Fix some additional compile options for the FAMSA code

CMakeLists.txt

@@ -3,22 +3,39 @@ project(${SKBUILD_PROJECT_NAME} VERSION ${SKBUILD_PROJECT_VERSION} LANGUAGES C C
 
 set(BUILD_SHARED_LIBS OFF)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-set(CMAKE_CXX_STANDARD 20)
 
-set_property(GLOBAL PROPERTY PYTHON_EXTENSIONS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED TRUE)
 
 message(STATUS "Building ${SKBUILD_PROJECT_NAME} for ${CMAKE_SYSTEM_PROCESSOR}")
 
 # --- Setup include folders ----------------------------------------------------
 
+set_property(GLOBAL PROPERTY PYTHON_EXTENSIONS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
 set(CYTHON_HEADERS_DIR ${CMAKE_CURRENT_LIST_DIR}/include)
 
+# --- Add global C++ flags -----------------------------------------------------
+
+include(CheckCXXCompilerFlag)
+
+check_cxx_compiler_flag(-funroll-loops HAVE_UNROLL_LOOPS)
+if(HAVE_UNROLL_LOOPS)
+    add_compile_options(-funroll-loops)
+endif()
+
+add_definitions(-DOLD_ATOMIC_FLAG -DNO_PROFILE_PAR)
+
+if(WIN32)
+    add_definitions(-D_WIN32)
+endif()
+
 # --- Add scripts for Cython ---------------------------------------------------
 
-# include("src/scripts/cmake/FindAVX1.cmake")
+include("src/scripts/cmake/FindAVX1.cmake")
 include("src/scripts/cmake/FindAVX2.cmake")
 # include("src/scripts/cmake/FindAVX512.cmake")
 include("src/scripts/cmake/FindNEON.cmake")
+include("src/scripts/cmake/FindPOPCNT.cmake")
 include("src/scripts/cmake/FindSSE2.cmake")
 include("src/scripts/cmake/FindSSE4.cmake")
 include("src/scripts/cmake/CythonExtension.cmake")

src/FAMSA/CMakeLists.txt

@@ -161,6 +161,10 @@ else()
     target_compile_definitions(famsa_lcs PRIVATE -DSIMD=0)
 endif()
 
+if(HAVE_POPCNT)
+    target_compile_options(famsa_lcs PRIVATE ${POPCNT_C_FLAGS})    
+endif()
+
 
 target_link_libraries(famsa PUBLIC famsa_lcs)
 

src/scripts/cmake/FindAVX1.cmake

@@ -0,0 +1,103 @@
+#.rst:
+# FindAVX1
+# --------
+#
+# Finds AVX1 support
+#
+# This module can be used to detect AVX1 support in a C compiler.  If
+# the compiler supports AVX1, the flags required to compile with
+# AVX1 support are returned in variables for the different languages.
+# The variables may be empty if the compiler does not need a special
+# flag to support AVX1.
+#
+# The following variables are set:
+#
+# ::
+#
+#    AVX1_C_FLAGS - flags to add to the C compiler for AVX1 support
+#    AVX1_FOUND - true if AVX1 is detected
+#
+#=============================================================================
+
+set(_AVX1_REQUIRED_VARS)
+set(CMAKE_REQUIRED_QUIET_SAVE ${CMAKE_REQUIRED_QUIET})
+set(CMAKE_REQUIRED_QUIET ${AVX1_FIND_QUIETLY})
+
+# sample AVX1 source code to test
+set(AVX1_C_TEST_SOURCE
+"
+#include <immintrin.h>
+void parasail_memset___m256i(__m256i *b, __m256i c, size_t len)
+{
+    size_t i;
+    for (i=0; i<len; ++i) {
+        _mm256_store_si256(&b[i], c);
+    }
+}
+int foo() {
+    __m256i vOne = _mm256_set1_epi16(1);
+    return _mm256_extract_epi16(vOne, 0);
+}
+int main(void) { return (int)foo(); }
+")
+
+# if these are set then do not try to find them again,
+# by avoiding any try_compiles for the flags
+if((DEFINED AVX1_C_FLAGS) OR (DEFINED HAVE_AVX1))
+else()
+  if(WIN32)
+    # MSVC can compile AVX intrinsics without the arch flag, however it
+    # will detect that AVX code is found and "consider using /arch:AVX".
+    set(AVX1_C_FLAG_CANDIDATES
+      "/arch:AVX"
+    )
+  else()
+    set(AVX1_C_FLAG_CANDIDATES
+      #Empty, if compiler automatically accepts AVX1
+      " "
+      #clang
+      "-mavx"
+      #GNU, Intel
+      "-march=core-avx-i"
+    )
+  endif()
+
+  include(CheckCSourceCompiles)
+
+  foreach(FLAG IN LISTS AVX1_C_FLAG_CANDIDATES)
+    set(SAFE_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
+    set(CMAKE_REQUIRED_FLAGS "${FLAG}")
+    unset(HAVE_AVX1 CACHE)
+    if(NOT CMAKE_REQUIRED_QUIET)
+      message(STATUS "Try AVX1 C flag = [${FLAG}]")
+    endif()
+    check_c_source_compiles("${AVX1_C_TEST_SOURCE}" HAVE_AVX1)
+    set(CMAKE_REQUIRED_FLAGS "${SAFE_CMAKE_REQUIRED_FLAGS}")
+    if(HAVE_AVX1)
+      set(AVX1_C_FLAGS_INTERNAL "${FLAG}")
+      break()
+    endif()
+  endforeach()
+
+  unset(AVX1_C_FLAG_CANDIDATES)
+
+  set(AVX1_C_FLAGS "${AVX1_C_FLAGS_INTERNAL}"
+    CACHE STRING "C compiler flags for AVX1 intrinsics")
+endif()
+
+list(APPEND _AVX1_REQUIRED_VARS AVX1_C_FLAGS)
+
+set(CMAKE_REQUIRED_QUIET ${CMAKE_REQUIRED_QUIET_SAVE})
+
+if(_AVX1_REQUIRED_VARS)
+  include(FindPackageHandleStandardArgs)
+
+  find_package_handle_standard_args(AVX1
+                                    REQUIRED_VARS ${_AVX1_REQUIRED_VARS})
+
+  mark_as_advanced(${_AVX1_REQUIRED_VARS})
+
+  unset(_AVX1_REQUIRED_VARS)
+else()
+  message(SEND_ERROR "FindAVX1 requires C or CXX language to be enabled")
+endif()

src/scripts/cmake/FindPOPCNT.cmake

@@ -0,0 +1,92 @@
+#.rst:
+# FindPOPCNT
+# --------
+#
+# Finds POPCNT support
+#
+# This module can be used to detect POPCNT support in a C compiler.  If
+# the compiler supports POPCNT, the flags required to compile with
+# POPCNT support are returned in variables for the different languages.
+# The variables may be empty if the compiler does not need a special
+# flag to support POPCNT.
+#
+# The following variables are set:
+#
+# ::
+#
+#    POPCNT_C_FLAGS - flags to add to the C compiler for POPCNT support
+#    POPCNT_FOUND - true if POPCNT is detected
+#
+#=============================================================================
+
+set(_POPCNT_REQUIRED_VARS)
+set(CMAKE_REQUIRED_QUIET_SAVE ${CMAKE_REQUIRED_QUIET})
+set(CMAKE_REQUIRED_QUIET ${POPCNT_FIND_QUIETLY})
+
+# sample POPCNT source code to test
+set(POPCNT_C_TEST_SOURCE
+"
+#include <immintrin.h>
+int foo(long long int a)
+{
+    return _popcnt64(a);
+}
+int main(void) { return (int)foo(0); }
+")
+
+# if these are set then do not try to find them again,
+# by avoiding any try_compiles for the flags
+if((DEFINED POPCNT_C_FLAGS) OR (DEFINED HAVE_POPCNT))
+else()
+  if(WIN32)
+    # MSVC can compile AVX intrinsics without the arch flag, however it
+    # will detect that AVX code is found and "consider using /arch:AVX".
+    set(POPCNT_C_FLAG_CANDIDATES
+      "/arch:SSE4.2"
+    )
+  else()
+    set(POPCNT_C_FLAG_CANDIDATES
+      #clang,GNU,Intel
+      "-mpopcnt"
+    )
+  endif()
+
+  include(CheckCSourceCompiles)
+
+  foreach(FLAG IN LISTS POPCNT_C_FLAG_CANDIDATES)
+    set(SAFE_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
+    set(CMAKE_REQUIRED_FLAGS "${FLAG}")
+    unset(HAVE_POPCNT CACHE)
+    if(NOT CMAKE_REQUIRED_QUIET)
+      message(STATUS "Try POPCNT C flag = [${FLAG}]")
+    endif()
+    check_c_source_compiles("${POPCNT_C_TEST_SOURCE}" HAVE_POPCNT)
+    set(CMAKE_REQUIRED_FLAGS "${SAFE_CMAKE_REQUIRED_FLAGS}")
+    if(HAVE_POPCNT)
+      set(POPCNT_C_FLAGS_INTERNAL "${FLAG}")
+      break()
+    endif()
+  endforeach()
+
+  unset(POPCNT_C_FLAG_CANDIDATES)
+
+  set(POPCNT_C_FLAGS "${POPCNT_C_FLAGS_INTERNAL}"
+    CACHE STRING "C compiler flags for POPCNT intrinsics")
+endif()
+
+list(APPEND _POPCNT_REQUIRED_VARS POPCNT_C_FLAGS)
+
+set(CMAKE_REQUIRED_QUIET ${CMAKE_REQUIRED_QUIET_SAVE})
+
+if(_POPCNT_REQUIRED_VARS)
+  include(FindPackageHandleStandardArgs)
+
+  find_package_handle_standard_args(POPCNT
+                                    REQUIRED_VARS ${_POPCNT_REQUIRED_VARS})
+
+  mark_as_advanced(${_POPCNT_REQUIRED_VARS})
+
+  unset(_POPCNT_REQUIRED_VARS)
+else()
+  message(SEND_ERROR "FindPOPCNT requires C or CXX language to be enabled")
+endif()