blob: fa7460e95be1404c85d99e18649b0044829590d3 (
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
|
# Generic Makefile for GEMMA
#
# Supported platforms
#
# Unix / Linux LNX (default)
# Mac MAC
#
# Compilation options
# 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
GEMMA_VERSION = $(shell cat ./VERSION)
# Set this variable to either LNX or MAC
SYS = MAC # LNX|MAC (Linux is the default)
# Leave blank after "=" to disable; put "= 1" to enable
DIST_NAME = gemma-$(GEMMA_VERSION)
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 \
-I/System/Library/Frameworks/Accelerate.framework/Versions/Current/Frameworks/vecLib.framework/Headers
TRAVIS_CI = # used by TRAVIS for testing
EIGEN_INCLUDE_PATH=
CXX = g++
# --------------------------------------------------------------------
# Edit below this line with caution
# --------------------------------------------------------------------
BIN_DIR = ./bin
SRC_DIR = ./src
TEST_SRC_DIR = ./test/src
ifdef CXX # CXX defined in environment
CPP = $(CXX)
CC = $(CXX)
else
CPP = g++
endif
ifdef OPENBLAS
WITH_LAPACK = # OPENBLAS usually includes LAPACK
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
OUTPUT = $(BIN_DIR)/gemma
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
HDR = $(wildcard src/*.h) ./src/version.h
SOURCES = $(wildcard src/*.cpp)
# all
OBJS = $(SOURCES:.cpp=.o)
all: $(OUTPUT)
./src/version.h:
./scripts/gen_version_info.sh > src/version.h
<print-% : ; @echo $* = $($*)
$(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/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 -vf $(SRC_DIR)/version.h
rm -vf $(SRC_DIR)/*.o
rm -vf $(SRC_DIR)/*~
rm -vf $(TEST_SRC_DIR)/*.o
rm -vf $(OUTPUT)
rm -vf ./bin/unittests-gemma
DIST_COMMON = COPYING.txt README.txt Makefile
DIST_SUBDIRS = src doc example bin
tar:
mkdir -p ./$(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)
|
