blob: 95f7e654bdbed8341ac5fd5cc4de003151bd3ae0 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
|
#Makefile
# Supported platforms
# Unix / Linux LNX
# Mac MAC
# Compilation options
# 32-bit binary FORCE_32BIT
# dynamic compilation FORCE_DYNAMIC
# Set this variable to either LNX or MAC
SYS = LNX
# Leave blank after "=" to disable; put "= 1" to enable
SHOW_COMPILER_WARNINGS =
WITH_LAPACK = 1
WITH_OPENBLAS =
NO_INTEL_COMPAT =
FORCE_32BIT =
FORCE_DYNAMIC =
GCC_FLAGS = -O3 # extra flags -Wl,--allow-multiple-definition
DIST_NAME = gemma-0.97.2
TRAVIS_CI =
# --------------------------------------------------------------------
# Edit below this line with caution
# --------------------------------------------------------------------
EIGEN_INCLUDE_PATH=/usr/include/eigen3
BIN_DIR = ./bin
SRC_DIR = ./src
TEST_SRC_DIR = ./test/src
ifdef CXX
CPP = $(CXX)
CC = $(CXX)
else
CPP = g++
endif
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
ifdef SHOW_COMPILER_WARNINGS
CPPFLAGS += -Wall
endif
ifdef FORCE_DYNAMIC
LIBS = -lgsl -lgslcblas -pthread -lz
else
ifndef TRAVIS_CI # Travis static compile we cheat a little
CPPFLAGS += -static
endif
endif
OUTPUT = $(BIN_DIR)/gemma
SOURCES = $(SRC_DIR)/main.cpp
HDR =
# Detailed libary paths, D for dynamic and S for static
LIBS_LNX_D_LAPACK = -llapack
LIBS_LNX_D_BLAS = -lblas
LIBS_LNX_D_OPENBLAS = -lopenblas
LIBS_MAC_D_LAPACK = -framework Veclib
# LIBS_LNX_S_LAPACK = /usr/lib/libgsl.a /usr/lib/libgslcblas.a /usr/lib/lapack/liblapack.a -lz
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
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 $(SRC_DIR)/debug.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 += $(SRC_DIR)/lapack.o
ifeq ($(SYS), MAC)
LIBS += $(LIBS_MAC_D_LAPACK)
else
ifdef FORCE_DYNAMIC
ifdef WITH_OPENBLAS
LIBS += $(LIBS_LNX_D_OPENBLAS)
else
LIBS += $(LIBS_LNX_D_BLAS)
endif
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 NO_INTEL_COMPAT
else
ifdef FORCE_32BIT
CPPFLAGS += -m32
else
CPPFLAGS += -m64
endif
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)
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_DIR)/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests
./bin/unittests
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
check: fast-check slow-check
clean:
rm -vf $(SRC_DIR)/*.o
rm -vf $(SRC_DIR)/*~
rm -vf $(TEST_SRC_DIR)/*.o
rm -vf $(OUTPUT)
rm -vf ./bin/unittests
DIST_COMMON = COPYING.txt README.txt Makefile
DIST_SUBDIRS = src doc example bin
tar:
mkdir -p ./$(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)
|
