Fix handling of required SIMD flags in CMake

CMakeLists.txt

@@ -10,13 +10,32 @@ set_property(GLOBAL PROPERTY PYTHON_EXTENSIONS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE
 
 include("src/scripts/cmake/FindNEON.cmake")
 include("src/scripts/cmake/FindSSE2.cmake")
+include("src/scripts/cmake/FindSSE4.cmake")
 # include("src/scripts/cmake/FindVMX.cmake")
 include("src/scripts/cmake/Destatic.cmake")
 include("src/scripts/cmake/CythonExtension.cmake")
 
+if(HAVE_SSE4)
+    set(eslENABLE_SSE4 true)
+    if(SSE4_C_FLAGS)
+        add_compile_options(${SSE4_C_FLAGS})
+    endif()
+endif()
+
 if(HAVE_SSE2)
     set(eslENABLE_SSE true)
     set(HMMER_IMPL "SSE")
+    if(SSE2_C_FLAGS)
+        add_compile_options(${SSE2_C_FLAGS})
+    endif()
+elseif(HAVE_NEON)
+    set(eslENABLE_NEON true)
+    set(HMMER_IMPL "NEON")
+    if(NEON_C_FLAGS)
+        add_compile_options(${NEON_C_FLAGS})
+    endif()
+else()
+    error("Unsupported platform, neither SSE2 nor NEON available.")
 endif()
 
 # --- Setup include folders ----------------------------------------------------

src/scripts/cmake/FindAVX2.cmake

@@ -81,6 +81,7 @@ else()
   endforeach()
 
   unset(AVX2_C_FLAG_CANDIDATES)
+  string(STRIP "${AVX2_C_FLAGS_INTERNAL}" AVX2_C_FLAGS_INTERNAL)
   
   set(AVX2_C_FLAGS "${AVX2_C_FLAGS_INTERNAL}"
     CACHE STRING "C compiler flags for AVX2 intrinsics")

src/scripts/cmake/FindNEON.cmake

@@ -74,6 +74,7 @@ else()
   endforeach()
 
   unset(NEON_C_FLAG_CANDIDATES)
+  string(STRIP "${NEON_C_FLAGS_INTERNAL}" NEON_C_FLAGS_INTERNAL)
   
   set(NEON_C_FLAGS "${NEON_C_FLAGS_INTERNAL}"
     CACHE STRING "C compiler flags for NEON intrinsics")

src/scripts/cmake/FindSSE2.cmake

@@ -77,6 +77,7 @@ else()
   endforeach()
 
   unset(SSE2_C_FLAG_CANDIDATES)
+  string(STRIP "${SSE2_C_FLAGS_INTERNAL}" SSE2_C_FLAGS_INTERNAL)
 
   set(SSE2_C_FLAGS "${SSE2_C_FLAGS_INTERNAL}"
     CACHE STRING "C compiler flags for SSE2 intrinsics")

src/scripts/cmake/FindSSE4.cmake

+#.rst:
+# FindSSE4
+# --------
+#
+# Finds SSE4 support
+#
+# This module can be used to detect SSE4 support in a C compiler.  If
+# the compiler supports SSE4, the flags required to compile with
+# SSE4 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 SSE4.
+#
+# The following variables are set:
+#
+# ::
+#
+#    SSE4_C_FLAGS - flags to add to the C compiler for SSE4 support
+#    SSE4_FOUND - true if SSE4 is detected
+#
+#=============================================================================
+
+set(_SSE4_REQUIRED_VARS)
+set(CMAKE_REQUIRED_QUIET_SAVE ${CMAKE_REQUIRED_QUIET})
+set(CMAKE_REQUIRED_QUIET ${SSE4_FIND_QUIETLY})
+
+# sample SSE4 source code to test
+set(SSE4_C_TEST_SOURCE
+"
+#if defined(_MSC_VER)
+#include <intrin.h>
+#else
+#include <smmintrin.h>
+#endif
+int foo() {
+    __m128  a = _mm_set1_ps(1.0);
+            a = _mm_blend_ps(a, _mm_setzero_ps(), 0b1111);
+    float   x = _mm_extract_ps(a, 1);
+    return (x == 1) ? 0 : 1;
+}
+int main(void) { return foo(); }
+")
+
+# if these are set then do not try to find them again,
+# by avoiding any try_compiles for the flags
+if((DEFINED SSE4_C_FLAGS) OR (DEFINED HAVE_SSE4))
+else()
+  if(WIN32)
+    set(SSE4_C_FLAG_CANDIDATES
+      #Empty, if compiler automatically accepts SSE4
+      " "
+      "/arch:SSE4")
+  else()
+    set(SSE4_C_FLAG_CANDIDATES
+      #Empty, if compiler automatically accepts SSE4
+      " "
+      #clang
+      "-msse4.1"
+    )
+  endif()
+
+  include(CheckCSourceCompiles)
+
+  foreach(FLAG IN LISTS SSE4_C_FLAG_CANDIDATES)
+    set(SAFE_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
+    set(CMAKE_REQUIRED_FLAGS "${FLAG}")
+    unset(HAVE_SSE4 CACHE)
+    if(NOT CMAKE_REQUIRED_QUIET)
+      message(STATUS "Try SSE4 C flag = [${FLAG}]")
+    endif()
+    check_c_source_compiles("${SSE4_C_TEST_SOURCE}" HAVE_SSE4)
+    set(CMAKE_REQUIRED_FLAGS "${SAFE_CMAKE_REQUIRED_FLAGS}")
+    if(HAVE_SSE4)
+      set(SSE4_C_FLAGS_INTERNAL "${FLAG}")
+      break()
+    endif()
+  endforeach()
+
+  unset(SSE4_C_FLAG_CANDIDATES)
+  string(STRIP "${SSE4_C_FLAGS_INTERNAL}" SSE4_C_FLAGS_INTERNAL)
+
+  set(SSE4_C_FLAGS "${SSE4_C_FLAGS_INTERNAL}"
+    CACHE STRING "C compiler flags for SSE4 intrinsics")
+endif()
+
+list(APPEND _SSE4_REQUIRED_VARS SSE4_C_FLAGS)
+
+set(CMAKE_REQUIRED_QUIET ${CMAKE_REQUIRED_QUIET_SAVE})
+
+if(_SSE4_REQUIRED_VARS)
+  include(FindPackageHandleStandardArgs)
+
+  find_package_handle_standard_args(SSE4
+                                    REQUIRED_VARS ${_SSE4_REQUIRED_VARS})
+
+  mark_as_advanced(${_SSE4_REQUIRED_VARS})
+
+  unset(_SSE4_REQUIRED_VARS)
+else()
+  message(SEND_ERROR "FindSSE4 requires C or CXX language to be enabled")
+endif()