Merge pull request #93 from ekg/cmake_tweaks

`cmake` tweaks and `atomic_queue` update for future portability

.github/workflows/build_and_test_on_push.yml

@@ -23,7 +23,7 @@ jobs:
       - name: Init and update submodules
         run: git submodule update --init --recursive
       - name: Build seqwish
-        run: sed -i 's/CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -mcx16 -g/CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O -mcx16 -g -fsanitize=address/g' CMakeLists.txt && sed -i 's/CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -mcx16 -g/CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O -mcx16 -g -fsanitize=address/g' CMakeLists.txt && cmake -H. -Bbuild && cmake --build build -- -j 2
+        run: cmake -H. -DCMAKE_BUILD_TYPE=Debug -Bbuild && cmake --build build -- -j 2
       - name: Execute tests
         run: cd test && ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 make test
 

CMakeLists.txt

@@ -10,11 +10,30 @@ set(CMAKE_CXX_STANDARD 14)
 set(THREADS_PREFER_PTHREAD_FLAG ON)
 find_package(Threads REQUIRED)
 
-# Use all standard-compliant optimizations
-set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -mcx16 -g")
-set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -mcx16 -g")
-#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O -mcx16 -g -fsanitize=address")
-#set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O -mcx16 -g -fsanitize=address")
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Release CACHE STRING
+          "Choose the type of build, options are: Release Debug Generic." FORCE)
+endif()
+
+# set(CMAKE_BUILD_TYPE Debug) -- don't uncomment this, instead run
+#   cmake -DCMAKE_BUILD_TYPE=Debug ..
+
+message(STATUS "CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}")
+
+if (${CMAKE_BUILD_TYPE} MATCHES Release)
+  set(EXTRA_FLAGS "-Ofast -march=native")
+  set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast
+endif ()
+
+if (${CMAKE_BUILD_TYPE} MATCHES Debug)
+  # Debug use the defaults
+  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O -mcx16 -g -fsanitize=address")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O -mcx16 -g -fsanitize=address")
+else()
+  # Use all standard-compliant optimizations - always add these:
+  set (CMAKE_C_FLAGS "${OpenMP_C_FLAGS} ${PIC_FLAG} ${EXTRA_FLAGS} -mcx16")
+  set (CMAKE_CXX_FLAGS "${OpenMP_CXX_FLAGS} ${PIC_FLAG} ${EXTRA_FLAGS} -mcx16")
+endif ()
 
 # Set the output folder where your program will be created
 set(CMAKE_BINARY_DIR ${CMAKE_SOURCE_DIR}/bin)
@@ -114,7 +133,7 @@ ExternalProject_Add(atomicqueue
   BUILD_COMMAND ""
   CONFIGURE_COMMAND "")
 ExternalProject_Get_property(atomicqueue SOURCE_DIR)
-set(atomicqueue_INCLUDE "${SOURCE_DIR}")
+set(atomicqueue_INCLUDE "${SOURCE_DIR}/include/atomic_queue")
 
 # ska
 ExternalProject_Add(ska

README.md

@@ -96,6 +96,13 @@ cmake -DBUILD_STATIC=1 -H. -Bbuild && cmake --build build -- -j 3
 You'll need to set this flag to 0 or remove and rebuild your build directory if you want to unset this behavior.
 Static builds are unlikely to be supported on OSX, and require appropriate static libraries on linux.
 
+#### Notes for distribution
+
+If you need to avoid machine-specific optimizations, use the `CMAKE_BUILD_TYPE=Generic` build type:
+
+```shell
+cmake -H. -Bbuild -DCMAKE_BUILD_TYPE=Generic && cmake --build build -- -j 3
+```
 
 ### Docker
 

src/dset64-gccAtomic.hpp

@@ -60,11 +60,6 @@
  *
  */
 
-// Sanity check that we are compiling on x86_64.
-#if !__x86_64__
-#error "seqwish can only be built on an x86_64 machine (64-bit Intel/AMD)"
-#endif
-
 namespace seqwish {
 
 class DisjointSets {

src/dset64.hpp

@@ -57,11 +57,6 @@
  *
  */
 
-// Sanity check that we are compiling on x86_64.
-#if !__x86_64__
-#error "seqwish can only be built on an x86_64 machine (64-bit Intel/AMD)"
-#endif
-
 namespace seqwish {
 
 class DisjointSets {