45 lines
1.4 KiB
Makefile
45 lines
1.4 KiB
Makefile
OMPCFLAGS=-fopenmp
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#OMPLDFLAGS=-lgomp
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#CFLAGS=-O2 -std=c++11 -W -Wall -march=corei7-avx -Wa,-q -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas
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#CFLAGS=-O2 -W -Wall -march=corei7 -mfpmath=sse -msse4.2 -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas
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JAVA_ROOT=/opt/jdk1.7.0_25/
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JNI_COMPILATION_FLAGS=-D_REENTRANT -fPIC -I${JAVA_ROOT}/include -I${JAVA_ROOT}/include/linux
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CFLAGS=-O3 -W -Wall -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas -xAVX
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CXXFLAGS=$(CFLAGS)
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CC=icc
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CXX=icc
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LDFLAGS=-lm $(OMPLDFLAGS)
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#BIN:=pairhmm-1-base #pairhmm-2-omp pairhmm-3-hybrid-float-double pairhmm-4-hybrid-diagonal pairhmm-5-hybrid-diagonal-homogeneus pairhmm-6-onlythreediags pairhmm-7-presse pairhmm-8-sse #pairhmm-dev
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BIN:=libJNILoglessPairHMM.so pairhmm-template-main
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#SOURCES=pairhmm-1-base.cc input.cc
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LIBSOURCES=org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc hmm_mask.cc
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SOURCES=$(LIBSOURCES) pairhmm-template-main.cc
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LIBOBJECTS=$(LIBSOURCES:.cc=.o)
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DEPDIR=.deps
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DF=$(DEPDIR)/$(*).d
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all: $(BIN)
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-include $(addprefix $(DEPDIR)/,$(SOURCES:.cc=.d))
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pairhmm-template-main: pairhmm-template-main.o hmm_mask.o
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$(CXX) -fopenmp -o $@ $^ $(LDFLAGS)
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libJNILoglessPairHMM.so: $(LIBOBJECTS)
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$(CXX) -shared -o $@ $(LIBOBJECTS)
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%.o: %.cc
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@mkdir -p $(DEPDIR)
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$(COMPILE.cpp) -MMD -MF $(DF) $(JNI_COMPILATION_FLAGS) $(CXXFLAGS) $(OUTPUT_OPTION) $<
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clean:
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rm -f $(BIN) *.o
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