forked from arun-sub/genomicsbench
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathMakefile
89 lines (58 loc) · 2.29 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
CXX=g++
CC=gcc
ARCH=avx2
#VTUNE_HOME=/opt/intel/oneapi/vtune/2021.1.1
MKLROOT=/opt/intel/oneapi/mkl/2021.1.1
MKL_IOMP5_DIR=/opt/intel/oneapi/compiler/2021.1.2/linux/compiler/lib/intel64_lin
CUDA_LIB=/usr/local/cuda
uname_arch := $(shell uname -m)
ifeq ($(uname_arch),aarch64)
MINIMAP_FLAGS=arm_neon=1 aarch64=1 -f Makefile.simde CFLAGS='-O3 -mcpu=native -g'
endif
.PHONY: clean
TARGETS=fmi bsw dbg phmm chain poa pileup kmer-cnt
all: $(TARGETS)
htslib:
cd tools/htslib && autoreconf -i && ./configure && $(MAKE) LDFLAGS="-fopenmp"
bwa-mem2:
cd tools/bwa-mem2 ; $(MAKE) CC=$(CC) CXX=$(CXX) VTUNE_HOME=$(VTUNE_HOME)
fmi: bwa-mem2
cd benchmarks/fmi; $(MAKE) CXX=$(CXX) VTUNE_HOME=$(VTUNE_HOME)
bsw:
cd benchmarks/bsw; $(MAKE) CXX=$(CXX) VTUNE_HOME=$(VTUNE_HOME)
dbg: htslib
cd benchmarks/dbg; $(MAKE) CXX=$(CXX) VTUNE_HOME=$(VTUNE_HOME)
gkl_phmm:
cd tools/GKL; ./gradlew cmakeConfig -Pcxx=$(CXX) -Pcc=$(CC) -Pcflags="$(CFLAGS)" && make -C build/native/src/main/native/pairhmm && make -C build/native/src/main/native/pairhmm install
phmm: gkl_phmm
cd benchmarks/phmm; $(MAKE) CC=$(CC) VTUNE_HOME=$(VTUNE_HOME)
minimap2:
cd tools/minimap2; $(MAKE) $(MINIMAP_FLAGS)
chain: minimap2
cd benchmarks/chain; $(MAKE) CXX=$(CXX) VTUNE_HOME=$(VTUNE_HOME)
spoa:
cd tools/spoa; mkdir build; cd build; cmake -DCMAKE_BUILD_TYPE=Release -Dspoa_optimize_for_native=OFF ..; $(MAKE)
poa: spoa
cd benchmarks/poa; $(MAKE) CXX=$(CXX) VTUNE_HOME=$(VTUNE_HOME)
pileup: htslib
cd benchmarks/pileup; CC=$(CC) $(MAKE) VTUNE_HOME=$(VTUNE_HOME)
kmer-cnt:
cd benchmarks/kmer-cnt; $(MAKE) CXX=$(CXX) VTUNE_HOME=$(VTUNE_HOME)
#grm: htslib
# cd benchmarks/grm/2.0/build_dynamic; $(MAKE) CC=$(CC) CXX=$(CXX) arch=$(ARCH) VTUNE_HOME=$(VTUNE_HOME) MKLROOT=$(MKLROOT) MKL_IOMP5_DIR=$(MKL_IOMP5_DIR) #needs MKL
gpu:
cd benchmarks/abea; $(MAKE) CUDA_LIB=$(CUDA_LIB)
clean:
cd tools/bwa-mem2; $(MAKE) clean
cd benchmarks/fmi; $(MAKE) clean
cd benchmarks/bsw; $(MAKE) clean
cd benchmarks/dbg; $(MAKE) clean
cd tools/htslib; $(MAKE) clean
cd tools/GKL; ./gradlew clean
cd benchmarks/phmm; $(MAKE) clean
cd tools/minimap2; $(MAKE)
cd benchmarks/chain; $(MAKE) clean
cd benchmarks/poa; $(MAKE) clean
cd benchmarks/pileup; $(MAKE) clean
cd benchmarks/kmer-cnt; $(MAKE) clean
cd benchmarks/grm/2.0/build_dynamic; $(MAKE) clean