 && array1.type <= BSP_INT64) ||
+      array1.type == BSP_BINT8) {
+    mm_type1 = BSP_MM_INTEGER;
+  } else if (array1.type >= BSP_FLOAT32 && array1.type <= BSP_FLOAT64) {
+    mm_type1 = BSP_MM_REAL;
+  } else if (array1.type == BSP_COMPLEX_FLOAT32 ||
+             array1.type == BSP_COMPLEX_FLOAT64) {
+    mm_type1 = BSP_MM_COMPLEX;
+  } else {
+    fprintf(stderr, "Unhandled array type.\n");
+    return 2;
+  }
+
+  bsp_matrix_market_type_t mm_type2 = BSP_MM_REAL;
+
+  if ((array2.type >= BSP_UINT8 && array2.type <= BSP_INT64) ||
+      array2.type == BSP_BINT8) {
+    mm_type2 = BSP_MM_INTEGER;
+  } else if (array2.type >= BSP_FLOAT32 && array2.type <= BSP_FLOAT64) {
+    mm_type2 = BSP_MM_REAL;
+  } else if (array2.type == BSP_COMPLEX_FLOAT32 ||
+             array2.type == BSP_COMPLEX_FLOAT64) {
+    mm_type2 = BSP_MM_COMPLEX;
+  } else {
+    fprintf(stderr, "Unhandled array type.\n");
+    return 2;
+  }
+
+  if (mm_type1 != mm_type2) {
+    fprintf(stderr, "Array types do not match.\n");
+    return 3;
+  }
+
+  for (size_t i = 0; i < array1.size; i++) {
+    if (mm_type1 == BSP_MM_INTEGER) {
+      size_t value1, value2;
+      bsp_array_read(array1, i, value1);
+      bsp_array_read(array2, i, value2);
+
+      if (value1 != value2) {
+        fprintf(stderr, "Array values are not equal. (%zu != %zu)\n", value1,
+                value2);
+        return 4;
+      }
+    } else if (mm_type1 == BSP_MM_REAL) {
+      double value1, value2;
+      bsp_array_read(array1, i, value1);
+      bsp_array_read(array2, i, value2);
+
+      if (value1 != value2) {
+        fprintf(stderr, "Array values are not equal. (%.17lg != %.17lg)\n",
+                value1, value2);
+        return 4;
+      }
+    } else if (mm_type1 == BSP_MM_COMPLEX) {
+      double _Complex value1, value2;
+      bsp_array_read(array1, i, value1);
+      bsp_array_read(array2, i, value2);
+
+      if (value1 != value2) {
+        fprintf(stderr,
+                "Array values are not equal. (%.17lg + i%.17lg != %.17lg + "
+                "i%.17lg)\n",
+                __real__ value1, __imag__ value1, __real__ value2,
+                __imag__ value2);
+        return 4;
+      }
+    }
+  }
+
+  return 0;
+}
+
+int main(int argc, char** argv) {
+  if (argc < 3) {
+    printf(
+        "usage: ./check_equivalence [file1.{mtx/hdf5}] [file2.{mtx/hdf5}]\n");
+
+    printf("  Note: the second argument will be read in parallel if it is a "
+           "Binsparse file.\n");
+    return 1;
+  }
+
+  char* file1 = argv[1];
+  char* file2 = argv[2];
+
+  int num_threads = 6;
+
+  bsp_fdataset_info_t info1 = bsp_parse_fdataset_string(argv[1]);
+  bsp_fdataset_info_t info2 = bsp_parse_fdataset_string(argv[2]);
+
+  printf("Matrix 1: %s and %s\n", info1.fname,
+         (info1.dataset == NULL) ? "root" : info1.dataset);
+  printf("Matrix 2: %s and %s\n", info2.fname,
+         (info2.dataset == NULL) ? "root" : info2.dataset);
+
+  fflush(stdout);
+
+  bsp_matrix_t matrix1 = bsp_read_matrix(info1.fname, info1.dataset);
+  bsp_matrix_t matrix2 =
+      bsp_read_matrix_parallel(info2.fname, info2.dataset, num_threads);
+
+  bool perform_suitesparse_declamping = true;
+  if (perform_suitesparse_declamping &&
+      strcmp(bsp_get_file_extension(file1), ".mtx") == 0) {
+    bsp_matrix_declamp_values(matrix1);
+  }
+
+  if (perform_suitesparse_declamping &&
+      strcmp(bsp_get_file_extension(file2), ".mtx") == 0) {
+    bsp_matrix_declamp_values(matrix2);
+  }
+
+  // If matrices are not the same format, try to convert.
+  if (matrix1.format != matrix2.format) {
+    if (matrix1.format != BSP_COOR) {
+      bsp_matrix_t intermediate = bsp_convert_matrix(matrix1, BSP_COOR);
+      bsp_destroy_matrix_t(matrix1);
+      matrix1 = intermediate;
+    }
+
+    if (matrix2.format != BSP_COOR) {
+      bsp_matrix_t intermediate = bsp_convert_matrix(matrix2, BSP_COOR);
+      bsp_destroy_matrix_t(matrix2);
+      matrix2 = intermediate;
+    }
+  }
+
+  if (matrix1.format != matrix2.format) {
+    fprintf(stderr, "Formats do not match. (%s != %s)\n",
+            bsp_get_matrix_format_string(matrix1.format),
+            bsp_get_matrix_format_string(matrix2.format));
+    fprintf(stderr, "FAIL!\n");
+    return 1;
+  }
+
+  if (matrix1.structure != matrix2.structure) {
+    fprintf(stderr, "Structures do not match. (%s != %s)\n",
+            bsp_get_structure_string(matrix1.structure),
+            bsp_get_structure_string(matrix2.structure));
+    fprintf(stderr, "FAIL!\n");
+    return 2;
+  }
+
+  if (matrix1.nrows != matrix2.nrows || matrix1.ncols != matrix2.ncols) {
+    fprintf(stderr, "Dimensions do not match. (%zu, %zu) != (%zu, %zu)\n",
+            matrix1.nrows, matrix1.ncols, matrix2.nrows, matrix2.ncols);
+    fprintf(stderr, "FAIL!\n");
+    return 3;
+  }
+
+  if (matrix1.nnz != matrix2.nnz) {
+    fprintf(stderr, "Number of stored values does not match. %zu != %zu\n",
+            matrix1.nnz, matrix2.nnz);
+    fprintf(stderr, "FAIL!\n");
+    return 4;
+  }
+
+  if (matrix1.is_iso != matrix2.is_iso) {
+    fprintf(stderr, "ISO-ness does not match. %s != %s\n",
+            (matrix1.is_iso) ? "true" : "false",
+            (matrix2.is_iso) ? "true" : "false");
+    fprintf(stderr, "FAIL!\n");
+    return 5;
+  }
+
+  if (check_array_equivalence(matrix1.values, matrix2.values) != 0) {
+    fprintf(stderr, "Value arrays not equivalent.\n");
+    fprintf(stderr, "FAIL!\n");
+    return 6;
+  }
+
+  if (check_array_equivalence(matrix1.indices_0, matrix2.indices_0) != 0) {
+    fprintf(stderr, "Indices_0 arrays not equivalent.\n");
+    fprintf(stderr, "FAIL!\n");
+    return 7;
+  }
+
+  if (check_array_equivalence(matrix1.indices_1, matrix2.indices_1) != 0) {
+    fprintf(stderr, "Indices_1 arrays not equivalent.\n");
+    fprintf(stderr, "FAIL!\n");
+    return 8;
+  }
+
+  if (check_array_equivalence(matrix1.pointers_to_1, matrix2.pointers_to_1) !=
+      0) {
+    fprintf(stderr, "Pointers_to_1 arrays not equivalent.\n");
+    fprintf(stderr, "FAIL!\n");
+    return 9;
+  }
+
+  printf("The files are equivalent.\n");
+  printf("OK!\n");
+
+  return 0;
+}