-
Notifications
You must be signed in to change notification settings - Fork 3
/
Copy pathMakefile
221 lines (178 loc) · 7.95 KB
/
Makefile
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
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
######################### configure ################
VERSION=0.5.0
# detect OS architecture and add flags
Platform := $(shell uname -s)
$(info "building PCAone on ${Platform} -- version ${VERSION}")
# MKLROOT=/opt/intel/oneapi/mkl/latest
MKLROOT =
# /opt/intel/oneapi/compiler/latest/lib/
ONEAPI_COMPILER := ${MKLROOT}
ONEAPI_OMP5 := $(ONEAPI_COMPILER)/lib/libiomp5.a
# make sure libiomp5 can be found on mac
# ln -s /opt/intel/oneapi/compiler/latest/mac/compiler/lib/libiomp5.dylib /opt/intel/oneapi/mkl/latest/lib/
# for MacOS use accelerate framework in default
# install openblas lapack on mac with brew install openblas lapack
OPENBLAS =
STATIC = 0 # by default dynamical linking
IOMP5 = 1 # use libiomp5 for mkl
DEBUG = 0 # debug
AVX = # 1: enable avx2 fma, 0: do nothing
########################### end ###########################
####### INC, LPATHS, LIBS, MYFLAGS
program = PCAone
CXX ?= g++ # use default g++ only if not set in env
CXXSTD = c++17
CXXFLAGS += -O3 -Wall -std=$(CXXSTD) -m64
MYFLAGS = -DVERSION=\"$(VERSION)\"
# CURRENT_DIR = $(shell pwd)
INC = -I./external -I./external/zstd/lib
PCALIB = libpcaone.a
ifeq ($(Platform), Darwin)
CXXFLAGS += -march=native
else
ifeq ($(strip $(AVX)),)
CXXFLAGS += -march=native
else ifeq ($(strip $(AVX)),1)
CXXFLAGS += -mavx2 -mfma
endif
endif
ifeq ($(strip $(DEBUG)),1)
MYFLAGS += -DDEBUG
endif
ifeq ($(Platform),Linux)
###### for linux
MYFLAGS += -fopenmp
ifneq ($(strip $(MKLROOT)),)
MYFLAGS += -DWITH_MKL -DEIGEN_USE_MKL_ALL
INC += -I${MKLROOT}/include/
ifeq ($(strip $(STATIC)),1)
ifeq ($(strip $(IOMP5)), 1)
SLIBS += -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a ${ONEAPI_OMP5} -Wl,--end-group -L${ONEAPI_COMPILER}/lib
else
SLIBS += -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_gnu_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -lgomp
endif
else
DLIBS += -Wl,--no-as-needed -Wl,-rpath,${ONEAPI_COMPILER}/lib,-rpath,${MKLROOT}/lib/intel64 -L${ONEAPI_COMPILER}/lib -L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5
endif
else ifneq ($(strip $(OPENBLAS)),)
MYFLAGS += -DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE
DLIBS += -llapack -llapacke -lopenblas -lgfortran -lgomp
else
DLIBS += -lgomp
endif
else ifeq ($(Platform),Darwin)
###### for mac
MYFLAGS += -Xpreprocessor -fopenmp
ifneq ($(strip $(OPENBLAS)),)
MYFLAGS += -DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE
ifeq ($(strip $(STATIC)),1)
# SLIBS += /usr/local/opt/gcc/lib/gcc/11/libgomp.a # gcc need libgomp.a
SLIBS += /opt/homebrew/opt/openblas/lib/libopenblas.a /opt/homebrew/opt/libomp/lib/libomp.a -L/opt/homebrew/opt/gcc/lib/gcc/14/ -lgfortran
else
DLIBS += -lopenblas -lomp
endif
else
MYFLAGS += -DEIGEN_USE_BLAS
ifeq ($(strip $(STATIC)),1)
SLIBS += /opt/homebrew/opt/libomp/lib/libomp.a -framework Accelerate
else
DLIBS += -lomp -framework Accelerate
endif
endif
endif
## libz
ifeq ($(strip $(STATIC)),1)
ifeq ($(Platform), Darwin)
SLIBS += /opt/homebrew/opt/zlib/lib/libz.a
# CXXFLAGS += -stdlib=libc++
else
SLIBS += /usr/lib/x86_64-linux-gnu/libz.a # /usr/lib64/libz.a #
CXXFLAGS += -static
# CXXFLAGS += -static-libgcc -static-libstdc++
endif
else
DLIBS += -lz
endif
# OBJ = $(patsubst %.cpp, %.o, $(wildcard ./src/*.cpp))
# tar OBJ as libpcaone.a
OBJ = src/Arnoldi.o src/Halko.o src/Data.o src/Utils.o src/Cmd.o \
src/FileBeagle.o src/FileCsv.o src/FileBgen.o src/FilePlink.o \
src/FileBinary.o src/FileUSV.o src/LD.o src/Projection.o src/Inbreeding.o \
src/kfunc.o
SLIBS += ./external/bgen/bgenlib.a ./external/zstd/lib/libzstd.a
LIBS += ${SLIBS} ${DLIBS} -lpthread -ldl -lm
.PHONY: all clean ld_matrix ld_r2 ld_prune ld_clump ld_tests
all: ${program}
${program}: zstdlib bgenlib pcaonelib src/Main.o
$(CXX) $(CXXFLAGS) -o $(program) src/Main.o ${PCALIB} ${LPATHS} ${LIBS} ${LDFLAGS}
%.o: %.cpp
${CXX} ${CXXFLAGS} ${MYFLAGS} -o $@ -c $< ${INC} ${CPPFLAGS}
zstdlib:
(cd ./external/zstd/lib/; $(MAKE) lib-nomt)
bgenlib:
(cd ./external/bgen/; $(MAKE))
pcaonelib:$(OBJ)
ar -rcs $(PCALIB) $?
rm:
(rm -f src/*.o $(program))
(cd ./external/bgen/; $(MAKE) clean)
clean:
(rm -f src/*.o $(program))
(cd ./external/bgen/; $(MAKE) clean)
(cd ./external/zstd/lib/; $(MAKE) clean)
data:
wget http://popgen.dk/zilong/datahub/pca/example.tar.gz
tar -xzf example.tar.gz && rm -f example.tar.gz
example_tests:
./PCAone -g example/test.bgen -n4 -o m0
./PCAone -g example/test.bgen -n4 -m0.1 -o m1
diff m0.eigvals m1.eigvals
./PCAone --csv example/BrainSpinalCord.csv.zst -k 10 -m 2 --scale 2 -S
hwe:
./PCAone -b example/plink -k 3 -V
./PCAone -b example/plink --USV pcaone --inbreed 1 -o inbreed_m0
./PCAone -b example/plink --USV pcaone --inbreed 1 -o inbreed_m1 -m 1
diff inbreed_m0.hwe inbreed_m1.hwe
rm -f inbreed* pcaone.*
ld_matrix:
./PCAone -b example/plink -k 3 --ld -o adj -d 2
./PCAone -b example/plink -k 3 --ld -o pcaone -d 2 -m 2
diff adj.mbim pcaone.mbim
cut -f1 adj.mbim | sort -cn ## check if sorted
awk '$$1==3' adj.mbim | cut -f4 | sort -cn
rm -f pcaone.*
ld_r2:
./PCAone -B adj.residuals --match-bim adj.mbim --ld-bp 1000 --print-r2 -o adj_r2
ld_prune:
./PCAone -B adj.residuals --match-bim adj.mbim --ld-r2 0.8 --ld-bp 1000000 -o adj_prune_m0 -m 0
./PCAone -B adj.residuals --match-bim adj.mbim --ld-r2 0.8 --ld-bp 1000000 -o adj_prune_m1 -m 1
diff adj_prune_m0.ld.prune.out adj_prune_m1.ld.prune.out > /dev/null
ld_clump:
./PCAone -B adj.residuals --match-bim adj.mbim --clump example/plink.pheno0.assoc --clump-p1 0.01 --clump-p2 0.05 --clump-r2 0.1 --clump-bp 10000000 -m 0 -o adj_clump_m0
./PCAone -B adj.residuals --match-bim adj.mbim --clump example/plink.pheno0.assoc --clump-p1 0.01 --clump-p2 0.05 --clump-r2 0.1 --clump-bp 10000000 -m 1 -o adj_clump_m1
diff adj_clump_m0.p0.clump adj_clump_m1.p0.clump > /dev/null
ld_tests:
./PCAone -b example/plink -k 3 --ld -o adj -d 0 --maf 0.1
./PCAone -B adj.residuals --match-bim adj.mbim --ld-r2 0.8 --ld-bp 1000000 -o adj_prune_m0 -m 0
./PCAone -B adj.residuals --match-bim adj.mbim --ld-r2 0.8 --ld-bp 1000000 -o adj_prune_m1 -m 2
diff adj_prune_m0.ld.prune.out adj_prune_m1.ld.prune.out > /dev/null
./PCAone -b example/plink -k 3 --ld -o adj -d 0 -m 4
./PCAone -B adj.residuals --match-bim adj.mbim --ld-r2 0.8 --ld-bp 1000000 -o adj_prune_m0 -m 0
./PCAone -B adj.residuals --match-bim adj.mbim --ld-r2 0.8 --ld-bp 1000000 -o adj_prune_m1 -m 2
diff adj_prune_m0.ld.prune.out adj_prune_m1.ld.prune.out > /dev/null
./PCAone -b example/plink -k 3 --ld -o adj -d 1 --maf 0.1
./PCAone -B adj.residuals --match-bim adj.mbim --ld-r2 0.8 --ld-bp 1000000 -o adj_prune_m0 -m 0
./PCAone -B adj.residuals --match-bim adj.mbim --ld-r2 0.8 --ld-bp 1000000 -o adj_prune_m1 -m 2
diff adj_prune_m0.ld.prune.out adj_prune_m1.ld.prune.out > /dev/null
./PCAone -b example/plink -k 3 --ld -o adj -d 1 -m 4
./PCAone -B adj.residuals --match-bim adj.mbim --ld-r2 0.8 --ld-bp 1000000 -o adj_prune_m0 -m 0
./PCAone -B adj.residuals --match-bim adj.mbim --ld-r2 0.8 --ld-bp 1000000 -o adj_prune_m1 -m 2
diff adj_prune_m0.ld.prune.out adj_prune_m1.ld.prune.out > /dev/null
./PCAone -b example/plink -k 3 --ld -o adj -d 2 --maf 0.1
./PCAone -B adj.residuals --match-bim adj.mbim --ld-r2 0.8 --ld-bp 1000000 -o adj_prune_m0 -m 0
./PCAone -B adj.residuals --match-bim adj.mbim --ld-r2 0.8 --ld-bp 1000000 -o adj_prune_m1 -m 2
diff adj_prune_m0.ld.prune.out adj_prune_m1.ld.prune.out > /dev/null
./PCAone -b example/plink -k 3 --ld -o adj -d 2 -m 4
./PCAone -B adj.residuals --match-bim adj.mbim --ld-r2 0.8 --ld-bp 1000000 -o adj_prune_m0 -m 0
./PCAone -B adj.residuals --match-bim adj.mbim --ld-r2 0.8 --ld-bp 1000000 -o adj_prune_m1 -m 2
diff adj_prune_m0.ld.prune.out adj_prune_m1.ld.prune.out > /dev/null