Implement runtime dispatch of SIMD code

.github/workflows/build.yml

@@ -25,6 +25,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
+        with:
+            submodules: true
       - name: Build trimal for Linux x86_64
         if: matrix.arch == 'x86_64' && matrix.cpu_instr == 'non_SIMD' 
         run: cmake . -DDISABLE_SSE2=1 -DDISABLE_AVX2=1 && make && file bin/trimal && file bin/readal &&
@@ -67,4 +69,4 @@ jobs:
             apt-get install -q -y cmake make g++ file
           run: |
             cmake . -DDISABLE_SSE2=1 -DDISABLE_AVX2=1 && make && file bin/trimal && file bin/readal &&
-            ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh
+            ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "vendor/cpu_features"]
+	path = vendor/cpu_features
+	url = https://github.com/google/cpu_features

CMakeLists.txt

@@ -62,6 +62,12 @@ add_executable(test
         ${TRIMAL_OBJECTS})
 SET_TARGET_PROPERTIES(test PROPERTIES EXCLUDE_FROM_ALL True)
 
+# Add `cpu_features` for detecting supported SIMD at compile time
+add_subdirectory(vendor/cpu_features)
+include_directories(vendor/cpu_features/include)
+target_link_libraries(trimal cpu_features)
+target_link_libraries(readal cpu_features)
+
 # Link the mathematical library to the targets
 target_link_libraries(trimal m)
 target_link_libraries(readal m)

include/Statistics/Manager.h

@@ -45,13 +45,27 @@ namespace statistics {
     class Identity;
     class Overlap;
 
+    /**
+     * \brief Enum to store the different supported compute kernels for the statistics.
+     */
+    enum ComputePlatform {
+        NONE,
+        SSE2,
+        AVX2,
+        NEON,
+    };
+
     /**
      * \brief Class to handle the interaction with Alignment and statistics objects.\n
      * It serves as a wrapper or intermediate between the alignment and each specific stat.\n
      * It also encapsulates the similarityMatrix.
      */
     class Manager {
     public:
+        /**
+         * \brief
+         * */
+        ComputePlatform platform = ComputePlatform::NONE;
 
         /**
          * \brief Gaps submodule

include/reportsystem.h

@@ -305,6 +305,8 @@ enum InfoCode {
 
     RemovingDuplicateSequences                  = 4,
 
+    UsingPlatform                               = 5,
+
 
     __MAXINFO
 };