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‎.gitignore‎

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build/
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examples/*.perm

‎CMakeLists.txt‎

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cmake_minimum_required(VERSION 3.22)
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project(ParAMD VERSION 1.0 LANGUAGES C CXX)
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# Default to Release build
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if(NOT CMAKE_BUILD_TYPE)
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set(CMAKE_BUILD_TYPE Release CACHE STRING "Build type" FORCE)
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endif()
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# Set C++ standard
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set(CMAKE_CXX_STANDARD 17)
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set(CMAKE_CXX_STANDARD_REQUIRED ON)
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# Set the installation path SuiteSparse is installed
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set(SUITESPARSE_ROOT "" CACHE PATH "Path to the SuiteSparse installation")
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# Add preprocessor macro if SuiteSparse is installed
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if (SUITESPARSE_ROOT)
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message(STATUS "SuiteSparse root directory: ${SUITESPARSE_ROOT}")
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# Define a preprocessor macro USE_SUITESPARSE to indicate that SuiteSparse is being used
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add_definitions(-DUSE_SUITESPARSE)
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# Set SuiteSparse include and library paths based on SUITESPARSE_ROOT
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set(SUITESPARSE_INCLUDE_DIR "${SUITESPARSE_ROOT}/include")
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set(SUITESPARSE_LIB_DIR_64 "${SUITESPARSE_ROOT}/lib64")
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set(SUITESPARSE_LIB_DIR "${SUITESPARSE_ROOT}/lib")
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# Check that the necessary directories exist
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if (NOT EXISTS "${SUITESPARSE_INCLUDE_DIR}/suitesparse/amd.h")
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message(FATAL_ERROR "SuiteSparse AMD (suitesparse/amd.h) not found!")
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endif()
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if (NOT EXISTS "${SUITESPARSE_LIB_DIR_64}/libamd.so" AND NOT EXISTS "${SUITESPARSE_LIB_DIR_64}/libamd.a")
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if (NOT EXISTS "${SUITESPARSE_LIB_DIR}/libamd.so" AND NOT EXISTS "${SUITESPARSE_LIB_DIR}/libamd.a")
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message(FATAL_ERROR "SuiteSparse library (libamd) not found!")
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endif()
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endif()
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# Find the SuiteSparse AMD library
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find_library(SUITESPARSE_AMD_LIB NAMES amd
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PATHS ${SUITESPARSE_LIB_DIR_64} ${SUITESPARSE_LIB_DIR}
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NO_DEFAULT_PATH
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)
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if (NOT SUITESPARSE_AMD_LIB)
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message(FATAL_ERROR "Could not find SuiteSparse AMD library!")
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endif()
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# Include the SuiteSparse headers
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include_directories(${SUITESPARSE_INCLUDE_DIR})
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else()
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message(STATUS "SUITESPARSE_ROOT not specified, SuiteSparse will not be used.")
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endif()
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include_directories(include)
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set(SOURCES
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src/config.cpp
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src/matrix.cpp
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src/paramd.cpp
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src/utils.cpp
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)
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add_library(paramd_lib SHARED ${SOURCES})
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set_target_properties(paramd_lib PROPERTIES
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OUTPUT_NAME paramd
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VERSION ${PROJECT_VERSION}
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SOVERSION 1
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PUBLIC_HEADER include/paramd/paramd.h
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)
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add_executable(paramd bin/main.cpp)
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target_link_libraries(paramd PRIVATE paramd_lib)
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if (SUITESPARSE_AMD_LIB)
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target_link_libraries(paramd PRIVATE ${SUITESPARSE_AMD_LIB})
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endif()
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find_package(OpenMP REQUIRED)
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if(OpenMP_CXX_FOUND)
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target_link_libraries(paramd_lib PRIVATE OpenMP::OpenMP_CXX)
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target_link_libraries(paramd PRIVATE OpenMP::OpenMP_CXX)
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endif()
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install(TARGETS paramd_lib
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LIBRARY DESTINATION lib
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PUBLIC_HEADER DESTINATION include/paramd
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)
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install(TARGETS paramd
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RUNTIME DESTINATION bin
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)

‎LICENSE‎

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BSD 3-Clause License
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Copyright (c) 2025, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎README.md‎

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‎bin/main.cpp‎

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#include <chrono>
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#include <iostream>
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#include <omp.h>
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#include <string>
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#ifdef USE_SUITESPARSE
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#include "suitesparse/amd.h"
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#endif
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#include "paramd/paramd.h"
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// Display help information
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static void show_help() {
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std::cout << "Usage: paramd [OPTIONS]\n"
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<< "Options:\n"
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<< " -h, --help Show this help message\n"
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<< " --matrix <path> Path to the input matrix in mtx format (required)\n"
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<< " --algo <paramd, amd (if available)> Algorithm to benchmark (default: paramd) \n"
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<< " --mult <double> Multiplicative relaxation factor (default: 1.1)\n"
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<< " --lim <double> Limitation factor (default: 8192), will be divided by #threads\n"
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<< " --mem <double> Extra memory factor (default: 1.5)\n"
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<< " --seed <64-bit integer> Seed used to randomly permute the matrix (default: 1)\n"
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<< " --breakdown Enable time breakdown (default: false)\n"
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<< " --stat Enable statistics (default: false)\n"
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<< " --sym Specify sym if the matrix is known to be symmetric (default: false)\n";
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}
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int main(int argc, char* argv[]) {
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paramd::config config;
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std::string matrix = "", algo = "paramd";
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// Parse arguments
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for (int i = 1; i < argc; i++) {
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std::string arg = argv[i];
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if (arg == "-h" || arg == "--help") {
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show_help();
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return 0;
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} else if (arg == "--matrix" && i + 1 < argc) {
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matrix = std::string(argv[++i]);
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} else if (arg == "--algo" && i + 1 < argc) {
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algo = std::string(argv[++i]);
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if (algo != "amd" && algo != "paramd") {
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std::cerr << algo << " is not in the algo list!" << std::endl;
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show_help();
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exit(1);
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}
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} else if (arg == "--mult" && i + 1 < argc) {
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config.mult = std::stod(argv[++i]);
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} else if (arg == "--lim" && i + 1 < argc) {
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config.lim = std::stod(argv[++i]);
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} else if (arg == "--mem" && i + 1 < argc) {
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config.mem = std::stod(argv[++i]);
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} else if (arg == "--seed" && i + 1 < argc) {
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config.seed = std::stoull(argv[++i]);
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} else if (arg == "--breakdown") {
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config.breakdown = true;
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} else if (arg == "--stat") {
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config.stat = true;
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} else if (arg == "--sym") {
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config.sym = true;
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} else {
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std::cerr << "Unknown option: " << arg << std::endl;
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show_help();
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exit(1);
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}
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}
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if (matrix == "") {
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std::cerr << "Please specify the input matrix!" << std::endl;
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show_help();
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exit(1);
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}
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std::cout << "Reading matrix market file: " << matrix << std::endl;
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paramd::matrix A(matrix);
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std::cout << "Applying random inverse permutation with seed: " << config.seed << std::endl;
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std::vector<paramd::vtype> rand_iperm = paramd::random_inverse_permutation(A.n, config.seed);
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A.apply_inverse_permutation(rand_iperm);
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std::vector<paramd::vtype> perm(A.n);
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std::cout << "Ordering using algorithm: " << algo << std::endl;
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uint64_t fill = 0;
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double start = 0, end = 0;
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if (algo == "paramd") {
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start = omp_get_wtime();
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fill = paramd::paramd(A.n, A.rowptr.data(), A.colidx.data(), perm.data(), config);
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end = omp_get_wtime();
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} else {
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#ifdef USE_SUITESPARSE
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double info[AMD_INFO];
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start = omp_get_wtime();
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amd_order(A.n, A.rowptr.data(), A.colidx.data(), perm.data(), NULL, info);
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end = omp_get_wtime();
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if (info[AMD_STATUS] != AMD_OK) {
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std::cout << "AMD returns errors. Fall back to 64-bit mode" << std::endl;
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int64_t n64 = A.n;
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std::vector<int64_t> rowptr64(A.rowptr.size());
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std::vector<int64_t> colidx64(A.colidx.size());
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std::vector<int64_t> perm64(perm.size());
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#pragma omp parallel for
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for (size_t i = 0; i < rowptr64.size(); ++i)
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rowptr64[i] = A.rowptr[i];
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#pragma omp parallel for
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for (size_t i = 0; i < colidx64.size(); ++i)
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colidx64[i] = A.colidx[i];
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std::cout << "Ordering using algorithm: amd_l" << std::endl;
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start = omp_get_wtime();
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amd_l_order(n64, rowptr64.data(), colidx64.data(), perm64.data(), NULL, info);
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end = omp_get_wtime();
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if (info[AMD_STATUS] != AMD_OK) {
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std::cerr << "AMD returns error code: " << info[AMD_STATUS] << std::endl;
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exit(1);
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}
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#pragma omp parallel for
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for (size_t i = 0; i < A.n; ++i)
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perm[i] = perm64[i];
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}
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fill = uint64_t(info[AMD_LNZ]);
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#else
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std::cerr << "AMD not found. Please specify the AMD installation path via CMake!" << std::endl;
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exit(1);
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#endif
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}
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std::cout << "#Fill = " << fill << std::endl;
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std::cout << "Ordering Time = " << end - start << " seconds" << std::endl;
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std::cout << "Reverting random inverse permutation with seed: " << config.seed << std::endl;
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std::vector<paramd::vtype> rand_perm = paramd::inverse_permutation(rand_iperm);
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perm = paramd::apply_function(perm, rand_perm);
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std::string out_perm_fp = matrix + ".perm";
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std::cout << "Writing permutation to: " << out_perm_fp << std::endl;
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paramd::write_perm(out_perm_fp, perm);
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return 0;
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}

‎environment.yml‎

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name: paramd-benchmarks
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channels:
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- conda-forge
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dependencies:
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- cmake>=3.22
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- python>=3.13
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- matplotlib>=3.10.1
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- numpy>=2.2.5
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- pandas>=2.2.3
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- seaborn>=0.13.2

‎examples/dumbbell.mtx‎

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%%MatrixMarket matrix coordinate real symmetric
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10 10 25
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1 1 4
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2 1 -1
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3 1 -1
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4 1 -1
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2 2 4
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3 2 -1
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4 2 -1
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‎examples/test.mtx‎

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%%MatrixMarket matrix coordinate real general
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10 10 46
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1 1 3
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4 1 -1
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6 1 -1
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2 2 4
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5 2 -1
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6 2 -1
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5 3 -1
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