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Makefile
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Makefile
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CXX := h5c++
PLATFORM := $(shell uname -s)
COMPILER := $(shell ($(CXX) -v 2>&1) | tr A-Z a-z )
ifdef DEBUG
ifneq (,$(findstring pgi,$(COMPILER)))
OPT = -g
else
OPT = -O0 -DDEBUG=1 --debug -g -ggdb
endif
else
ifneq (,$(findstring pgi,$(COMPILER)))
OPT = -fast
else
ifneq (,$(findstring gcc,$(COMPILER)))
OPT = -O4
TGTFLAGS = -fwhole-program
else
OPT = -O3
endif
endif
endif
ifeq ($(PREFIX),)
PREFIX := $(CONDA_PREFIX)
endif
ifeq ($(PLATFORM),Darwin)
AVX2 := $(shell sysctl -a | grep -c AVX2)
LDDFLAGS = -dynamiclib -install_name @rpath/libssu.so
else
AVX2 := $(shell grep "^flags" /proc/cpuinfo | head -n 1 | grep -c avx2)
LDDFLAGS = -shared
endif
EXEFLAGS =
ifneq (,$(findstring pgi,$(COMPILER)))
MPFLAG = -mp
else
MPFLAG = -fopenmp
endif
LDDFLAGS += $(MPFLAG)
CPPFLAGS += $(MPFLAG)
UNIFRAC_FILES = unifrac_internal.o unifrac_cmp_cpu.o
ifndef NOGPU
ifneq (,$(findstring pgi,$(COMPILER)))
CPPFLAGS += -DUNIFRAC_ENABLE_ACC=1
UNIFRAC_FILES += unifrac_cmp_acc.o
ACCCPPFLAGS += -acc
ifeq ($(PERFORMING_CONDA_BUILD),True)
ACCCPPFLAGS += -ta=tesla:ccall
else
ACCCPPFLAGS += -ta=tesla
endif
# optional info
ACCCPPFLAGS += -Minfo=accel
LDDFLAGS += -shlib -acc -Bstatic_pgi
EXEFLAGS += -acc -Bstatic_pgi
endif
endif
ifneq (,$(findstring pgi,$(COMPILER)))
ifeq ($(PERFORMING_CONDA_BUILD),True)
CPPFLAGS += -tp=px
endif
else
ifeq ($(PERFORMING_CONDA_BUILD),True)
CPPFLAGS += -mtune=generic
else
CPPFLAGS += -mfma -march=native
endif
endif
ifeq (,$(findstring pgi,$(COMPILER)))
# basically, not gcc
CPPFLAGS += -Wextra -Wno-unused-parameter
endif
ifeq ($(PLATFORM),Darwin)
BLASLIB=-llapacke -lcblas
else
BLASLIB=-lcblas
endif
CPPFLAGS += -Wall -std=c++11 -pedantic -I. $(OPT) -fPIC -L$(CONDA_PREFIX)/lib
test: tree.o test_su.cpp biom.o unifrac.o skbio_alt.o api.o $(UNIFRAC_FILES)
$(CXX) $(CPPFLAGS) $(EXEFLAGS) test_su.cpp -o test_su tree.o biom.o $(UNIFRAC_FILES) unifrac.o skbio_alt.o api.o -llz4 $(BLASLIB) -lpthread
$(CXX) $(CPPFLAGS) $(EXEFLAGS) test_ska.cpp -o test_ska skbio_alt.o tree.o biom.o $(UNIFRAC_FILES) unifrac.o api.o -llz4 $(BLASLIB) -lpthread
$(CXX) $(CPPFLAGS) $(EXEFLAGS) test_api.cpp -o test_api tree.o biom.o $(UNIFRAC_FILES) unifrac.o skbio_alt.o api.o -llz4 $(BLASLIB) -lpthread
main: tree.o biom.o unifrac.o cmd.o skbio_alt.o api.o $(UNIFRAC_FILES)
$(CXX) $(CPPFLAGS) $(EXEFLAGS) su.cpp -o ssu tree.o biom.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 $(BLASLIB) -lpthread
$(CXX) $(CPPFLAGS) $(EXEFLAGS) faithpd.cpp -o faithpd tree.o biom.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 $(BLASLIB) -lpthread
cp ssu ${PREFIX}/bin/
cp faithpd ${PREFIX}/bin/
rapi_test: main
mkdir -p ~/.R
if [ -e ~/.R/Makevars ] ; \
then \
echo "WARNING: OVERWRITING ~/.R/Makevars" ; \
echo "The original Makevars file has been copied to ~/.R/Makevars" ;\
cp ~/.R/Makevars Makevars-original ; \
fi;
echo CXX1X=h5c++ > ~/.R/Makevars
echo CXX=h5c++ >> ~/.R/Makevars
echo CC=h5c++ >> ~/.R/Makevars
echo LDFLAGS= -llz4 $(BLASLIB) >> ~/.R/Makevars
rm -f *.o
Rscript R_interface/rapi_test.R
rm -f *.o
api: tree.o biom.o unifrac.o cmd.o skbio_alt.o api.o $(UNIFRAC_FILES)
$(CXX) $(LDDFLAGS) -o libssu.so tree.o biom.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 $(BLASLIB) -L$(PREFIX)/lib
cp libssu.so ${PREFIX}/lib/
capi_test: api
gcc -std=c99 capi_test.c -lssu -L${PREFIX}/lib -Wl,-rpath,${PREFIX}/lib -o capi_test
export LD_LIBRARY_PATH="${PREFIX}/lib":"./capi_test"
api.o: api.cpp api.hpp unifrac.hpp skbio_alt.hpp biom.hpp tree.hpp
$(CXX) $(CPPFLAGS) api.cpp -c -o api.o -fPIC
unifrac_cmp_cpu.o: unifrac_cmp.cpp unifrac_cmp.hpp unifrac_internal.hpp unifrac.hpp unifrac_task.cpp unifrac_task.hpp biom_interface.hpp tree.hpp
$(CXX) $(CPPFLAGS) -c $< -o $@
unifrac_cmp_acc.o: unifrac_cmp.cpp unifrac_cmp.hpp unifrac_internal.hpp unifrac.hpp unifrac_task.cpp unifrac_task.hpp biom_interface.hpp tree.hpp
$(CXX) $(CPPFLAGS) $(ACCCPPFLAGS) -c $< -o $@
%.o: %.cpp %.hpp
$(CXX) $(CPPFLAGS) -c $< -o $@
clean:
-rm -f *.o ssu