Support for static executable (#101)(#163)

* Build script: --static flag * Static compile flags in CMakeLists
iqbal-lab-org · Jan 25, 2022 · ef92c63 · ef92c63
1 parent 83d682b
commit ef92c63
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Showing 3 changed files with 63 additions and 26 deletions.
diff --git a/build.sh b/build.sh
@@ -1,20 +1,47 @@
 #!/usr/bin/env bash
 set -eu -o pipefail
 
+TARGETS="gram|all|test_main"
+BUILD_TYPES="DEBUG|REL_WITH_ASSERTS"
+
 usage(){
     echo "Builds the gramtools backend"
-    echo "usage: $0 [build_target] [build_mode]"
-    echo "\tbuild_target: $TARGETS (default: gram)"
-    echo "\tbuild_mode: $BUILD_TYPES (default: REL_WITH_ASSERTS)"
+    echo "usage: $0 [--target ($TARGETS)] [--build_type ($BUILD_TYPES)] [--static]"
+    echo -e "\tDefaults: --target gram --build_type REL_WITH_ASSERTS"
+    echo -e "\tPass --static to make a standalone executable"
     exit 0
 }
 
-TARGETS="gram|all|test_main"
-BUILD_TYPES="DEBUG|REL_WITH_ASSERTS"
-TARGET=${1:-gram}
-BUILD_TYPE=${2:-REL_WITH_ASSERTS}
-[[ "$BUILD_TYPE" =~ $BUILD_TYPES ]] || usage
-[[ "$TARGET" =~ $TARGETS ]] || usage
+while [[ $# -gt 0 ]]
+do
+    key="$1"
+    case $key in
+        --target)
+        TARGET="$2"
+        [[ "$TARGET" =~ $TARGETS ]] || usage
+        shift
+        shift
+        ;;
+        --build_type)
+        BUILD_TYPE="$2"
+        [[ "$BUILD_TYPE" =~ $BUILD_TYPES ]] || usage
+        shift
+        shift
+        ;;
+        --static)
+        STATIC="-static"
+        shift
+        ;;
+        *)    # unknown option
+        usage
+        ;;
+    esac
+done
+
+TARGET=${TARGET:-gram}
+BUILD_TYPE=${BUILD_TYPE:-REL_WITH_ASSERTS}
+STATIC=${STATIC:- }
+[[ "$STATIC" =~ -static| ]] || usage
 
 BASE_DIR=$(realpath $(dirname $0))
 CUR_DIR=$(pwd)
@@ -33,8 +60,10 @@ echo "Building in: ${BUILD_DIR}" >&1
 echo "Writing stdout to: ${STDOUT_FILE}" >&1
 mkdir -p "${BUILD_DIR}" && cd "${BUILD_DIR}"
 
+CMAKE_OPTS="-DCMAKE_EXE_LINKER_FLAGS=${STATIC} -DCMAKE_BUILD_TYPE=${BUILD_TYPE}"
+
 conan install .. -s compiler.libcxx=libstdc++11 --build=missing > "$STDOUT_FILE"
-CC=gcc CXX=g++ cmake -DCMAKE_BUILD_TYPE="${BUILD_TYPE}" .. >> "$STDOUT_FILE"
+CC=gcc CXX=g++ cmake "$CMAKE_OPTS" .. | tee -a "$STDOUT_FILE"
 make -j 4 "${TARGET}" | tee -a "$STDOUT_FILE"
 
 cd "$CUR_DIR"
diff --git a/libgramtools/CMakeLists.txt b/libgramtools/CMakeLists.txt
@@ -7,12 +7,10 @@ add_custom_target(py_git_version
         COMMAND make -C ${PROJECT_SOURCE_DIR}/gramtools/version)
 
 
-######################
-###  Compile flags ##
-######################
+###  Build type flags ##
 # add a RELEASE_WITH_ASSERTS build type. Use via `cmake -DCMAKE_BUILD_TYPE=REL_WITH_ASSERTS`
-# Note: this variable name NEEDS TO BE UPPERCASE (but not in cmake call)
-set(CMAKE_CXX_FLAGS_REL_WITH_ASSERTS "-O3")
+# Note: this variable name needs to be uppercased here
+set(CMAKE_CXX_FLAGS_REL_WITH_ASSERTS "${CMAKE_CXX_FLAGS_REL_WITH_ASSERTS} -O3")
 
 
 ######################
@@ -23,7 +21,14 @@ include(${PROJECT_SOURCE_DIR}/libgramtools/lib/htslib.cmake)
 include(${CMAKE_BINARY_DIR}/conanbuildinfo.cmake)
 conan_basic_setup(TARGETS)
 
-find_package(OpenMP REQUIRED)
+# Parallelisation
+if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+    set(MACOSX TRUE)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DNO_OPENMP")
+else ()
+    find_package(OpenMP REQUIRED)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
+endif()
 
 ### Include headers ####
 set(EXTERNAL_INCLUDE_DIR 
@@ -33,9 +38,10 @@ set(EXTERNAL_INCLUDE_DIR
 #### Link libraries ####
 link_directories(${CMAKE_CURRENT_BINARY_DIR}/lib)
 
-set(EXTERN_LIBS
-        divsufsort
-        divsufsort64
+set(SDSL_LIBS
+        -ldivsufsort
+        -ldivsufsort64
+        -lsdsl
         )
 
 #########################
@@ -54,27 +60,29 @@ file(GLOB_RECURSE HEADER_FILES
         ${INCLUDE}/*.hpp)
 
 
-
 #########################
 ####  libgramtools   ####
 #########################
+if (${CMAKE_EXE_LINKER_FLAGS} MATCHES "-static")
+    set(STATIC_FLAGS "-static-libgcc -static-libstdc++ -ldl")
+endif()
 add_library(gramtools STATIC
         ${SOURCE_FILES}
         ${HEADER_FILES} # For IDE to recognise header files as part of a target
         )
+
 target_include_directories(gramtools PUBLIC
         ${INCLUDE}
         ${EXTERNAL_INCLUDE_DIR}
         ${PROJECT_SOURCE_DIR}/libgramtools/lib
         )
 target_link_libraries(gramtools LINK_PUBLIC
-        ${EXTERN_LIBS}
-        ${CMAKE_CURRENT_BINARY_DIR}/lib/libsdsl.a
+        ${SDSL_LIBS}
         ${CMAKE_CURRENT_BINARY_DIR}/lib/libhts.a
         CONAN_PKG::boost
         CONAN_PKG::nlohmann_json
-        OpenMP::OpenMP_CXX
         -lstdc++fs -lpthread -lrt -lm -lz
+        ${STATIC_FLAGS}
 		)
 target_compile_features(gramtools PUBLIC cxx_std_17)
 set_target_properties(gramtools
@@ -134,8 +142,8 @@ if (EXISTS "${PROJECT_SOURCE_DIR}/libgramtools/tests")
             "${PROJECT_SOURCE_DIR}/libgramtools/tests/*"
             )
         include(CodeCoverage)
-        set(CMAKE_CXX_FLAGS "-O0")
-        set(CMAKE_C_FLAGS "-O0")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O0")
+        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O0")
         append_coverage_compiler_flags()
         setup_target_for_coverage_lcov(
             NAME test_coverage 

diff --git a/libgramtools/lib/htslib.cmake b/libgramtools/lib/htslib.cmake
@@ -2,7 +2,7 @@ ExternalProject_Add(htslib
         DOWNLOAD_COMMAND  wget https://github.com/samtools/htslib/releases/download/1.10/htslib-1.10.tar.bz2 --timestamping
         DOWNLOAD_DIR      "${CMAKE_CURRENT_BINARY_DIR}/download"
         CONFIGURE_COMMAND bash -c "cd ${CMAKE_CURRENT_BINARY_DIR}/src/htslib-1.10 && \
-            autoheader && autoconf && ./configure --prefix=${CMAKE_CURRENT_BINARY_DIR} \
+            ./configure --prefix=${CMAKE_CURRENT_BINARY_DIR} \
             --disable-bz2 --disable-lzma --enable-libcurl=no"
         BUILD_COMMAND     bash -c "cd ${CMAKE_CURRENT_BINARY_DIR}/src/htslib-1.10 && make && make install"
         INSTALL_COMMAND   ""