Added new Makefile that I found works well for compiling on CentOS/Sc…

…ientific Linux 7

Makefile.linux

@@ -0,0 +1,125 @@
+#Makefile
+
+# Supported platforms
+#       Unix / Linux               	LNX
+#       Mac                        	MAC
+# Compilation options
+#       link to LAPACK              WITH_LAPACK
+#       32-bit binary        		FORCE_32BIT
+#       dynamic compilation    		FORCE_DYNAMIC
+#       float precision				FORCE_FLOAT
+
+# Set this variable to either LNX or MAC
+SYS = LNX
+# 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 = 
+FORCE_FLOAT = 
+DIST_NAME = gemma-0.95.2alpha
+
+# --------------------------------------------------------------------
+# Edit below this line with caution
+# --------------------------------------------------------------------
+
+
+BIN_DIR  = ./bin
+
+SRC_DIR  = ./src
+
+CPP = g++
+
+CPPFLAGS = -Wall -Weffc++ -O3 -std=gnu++11
+
+LIBS = /software/gsl-2.2.1-el7-x86_64/lib/libgslcblas.a \
+       /software/gsl-2.2.1-el7-x86_64/lib/libgsl.a \
+       -pthread -lz
+
+# ifdef FORCE_DYNAMIC
+# LIBS = -lgsl -lgslcblas -lblas -pthread -lz
+# else
+# LIBS = -lgsl -lgslcblas -pthread -lz
+# endif
+
+OUTPUT = $(BIN_DIR)/gemma
+
+ifdef FORCE_FLOAT
+OUTPUT = $(BIN_DIR)/gemmaf
+endif
+
+SOURCES = $(SRC_DIR)/main.cpp
+
+HDR = 
+
+# Detailed libary paths, D for dynamic and S for static
+LIBS_LNX_D_LAPACK = -llapack
+LIBS_MAC_D_LAPACK = -framework Veclib
+LIBS_LNX_S_LAPACK = /software/atlas-3.10.3-el7-x86_64/lib/liblapack.a \
+   /software/atlas-3.10.3-el7-x86_64/lib/libcblas.a \
+   /software/atlas-3.10.3-el7-x86_64/lib/libf77blas.a \
+   /software/atlas-3.10.3-el7-x86_64/lib/libatlas.a -lgfortran \
+   -Wl,--allow-multiple-definition 
+
+# Options
+
+ifdef FORCE_FLOAT
+  CPPFLAGS += -DFORCE_FLOAT
+  SOURCES += $(SRC_DIR)/param_float.cpp $(SRC_DIR)/gemma_float.cpp $(SRC_DIR)/io_float.cpp $(SRC_DIR)/lm_float.cpp $(SRC_DIR)/vc_float.cpp $(SRC_DIR)/lmm_float.cpp $(SRC_DIR)/mvlmm_float.cpp $(SRC_DIR)/bslmm_float.cpp $(SRC_DIR)/prdt_float.cpp $(SRC_DIR)/mathfunc_float.cpp $(SRC_DIR)/gzstream.cpp $(SRC_DIR)/eigenlib.cpp
+  HDR += $(SRC_DIR)/param_float.h $(SRC_DIR)/gemma_float.h $(SRC_DIR)/io_float.h $(SRC_DIR)/lm_float.h $(SRC_DIR)/lmm_float.h $(SRC_DIR)/vc_float.h $(SRC_DIR)/mvlmm_float.h $(SRC_DIR)/bslmm_float.h $(SRC_DIR)/prdt_float.h $(SRC_DIR)/mathfunc_float.h $(SRC_DIR)/gzstream.h $(SRC_DIR)/eigenlib.h
+else
+  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
+endif
+
+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
+
+# all
+OBJS = $(SOURCES:.cpp=.o)
+
+all: $(OUTPUT)
+
+$(OUTPUT): $(OBJS)
+	$(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT)
+
+$(OBJS) : $(HDR)
+
+.cpp.o: 
+	$(CPP) $(CPPFLAGS) $(HEADERS) -c $*.cpp -o $*.o
+.SUFFIXES : .cpp .c .o $(SUFFIXES)
+
+
+clean:
+	rm -rf ${SRC_DIR}/*.o ${SRC_DIR}/*~ *~ ${SRC_DIR}/*_float.* $(OUTPUT)
+
+DIST_COMMON = COPYING.txt README.txt Makefile
+DIST_SUBDIRS = src doc example bin
+
+tar:
+	mkdir -p ./$(DIST_NAME)
+	cp $(DIST_COMMON) ./$(DIST_NAME)/
+	cp -r $(DIST_SUBDIRS) ./$(DIST_NAME)/
+	tar cvzf $(DIST_NAME).tar.gz ./$(DIST_NAME)/
+	rm -r ./$(DIST_NAME)
+