SpGEMM bad_alloc Error

examples/CMakeLists.txt

@@ -3,4 +3,5 @@ add_subdirectory(range)
 add_subdirectory(saxpy)
 add_subdirectory(spmv)
 add_subdirectory(spmm)
+add_subdirectory(spgemm)
 # end /* Add examples' subdirectories */

examples/spgemm/CMakeLists.txt

@@ -0,0 +1,16 @@
+# begin /* Add application */
+set(SOURCES
+ thread_mapped.cu
+)
+
+foreach(SOURCE IN LISTS SOURCES)
+ get_filename_component(TEST_NAME ${SOURCE} NAME_WLE)
+ add_executable(loops.spgemm.${TEST_NAME} ${SOURCE})
+ target_link_libraries(loops.spgemm.${TEST_NAME} PRIVATE loops)
+ set_target_properties(loops.spgemm.${TEST_NAME} 
+ PROPERTIES 
+ CUDA_ARCHITECTURES ${CMAKE_CUDA_ARCHITECTURES}
+ )
+ message(STATUS "Example Added: loops.spgemm.${TEST_NAME}")
+endforeach()
+# end /* Add application */

examples/spgemm/filter_zeros.ipynb

@@ -0,0 +1,109 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import scipy.io\n",
+ "import scipy.sparse\n",
+ "\n",
+ "import os\n",
+ "from pathlib import Path\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "\n",
+ "\n",
+ "def remove_zeros_and_save(input_file, output_file):\n",
+ " matrix = scipy.io.mmread(input_file)\n",
+ "\n",
+ " rows, cols, data = zip(*[(r, c, d) for r, c, d in zip(matrix.row, matrix.col, matrix.data) if d != 0])\n",
+ "\n",
+ " filtered_matrix = scipy.sparse.coo_matrix((data, (rows, cols)), shape=matrix.shape)\n",
+ "\n",
+ " scipy.io.mmwrite(output_file, filtered_matrix)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Processed matrix saved to /home/ychenfei/research/libs/loops/datasets/filtered_zeros/rma10.mtx\n"
+ ]
+ }
+ ],
+ "source": [
+ "remove_zeros_and_save('/data/toodemuy/datasets/floridaMatrices/rma10.mtx','/home/ychenfei/research/libs/loops/datasets/filtered_zeros/rma10.mtx')\n",
+ "print(f\"Processed matrix saved to {'/home/ychenfei/research/libs/loops/datasets/filtered_zeros/rma10.mtx'}\")\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "remove_zeros_and_save(input_file, output_file)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 22,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def filter_zero_in_bulk(dir):\n",
+ " path = Path(str(dir))\n",
+ " for file in path.iterdir():\n",
+ " # print(str(file))\n",
+ " file = str(file)\n",
+ " if file.endswith(\".mtx\"):\n",
+ " new_file = '/home/ychenfei/research/libs/loops/datasets/filtered_zeros/'+os.path.basename(file)\n",
+ " # print(new_file)\n",
+ " remove_zeros_and_save(file,new_file)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 23,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "filter_zero_in_bulk('/data/toodemuy/datasets/floridaMatrices/')"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.10.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

examples/spgemm/helpers.hxx

@@ -0,0 +1,78 @@
+/**
+ * @file helpers.hxx
+ * @author Muhammad Osama (mosama@ucdavis.edu)
+ * @brief Header file for SpGEMM.
+ * @version 0.1
+ * @copyright Copyright (c) 2022
+ *
+ */
+
+#pragma once
+
+#include <loops/util/generate.hxx>
+#include <loops/container/formats.hxx>
+#include <loops/container/vector.hxx>
+#include <loops/container/market.hxx>
+#include <loops/util/filepath.hxx>
+#include <loops/util/equal.hxx>
+#include <loops/util/device.hxx>
+#include <loops/util/timer.hxx>
+#include <loops/memory.hxx>
+#include <cxxopts.hpp>
+
+#include <algorithm>
+#include <iostream>
+
+struct parameters_t {
+ std::string filename;
+ bool validate;
+ bool verbose;
+ cxxopts::Options options;
+
+ /**
+ * @brief Construct a new parameters object and parse command line arguments.
+ *
+ * @param argc Number of command line arguments.
+ * @param argv Command line arguments.
+ */
+ parameters_t(int argc, char** argv)
+ : options(argv[0], "Sparse Matrix-Matrix Multiplication") {
+ // Add command line options
+ options.add_options()("h,help", "Print help") // help
+ ("m,market", "Matrix file", cxxopts::value<std::string>()) // mtx
+ ("validate", "CPU validation") // validate
+ ("v,verbose", "Verbose output"); // verbose
+
+ // Parse command line arguments
+ auto result = options.parse(argc, argv);
+
+ if (result.count("help") || (result.count("market") == 0)) {
+ std::cout << options.help({""}) << std::endl;
+ std::exit(0);
+ }
+
+ if (result.count("market") == 1) {
+ filename = result["market"].as<std::string>();
+ if (loops::is_market(filename)) {
+ } else {
+ std::cout << options.help({""}) << std::endl;
+ std::exit(0);
+ }
+ } else {
+ std::cout << options.help({""}) << std::endl;
+ std::exit(0);
+ }
+
+ if (result.count("validate") == 1) {
+ validate = true;
+ } else {
+ validate = false;
+ }
+
+ if (result.count("verbose") == 1) {
+ verbose = true;
+ } else {
+ verbose = false;
+ }
+ }
+};

examples/spgemm/run.sh

@@ -0,0 +1,70 @@
+# /home/ychenfei/research/libs/loops/build/bin/loops.spgemm.thread_mapped -m /home/ychenfei/research/sparse_matrix_perf_analysis/spgemm_dataflow_analysis/test_mtx/s100/ck104.mtx
+
+# filepath="/home/ychenfei/research/sparse_matrix_perf_analysis/spgemm_dataflow_analysis/test_mtx2/bcsstk17.mtx"
+# filename=$(basename "$filepath")
+
+# echo "$filename" >> /home/ychenfei/research/libs/loops/examples/spgemm/running_time.txt
+# /home/ychenfei/research/libs/loops/build/bin/loops.spgemm.thread_mapped -m /home/ychenfei/research/sparse_matrix_perf_analysis/spgemm_dataflow_analysis/test_mtx2/bcsstk17.mtx >> /home/ychenfei/research/libs/loops/examples/spgemm/running_time.txt
+
+############## Output matrix C in dense format ##############
+# export_file="/home/ychenfei/research/libs/loops/examples/spgemm/running_time/dense_C/dense_C_running_time_$(date +%Y-%m-%d).txt"
+
+# export_file="/home/ychenfei/research/libs/loops/examples/spgemm/running_time/dense_C/testing.txt"
+
+# exe="/home/ychenfei/research/libs/loops/build/bin/loops.spgemm.thread_mapped"
+
+# > $export_file
+
+# for f in /data/toodemuy/datasets/floridaMatrices/*.mtx
+# do
+# filename=$(basename "$f")
+# echo "$filename" >> $export_file
+# $exe -m $f >> $export_file
+# echo >> $export_file
+# done
+
+
+############## Count the nnz of input matrices without explicit zeros ##############
+# export_file="/home/ychenfei/research/libs/loops/examples/spgemm/running_time/nnz_C/non_explicit_zeros.txt"
+
+# exe="/home/ychenfei/research/libs/loops/build/bin/loops.spgemm.thread_mapped"
+
+# > $export_file
+
+# for f in /home/ychenfei/research/libs/loops/datasets/non_explicit_zeros/*.mtx
+# do
+# filename=$(basename "$f")
+# echo "$filename" >> $export_file
+# $exe -m $f >> $export_file
+# echo >> $export_file
+# done
+
+############## Count the explicit zeros from the input matrices when applying SpGEMM ##############
+export_file="/home/ychenfei/research/libs/loops/examples/spgemm/export_mtx/nnz_C/explicit_zeros.txt"
+
+exe="/home/ychenfei/research/libs/loops/build/bin/loops.spgemm.thread_mapped"
+
+> $export_file
+
+for f in /data/toodemuy/datasets/floridaMatrices/*.mtx
+do
+ filename=$(basename "$f")
+ echo "$filename" >> $export_file
+ $exe -m $f >> $export_file
+ echo >> $export_file
+done
+
+############## Count the NNZ of C with input matrices have explicit zeros ##############
+# export_file="/home/ychenfei/research/libs/loops/examples/spgemm/export_mtx/nnz_C/nnz_C_explicit_zeros_$(date +%Y-%m-%d).txt"
+
+# exe="/home/ychenfei/research/libs/loops/build/bin/loops.spgemm.thread_mapped"
+
+# > $export_file
+
+# for f in /data/toodemuy/datasets/floridaMatrices/*.mtx
+# do
+# filename=$(basename "$f")
+# echo "$filename" >> $export_file
+# $exe -m $f >> $export_file
+# echo >> $export_file
+# done

examples/spgemm/running_time.txt

@@ -0,0 +1,7 @@
+bcsstk17.mtx
+Elapsed (ms): 2458.75
+
+cant.mtx
+Elapsed (ms): 27056
+
+consph.mtx

examples/spgemm/running_time/dense_C/running_time_2023-11-06.txt

@@ -0,0 +1,20 @@
+bcsstk17.mtx
+Elapsed (ms): 2130.66
+
+cant.mtx
+Elapsed (ms): 23811.8
+
+consph.mtx
+Elapsed (ms): 48775.6
+
+mac_econ_fwd500.mtx
+
+pwtk.mtx
+
+rma10.mtx
+Elapsed (ms): 14880.4
+
+scircuit.mtx
+
+shipsec1.mtx
+

examples/spgemm/running_time/dense_C/testing.txt

@@ -0,0 +1,20 @@
+bcsstk17.mtx
+Elapsed (ms): 0.012288
+
+cant.mtx
+Elapsed (ms): 0.01536
+
+consph.mtx
+Elapsed (ms): 0.015328
+
+mac_econ_fwd500.mtx
+
+pwtk.mtx
+
+rma10.mtx
+Elapsed (ms): 0.018432
+
+scircuit.mtx
+
+shipsec1.mtx
+