Merge commit '234e2a2e008bd2b6f6e037111af510a49bb3e122' into update-sz3

silx-kit · Jan 19, 2024 · 1f0e7ed · 1f0e7ed
2 parents 160f999 + 234e2a2
commit 1f0e7ed
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Showing 70 changed files with 2,222 additions and 1,928 deletions.
diff --git a/src/SZ3/CMakeLists.txt b/src/SZ3/CMakeLists.txt
@@ -1,24 +1,24 @@
 cmake_minimum_required(VERSION 3.18)
-project(SZ3 VERSION 3.1.7)
+project(SZ3 VERSION 3.1.8)
 include(GNUInstallDirs)
 include(CTest)
 
 option(BUILD_SHARED_LIBS "build shared libraries by default" ON)
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 if (MSVC)
-    set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /bigobj")
-endif()
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /bigobj")
+endif ()
 set(default_build_type "Release")
-if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
-  message(STATUS "No build type was set. Setting build type to ${default_build_type}.")
-  set(CMAKE_BUILD_TYPE ${default_build_type} CACHE
-          STRING "Choose the type to build" FORCE)
-  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
-          "MinSizeRel" "RelWithDebInfo")
-endif()
+if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+    message(STATUS "No build type was set. Setting build type to ${default_build_type}.")
+    set(CMAKE_BUILD_TYPE ${default_build_type} CACHE
+            STRING "Choose the type to build" FORCE)
+    set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
+            "MinSizeRel" "RelWithDebInfo")
+endif ()
 
 find_package(PkgConfig)
-find_package(OpenMP)
+
 
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/include/SZ3/version.hpp.in ${CMAKE_CURRENT_BINARY_DIR}/include/SZ3/version.hpp)
 
@@ -28,80 +28,83 @@ target_include_directories(
         $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
         $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/include>
         $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
-        )
+)
 target_compile_features(${PROJECT_NAME}
-    INTERFACE cxx_std_17
-  )
+        INTERFACE cxx_std_17
+        )
 
-target_link_libraries(${PROJECT_NAME} INTERFACE OpenMP::OpenMP_CXX)
+find_package(OpenMP)
+if (OpenMP_FOUND)
+    target_link_libraries(${PROJECT_NAME} INTERFACE OpenMP::OpenMP_CXX)
+endif ()
 
 if (MSVC)
     option(SZ3_USE_BUNDLED_ZSTD "prefer the bundled version of Zstd" ON)
-else()
+else ()
     option(SZ3_USE_BUNDLED_ZSTD "prefer the bundled version of Zstd" OFF)
-endif()
-option(SZ3_DEBUG_TIMINGS "print debug timing information" ON)
+endif ()
 
-if(SZ3_DEBUG_TIMINGS)
-  target_compile_definitions(${PROJECT_NAME} INTERFACE SZ3_DEBUG_TIMINGS=1)
-else()
-  target_compile_definitions(${PROJECT_NAME} INTERFACE SZ3_DEBUG_TIMINGS=0)
-endif()
+option(SZ3_DEBUG_TIMINGS "print debug timing information" OFF)
+if (SZ3_DEBUG_TIMINGS)
+    target_compile_definitions(${PROJECT_NAME} INTERFACE SZ3_DEBUG_TIMINGS=1)
+else ()
+    target_compile_definitions(${PROJECT_NAME} INTERFACE SZ3_DEBUG_TIMINGS=0)
+endif ()
 
 pkg_search_module(ZSTD IMPORTED_TARGET libzstd)
-if(ZSTD_FOUND AND NOT SZ3_USE_BUNDLED_ZSTD)
-  target_link_libraries(${PROJECT_NAME} INTERFACE PkgConfig::ZSTD)
-else()
-  add_subdirectory(tools/zstd)
-  target_link_libraries(${PROJECT_NAME} INTERFACE zstd)
-endif()
+if (ZSTD_FOUND AND NOT SZ3_USE_BUNDLED_ZSTD)
+    target_link_libraries(${PROJECT_NAME} INTERFACE PkgConfig::ZSTD)
+else ()
+    add_subdirectory(tools/zstd)
+    target_link_libraries(${PROJECT_NAME} INTERFACE zstd)
+endif ()
 
 find_package(GSL)
 if (GSL_FOUND)
-  target_compile_definitions(${PROJECT_NAME} INTERFACE -DENABLE_GSL="TRUE")
-  target_link_libraries(${PROJECT_NAME} INTERFACE GSL::gsl)
-endif()
+    target_compile_definitions(${PROJECT_NAME} INTERFACE -DENABLE_GSL="TRUE")
+    target_link_libraries(${PROJECT_NAME} INTERFACE GSL::gsl)
+endif ()
 
 add_subdirectory(tools/sz3)
 add_subdirectory(tools/sz3c)
 
 
 option(BUILD_H5Z_FILTER "build the H5Z-SZ3 filter" OFF)
-if(BUILD_H5Z_FILTER)
-	add_subdirectory(tools/H5Z-SZ3)
-endif()
+if (BUILD_H5Z_FILTER)
+    add_subdirectory(tools/H5Z-SZ3)
+endif ()
 
 option(BUILD_MDZ "build MDZ (MMD-SZ)" OFF)
-if(BUILD_MDZ)
-  add_subdirectory(tools/mdz)
-endif()
+if (BUILD_MDZ)
+    add_subdirectory(tools/mdz)
+endif ()
 
 
-install(TARGETS ${PROJECT_NAME} 
-  EXPORT SZ3Targets
-  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-  INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
-  )
+install(TARGETS ${PROJECT_NAME}
+        EXPORT SZ3Targets
+        LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+        INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+        )
 install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/include/ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 install(FILES
-  "${CMAKE_CURRENT_BINARY_DIR}/include/SZ3/version.hpp"
-  DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/SZ3/"
-  )
+        "${CMAKE_CURRENT_BINARY_DIR}/include/SZ3/version.hpp"
+        DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/SZ3/"
+        )
 install(EXPORT SZ3Targets NAMESPACE SZ3:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/SZ3)
 include(CMakePackageConfigHelpers)
 configure_package_config_file(${CMAKE_CURRENT_SOURCE_DIR}/SZ3Config.cmake.in
-  "${CMAKE_CURRENT_BINARY_DIR}/SZ3Config.cmake"
-  INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/SZ3
-  )
+        "${CMAKE_CURRENT_BINARY_DIR}/SZ3Config.cmake"
+        INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/SZ3
+        )
 write_basic_package_version_file(
-  "${CMAKE_CURRENT_BINARY_DIR}/SZ3ConfigVersion.cmake"
-  VERSION ${PROJECT_VERSION}
-  COMPATIBILITY AnyNewerVersion
-  )
+        "${CMAKE_CURRENT_BINARY_DIR}/SZ3ConfigVersion.cmake"
+        VERSION ${PROJECT_VERSION}
+        COMPATIBILITY AnyNewerVersion
+)
 install(FILES
-  ${CMAKE_CURRENT_BINARY_DIR}/SZ3Config.cmake
-  ${CMAKE_CURRENT_BINARY_DIR}/SZ3ConfigVersion.cmake
-  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/SZ3
-  )
+        ${CMAKE_CURRENT_BINARY_DIR}/SZ3Config.cmake
+        ${CMAKE_CURRENT_BINARY_DIR}/SZ3ConfigVersion.cmake
+        DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/SZ3
+        )
 #export sz3 target for external use
 export(TARGETS SZ3 FILE SZ3.cmake)
diff --git a/src/SZ3/README.md b/src/SZ3/README.md
@@ -125,4 +125,5 @@ Version New features
 * SZ 3.1.4 Support running on Windows. Please refer to https://github.com/szcompressor/SZ3/issues/5#issuecomment-1094039224 for instructions.
 * SZ 3.1.5 Support HDF5 by H5Z-SZ3. Please add "-DBUILD_H5Z_FILTER=ON" to enable this function for CMake.
 * SZ 3.1.6 Support C API and Python API.
-* SZ 3.1.7 Initial MDZ(https://github.com/szcompressor/SZ3/tree/master/tools/mdz) support.
+* SZ 3.1.7 Initial MDZ(https://github.com/szcompressor/SZ3/tree/master/tools/mdz) support.
+* SZ 3.1.8 namespace changed from SZ to SZ3. H5Z-SZ3 supports configuration file now.
diff --git a/src/SZ3/include/SZ3/api/impl/SZDispatcher.hpp b/src/SZ3/include/SZ3/api/impl/SZDispatcher.hpp
@@ -8,43 +8,43 @@
 #include "SZ3/api/impl/SZLorenzoReg.hpp"
 #include <cmath>
 
-
-template<class T, SZ::uint N>
-char *SZ_compress_dispatcher(SZ::Config &conf, T *data, size_t &outSize) {
-
-    assert(N == conf.N);
-    SZ::calAbsErrorBound(conf, data);
-
-    char *cmpData;
-    if (conf.absErrorBound == 0) {
-        auto zstd = SZ::Lossless_zstd();
-        cmpData = (char *) zstd.compress((SZ::uchar *) data, conf.num * sizeof(T), outSize);
-    } else if (conf.cmprAlgo == SZ::ALGO_LORENZO_REG) {
-        cmpData = (char *) SZ_compress_LorenzoReg<T, N>(conf, data, outSize);
-    } else if (conf.cmprAlgo == SZ::ALGO_INTERP) {
-        cmpData = (char *) SZ_compress_Interp<T, N>(conf, data, outSize);
-    } else if (conf.cmprAlgo == SZ::ALGO_INTERP_LORENZO) {
-        cmpData = (char *) SZ_compress_Interp_lorenzo<T, N>(conf, data, outSize);
+namespace SZ3 {
+    template<class T, uint N>
+    char *SZ_compress_dispatcher(Config &conf, T *data, size_t &outSize) {
+
+        assert(N == conf.N);
+        calAbsErrorBound(conf, data);
+
+        char *cmpData;
+        if (conf.absErrorBound == 0) {
+            auto zstd = Lossless_zstd();
+            cmpData = (char *) zstd.compress((uchar *) data, conf.num * sizeof(T), outSize);
+        } else if (conf.cmprAlgo == ALGO_LORENZO_REG) {
+            cmpData = (char *) SZ_compress_LorenzoReg<T, N>(conf, data, outSize);
+        } else if (conf.cmprAlgo == ALGO_INTERP) {
+            cmpData = (char *) SZ_compress_Interp<T, N>(conf, data, outSize);
+        } else if (conf.cmprAlgo == ALGO_INTERP_LORENZO) {
+            cmpData = (char *) SZ_compress_Interp_lorenzo<T, N>(conf, data, outSize);
+        }
+        return cmpData;
     }
-    return cmpData;
-}
 
 
-template<class T, SZ::uint N>
-void SZ_decompress_dispatcher(SZ::Config &conf, char *cmpData, size_t cmpSize, T *decData) {
-    if (conf.absErrorBound == 0) {
-        auto zstd = SZ::Lossless_zstd();
-        auto zstdOut = zstd.decompress((SZ::uchar *) cmpData, cmpSize);
-        memcpy(decData, zstdOut, conf.num * sizeof(T));
-    } else if (conf.cmprAlgo == SZ::ALGO_LORENZO_REG) {
-        SZ_decompress_LorenzoReg<T, N>(conf, cmpData, cmpSize, decData);
-    } else if (conf.cmprAlgo == SZ::ALGO_INTERP) {
-        SZ_decompress_Interp<T, N>(conf, cmpData, cmpSize, decData);
-    } else {
-        printf("SZ_decompress_dispatcher, Method not supported\n");
-        exit(0);
-    }
+    template<class T, uint N>
+    void SZ_decompress_dispatcher(Config &conf, char *cmpData, size_t cmpSize, T *decData) {
+        if (conf.absErrorBound == 0) {
+            auto zstd = Lossless_zstd();
+            auto zstdOut = zstd.decompress((uchar *) cmpData, cmpSize);
+            memcpy(decData, zstdOut, conf.num * sizeof(T));
+        } else if (conf.cmprAlgo == ALGO_LORENZO_REG) {
+            SZ_decompress_LorenzoReg<T, N>(conf, cmpData, cmpSize, decData);
+        } else if (conf.cmprAlgo == ALGO_INTERP) {
+            SZ_decompress_Interp<T, N>(conf, cmpData, cmpSize, decData);
+        } else {
+            printf("SZ_decompress_dispatcher, Method not supported\n");
+            exit(0);
+        }
 
+    }
 }
-
 #endif
diff --git a/src/SZ3/include/SZ3/api/impl/SZImpl.hpp b/src/SZ3/include/SZ3/api/impl/SZImpl.hpp
@@ -6,33 +6,34 @@
 #include "SZ3/api/impl/SZImplOMP.hpp"
 #include <cmath>
 
-template<class T, SZ::uint N>
-char *SZ_compress_impl(SZ::Config &conf, const T *data, size_t &outSize) {
+namespace SZ3 {
+    template<class T, uint N>
+    char *SZ_compress_impl(Config &conf, const T *data, size_t &outSize) {
 #ifndef _OPENMP
-    conf.openmp=false;
+        conf.openmp=false;
 #endif
-    if (conf.openmp) {
-        //dataCopy for openMP is handled by each thread
-        return SZ_compress_OMP<T, N>(conf, data, outSize);
-    } else {
-        std::vector<T> dataCopy(data, data + conf.num);
-        return SZ_compress_dispatcher<T, N>(conf, dataCopy.data(), outSize);
+        if (conf.openmp) {
+            //dataCopy for openMP is handled by each thread
+            return SZ_compress_OMP<T, N>(conf, data, outSize);
+        } else {
+            std::vector<T> dataCopy(data, data + conf.num);
+            return SZ_compress_dispatcher<T, N>(conf, dataCopy.data(), outSize);
+        }
     }
-}
 
 
-template<class T, SZ::uint N>
-void SZ_decompress_impl(SZ::Config &conf, char *cmpData, size_t cmpSize, T *decData) {
+    template<class T, uint N>
+    void SZ_decompress_impl(Config &conf, char *cmpData, size_t cmpSize, T *decData) {
 
 
 #ifndef _OPENMP
-    conf.openmp=false;
+        conf.openmp=false;
 #endif
-    if (conf.openmp) {
-        SZ_decompress_OMP<T, N>(conf, cmpData, cmpSize, decData);
-    } else {
-        SZ_decompress_dispatcher<T, N>(conf, cmpData, cmpSize, decData);
+        if (conf.openmp) {
+            SZ_decompress_OMP<T, N>(conf, cmpData, cmpSize, decData);
+        } else {
+            SZ_decompress_dispatcher<T, N>(conf, cmpData, cmpSize, decData);
+        }
     }
 }
-
 #endif