115 lines
4.0 KiB
Makefile
115 lines
4.0 KiB
Makefile
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#Copyright (c) 2012 The Broad Institute
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#Permission is hereby granted, free of charge, to any person
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#obtaining a copy of this software and associated documentation
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#files (the "Software"), to deal in the Software without
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#restriction, including without limitation the rights to use,
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#copy, modify, merge, publish, distribute, sublicense, and/or sell
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#copies of the Software, and to permit persons to whom the
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#Software is furnished to do so, subject to the following
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#conditions:
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#The above copyright notice and this permission notice shall be
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#included in all copies or substantial portions of the Software.
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#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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#EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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#OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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#NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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#HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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#WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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#FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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#THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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#
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#OMPCFLAGS=-fopenmp
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#OMPLFLAGS=-fopenmp #-openmp-link static
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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 $(OMPCFLAGS) -Wno-unknown-pragmas
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JRE_HOME?=/opt/jdk1.7.0_25/jre
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JNI_COMPILATION_FLAGS=-D_REENTRANT -fPIC -I${JRE_HOME}/../include -I${JRE_HOME}/../include/linux
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COMMON_COMPILATION_FLAGS=$(JNI_COMPILATION_FLAGS) -O3 -W -Wall -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas
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CC=icc
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CXX=icc
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LDFLAGS=-lm -lrt $(OMPLDFLAGS)
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ifdef DISABLE_FTZ
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COMMON_COMPILATION_FLAGS+=-DDISABLE_FTZ -no-ftz
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endif
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PAPI_DIR=/home/karthikg/softwares/papi-5.3.0
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ifdef USE_PAPI
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ifeq ($(USE_PAPI),1)
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COMMON_COMPILATION_FLAGS+=-I$(PAPI_DIR)/include -DUSE_PAPI
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LDFLAGS+=-L$(PAPI_DIR)/lib -lpapi
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endif
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endif
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ifdef DISABLE_FTZ
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COMMON_COMPILATION_FLAGS+=-DDISABLE_FTZ -no-ftz
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endif
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BIN=libVectorLoglessPairHMM.so pairhmm-template-main checker
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#BIN=checker
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DEPDIR=.deps
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DF=$(DEPDIR)/$(*).d
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#Common across libJNI and sandbox
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COMMON_SOURCES=utils.cc avx_function_instantiations.cc baseline.cc sse_function_instantiations.cc LoadTimeInitializer.cc
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#Part of libJNI
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LIBSOURCES=org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc Sandbox.cc $(COMMON_SOURCES)
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SOURCES=$(LIBSOURCES) pairhmm-template-main.cc pairhmm-1-base.cc
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LIBOBJECTS=$(LIBSOURCES:.cc=.o)
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COMMON_OBJECTS=$(COMMON_SOURCES:.cc=.o)
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#No vectorization for these files
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NO_VECTOR_SOURCES=org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc pairhmm-template-main.cc pairhmm-1-base.cc utils.cc baseline.cc LoadTimeInitializer.cc Sandbox.cc
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#Use -xAVX for these files
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AVX_SOURCES=avx_function_instantiations.cc
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#Use -xSSE4.2 for these files
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SSE_SOURCES=sse_function_instantiations.cc
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NO_VECTOR_OBJECTS=$(NO_VECTOR_SOURCES:.cc=.o)
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AVX_OBJECTS=$(AVX_SOURCES:.cc=.o)
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SSE_OBJECTS=$(SSE_SOURCES:.cc=.o)
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$(NO_VECTOR_OBJECTS): CXXFLAGS=$(COMMON_COMPILATION_FLAGS)
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$(AVX_OBJECTS): CXXFLAGS=$(COMMON_COMPILATION_FLAGS) -xAVX
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$(SSE_OBJECTS): CXXFLAGS=$(COMMON_COMPILATION_FLAGS) -xSSE4.2
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OBJECTS=$(NO_VECTOR_OBJECTS) $(AVX_OBJECTS) $(SSE_OBJECTS)
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all: $(BIN) Sandbox.class copied_lib
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-include $(addprefix $(DEPDIR)/,$(SOURCES:.cc=.d))
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checker: pairhmm-1-base.o $(COMMON_OBJECTS)
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$(CXX) $(OMPLFLAGS) -o $@ $^ $(LDFLAGS)
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pairhmm-template-main: pairhmm-template-main.o $(COMMON_OBJECTS)
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$(CXX) $(OMPLFLAGS) -o $@ $^ $(LDFLAGS)
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libVectorLoglessPairHMM.so: $(LIBOBJECTS)
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$(CXX) $(OMPLFLAGS) -shared -static-intel -o $@ $(LIBOBJECTS) ${LDFLAGS}
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$(OBJECTS): %.o: %.cc
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@mkdir -p $(DEPDIR)
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$(CXX) -c -MMD -MF $(DF) $(CXXFLAGS) $(OUTPUT_OPTION) $<
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Sandbox.class: Sandbox.java
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javac Sandbox.java
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copied_lib: libVectorLoglessPairHMM.so
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ifdef OUTPUT_DIR
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mkdir -p $(OUTPUT_DIR)
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rsync -a libVectorLoglessPairHMM.so $(OUTPUT_DIR)/
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endif
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clean:
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rm -rf $(BIN) *.o $(DEPDIR) *.class
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