Updated/revised Makefile for MacOSX.

1 files changed, 96 insertions, 53 deletions

diff --git a/Makefile.macosx b/Makefile.macosx
index 5312288..d2c1d90 100644
--- a/Makefile.macosx
+++ b/Makefile.macosx
@@ -1,38 +1,78 @@
-#Makefile
-
+# Generic Makefile for GEMMA
+#
 # Supported platforms
-#       Unix / Linux               	LNX
+#
+#       Unix / Linux               	LNX (default)
 #       Mac                        	MAC
+#
 # Compilation options
-#       link to LAPACK              WITH_LAPACK
-#       32-bit binary        		FORCE_32BIT
-#       dynamic compilation    		FORCE_DYNAMIC
+#       static compilation    		FORCE_STATIC
+#
+# Examples:
+#
+#    Make GEMMA on Linux with OPENBLAS support:
+#
+#      make WITH_OPENBLAS=1
+#
+#    Disable debug info and checks (slightly faster release mode)
+#
+#      make WITH_OPENBLAS=1 DEBUG=
+#
+#    Force static compilation
+#
+#      make FORCE_STATIC=1
+#
+#    Run tests with
+#
+#      make check
+#
+#    See also the INSTALL.md document in the source tree at
+#
+#      https://github.com/genetics-statistics/GEMMA/blob/master/INSTALL.md
 
 # Set this variable to either LNX or MAC
-SYS = MAC
+SYS                    = MAC # LNX|MAC (Linux is the default)
 # Leave blank after "=" to disable; put "= 1" to enable
-# Disable WITH_LAPACK option can slow computation speed significantly and is not recommended
-# Disable WITH_ARPACK option only disable -apprx option in the software
-WITH_LAPACK = 1
-FORCE_32BIT =
-FORCE_DYNAMIC = 1
-DIST_NAME = gemma-0.97.2
+DIST_NAME              = gemma-0.97.2
+DEBUG                  =     # DEBUG mode, set DEBUG= for a release
+SHOW_COMPILER_WARNINGS =
+WITH_LAPACK            = 1
+WITH_OPENBLAS          =     # Defaults to LAPACK - OPENBLAS may be faster
+FORCE_STATIC           =     # Static linking of libraries
+GCC_FLAGS              = -O3 -I/usr/local/Cellar/gsl/2.4/include -I./eigen
+TRAVIS_CI              =     # used by TRAVIS for testing
+EIGEN_INCLUDE_PATH=
+CXX = g++
 
 # --------------------------------------------------------------------
 # Edit below this line with caution
 # --------------------------------------------------------------------
-BIN_DIR  = ./bin
 
+BIN_DIR  = ./bin
 SRC_DIR  = ./src
+TEST_SRC_DIR  = ./test/src
 
-CPP = g++
+ifdef CXX # CXX defined in environment
+  CPP = $(CXX)
+  CC = $(CXX)
+else
+  CPP = g++
+endif
+
+ifdef OPENBLAS
+  WITH_LAPACK =  # OPENBLAS usually includes LAPACK
+endif
 
-CPPFLAGS = -F /System/Library/Frameworks \
-  -O3 -I/usr/local/opt/gsl@1/include \
-  -I./eigen -Wc++11-narrowing -Wno-unused-value
+ifdef DEBUG
+  CPPFLAGS = -g $(GCC_FLAGS) -std=gnu++11 -isystem/$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
+else
+  # release mode
+  CPPFLAGS = -DNDEBUG $(GCC_FLAGS) -std=gnu++11 -isystem/$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
+endif
 
-LIBS = /usr/local/opt/gsl@1/lib/libgsl.a \
-       /usr/local/opt/gsl@1/lib/libgslcblas.a -lz
+ifdef SHOW_COMPILER_WARNINGS
+  CPPFLAGS += -Wall
+endif
 
 OUTPUT = $(BIN_DIR)/gemma
 
@@ -41,55 +81,59 @@ SOURCES = $(SRC_DIR)/main.cpp
 HDR =
 
 # Detailed libary paths, D for dynamic and S for static
+LIBS += -framework Accelerate \
+  /usr/local/opt/zlib/lib/libz.a \
+  /usr/local/Cellar/gsl/2.4/lib/libgsl.a \
+  /usr/local/Cellar/gsl/2.4/lib/libgslcblas.a
 
-LIBS_LNX_D_LAPACK = -llapack
-LIBS_MAC_D_LAPACK = -framework Accelerate
-LIBS_LNX_S_LAPACK = /usr/lib/lapack/liblapack.a -lgfortran  /usr/lib/atlas-base/libatlas.a /usr/lib/libblas/libblas.a -Wl,--allow-multiple-definition
-
-# Options
-
-SOURCES += $(SRC_DIR)/param.cpp $(SRC_DIR)/gemma.cpp $(SRC_DIR)/io.cpp $(SRC_DIR)/lm.cpp $(SRC_DIR)/lmm.cpp $(SRC_DIR)/vc.cpp $(SRC_DIR)/mvlmm.cpp $(SRC_DIR)/bslmm.cpp $(SRC_DIR)/prdt.cpp $(SRC_DIR)/mathfunc.cpp $(SRC_DIR)/gzstream.cpp $(SRC_DIR)/eigenlib.cpp $(SRC_DIR)/ldr.cpp $(SRC_DIR)/bslmmdap.cpp $(SRC_DIR)/logistic.cpp $(SRC_DIR)/varcov.cpp
-HDR += $(SRC_DIR)/param.h $(SRC_DIR)/gemma.h $(SRC_DIR)/io.h $(SRC_DIR)/lm.h $(SRC_DIR)/lmm.h $(SRC_DIR)/vc.h $(SRC_DIR)/mvlmm.h $(SRC_DIR)/bslmm.h $(SRC_DIR)/prdt.h $(SRC_DIR)/mathfunc.h $(SRC_DIR)/gzstream.h $(SRC_DIR)/eigenlib.h
-
-ifdef WITH_LAPACK
-  OBJS += $(SRC_DIR)/lapack.o
-  CPPFLAGS += -DWITH_LAPACK
-ifeq ($(SYS), MAC)
-  LIBS += $(LIBS_MAC_D_LAPACK)
-else
-ifdef FORCE_DYNAMIC
-  LIBS += $(LIBS_LNX_D_LAPACK)
-else
-  LIBS += $(LIBS_LNX_S_LAPACK)
-endif
-endif
-  SOURCES += $(SRC_DIR)/lapack.cpp
-  HDR += $(SRC_DIR)/lapack.h
-endif
-
-ifdef FORCE_32BIT
-  CPPFLAGS += -m32
-else
-  CPPFLAGS += -m64
-endif
+HDR          = $(wildcard src/*.h)
+SOURCES      = $(wildcard src/*.cpp)
 
 # all
 OBJS = $(SOURCES:.cpp=.o)
 
 all: $(OUTPUT)
 
+<print-% : ; @echo $* = $($*)
+
 $(OUTPUT): $(OBJS)
 	$(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT)
 
-$(OBJS) : $(HDR)
+$(OBJS)  : $(HDR)
 
 .cpp.o:
 	$(CPP) $(CPPFLAGS) $(HEADERS) -c $*.cpp -o $*.o
 .SUFFIXES : .cpp .c .o $(SUFFIXES)
 
+unittests: all contrib/catch-1.9.7/catch.hpp $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o
+	$(CPP) $(CPPFLAGS) $(TEST_SRC_DIR)/unittests-main.o  $(TEST_SRC_DIR)/unittests-math.o $(filter-out src/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests-gemma
+	./bin/unittests-gemma
+
+fast-check: all unittests
+	rm -vf test/output/*
+	cd test && ./dev_test_suite.sh | tee ../dev_test.log
+	grep -q 'success rate: 100%' dev_test.log
+
+slow-check: all
+	rm -vf test/output/*
+	cd test && ./test_suite.sh | tee ../test.log
+	grep -q 'success rate: 100%' test.log
+
+lengthy-check: all
+	rm -vf test/output/*
+	cd test && ./lengthy_test_suite.sh | tee ../lengthy_test.log
+	grep -q 'success rate: 100%' lengthy_test.log
+
+check: fast-check slow-check
+
+check-all: check lengthy-check
 
 clean:
-	rm -rf ${SRC_DIR}/*.o ${SRC_DIR}/*~ *~ $(OUTPUT)
+	rm -vf $(SRC_DIR)/*.o
+	rm -vf $(SRC_DIR)/*~
+	rm -vf $(TEST_SRC_DIR)/*.o
+	rm -vf $(OUTPUT)
+	rm -vf ./bin/unittests-gemma
 
 DIST_COMMON = COPYING.txt README.txt Makefile
 DIST_SUBDIRS = src doc example bin
@@ -100,4 +144,3 @@ tar:
 	cp -r $(DIST_SUBDIRS) ./$(DIST_NAME)/
 	tar cvzf $(DIST_NAME).tar.gz ./$(DIST_NAME)/
 	rm -r ./$(DIST_NAME)
-