Make ssu and faithpd use the shared library

biocore · Jan 24, 2025 · 817b7d7 · 817b7d7
1 parent 897ce3e
commit 817b7d7
Show file tree

Hide file tree

Showing 5 changed files with 23 additions and 119 deletions.
diff --git a/Makefile b/Makefile
@@ -6,20 +6,20 @@ PLATFORM := $(shell uname -s)
 COMPILER := $(shell ($(CXX) -v 2>&1) | tr A-Z a-z )
 
 ifeq ($(PLATFORM),Darwin)
-all: api main install test_binaries
+all: api install main install_main test_binaries
 
 else
 
 # Note: important that all_nv is after all_cpu_basic and all_nv_avx2 for tests to work
 all: all_cpu_basic all_nv_avx2 all_nv all_combined test_binaries_nv
 
-all_cpu_basic: api_cpu_basic main_cpu_basic install_cpu_basic
+all_cpu_basic: api_cpu_basic install_cpu_basic
 
-all_nv: api_nv main_nv install_nv
+all_nv: api_nv install_nv
 
-all_nv_avx2: api_nv_avx2 main_nv_avx2 install_nv_avx2
+all_nv_avx2: api_nv_avx2 install_nv_avx2
 
-all_combined: api_combined install_combined
+all_combined: api_combined install_combined main install_main
 
 endif
 
@@ -50,28 +50,22 @@ api_combined:
 main:
 	cd src && make main
 
-main_cpu_basic:
-	export BUILD_VARIANT=cpu_basic ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make main
-
-main_nv:
-	. ./setup_nv_h5.sh; export BUILD_VARIANT=nv ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make main
-
-main_nv_avx2:
-	. ./setup_nv_h5.sh; export BUILD_VARIANT=nv_avx2 ; export BUILD_FULL_OPTIMIZATION=True ; cd src && make main
+install_main:
+	cd src && make install
 
 ########### install
 
 install:
-	cd src && make install
+	cd src && make install_lib
 
 install_cpu_basic:
-	export BUILD_VARIANT=cpu_basic ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make install
+	export BUILD_VARIANT=cpu_basic ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make install_lib
 
 install_nv:
-	. ./setup_nv_h5.sh; export BUILD_VARIANT=nv ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make install
+	. ./setup_nv_h5.sh; export BUILD_VARIANT=nv ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make install_lib
 
 install_nv_avx2:
-	. ./setup_nv_h5.sh; export BUILD_VARIANT=nv_avx2 ; export BUILD_FULL_OPTIMIZATION=True ; cd src && make install
+	. ./setup_nv_h5.sh; export BUILD_VARIANT=nv_avx2 ; export BUILD_FULL_OPTIMIZATION=True ; cd src && make install_lib
 
 install_combined:
 	cd combined && make install

diff --git a/combined/Makefile b/combined/Makefile
@@ -19,9 +19,7 @@ libssu.so: libssu.o
 	$(CC) -shared -o libssu.so libssu.o -fPIC -ldl $(LDFLAGS)
 
 install: libssu.so
-	rm -f ${PREFIX}/lib//libssu.so; cp libssu.so ${PREFIX}/lib/
-	rm -f ${PREFIX}/bin/ssu; cp ssu ${PREFIX}/bin/
-	rm -f ${PREFIX}/bin/faithpd; cp faithpd ${PREFIX}/bin/
+	rm -f ${PREFIX}/lib/libssu.so; cp libssu.so ${PREFIX}/lib/
 
 clean:
 	rm -f libssu.o libssu.so
diff --git a/combined/faithpd b/combined/faithpd
diff --git a/combined/ssu b/combined/ssu
diff --git a/src/Makefile b/src/Makefile
@@ -1,4 +1,4 @@
-.PHONY: all main api test test_binaries install clean rapi_test
+.PHONY: all main api test test_binaries install install_lib clean rapi_test
 
 CXX := h5c++
 
@@ -138,7 +138,7 @@ endif
 
 CPPFLAGS += -Wall  -std=c++17 -pedantic -I. $(OPT) -fPIC -L$(PREFIX)/lib
 
-all: api main install
+all: api install_lib main install
 
 main: $(SSU) $(FPD)
 
@@ -153,11 +153,11 @@ test_ska: test_ska.cpp tree.o tsv.o test_su.cpp biom.o biom_inmem.o biom_subsamp
 test_api: test_api.cpp tree.o tsv.o test_su.cpp biom.o biom_inmem.o biom_subsampled.o unifrac.o skbio_alt.o api.o $(UNIFRAC_FILES)
 	$(CXX) $(CPPFLAGS) $(EXEFLAGS) test_api.cpp -o test_api tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o skbio_alt.o api.o -llz4 $(BLASLIB) -lpthread
 
-$(SSU): su.cpp tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac.o cmd.o skbio_alt.o api.o $(UNIFRAC_FILES)
-	$(CXX) $(CPPFLAGS) $(EXEFLAGS) su.cpp -o $(SSU) tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 $(BLASLIB) -lpthread
+$(SSU): su.cpp $(PREFIX)/lib/lib$(SSU).so
+	$(CXX) $(CPPFLAGS) $(EXEFLAGS) su.cpp -o $@ -l$(SSU)
 
-$(FPD): faithpd.cpp tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac.o cmd.o skbio_alt.o api.o $(UNIFRAC_FILES)
-	$(CXX) $(CPPFLAGS) $(EXEFLAGS) faithpd.cpp -o $(FPD) tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 $(BLASLIB) -lpthread
+$(FPD): faithpd.cpp $(PREFIX)/lib/lib$(SSU).so
+	$(CXX) $(CPPFLAGS) $(EXEFLAGS) faithpd.cpp -o $@ -l$(SSU)
 
 lib$(SSU).so: tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac.o cmd.o skbio_alt.o api.o $(UNIFRAC_FILES)
 	$(CXX) $(LDDFLAGS) -o lib$(SSU).so tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 $(BLASLIB) -L$(PREFIX)/lib -noshlib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
@@ -195,8 +195,11 @@ test: test_binaries
 	./test_ska
 	./test_api
 
-install: lib$(SSU).so $(SSU) $(FPD)
-	rm -f ${PREFIX}/lib//lib$(SSU).so; cp lib$(SSU).so ${PREFIX}/lib/
+install_lib: lib$(SSU).so
+	rm -f ${PREFIX}/lib/lib$(SSU).so; cp lib$(SSU).so ${PREFIX}/lib/
+
+
+install: $(SSU) $(FPD)
 	rm -f ${PREFIX}/bin/$(SSU); cp $(SSU) ${PREFIX}/bin/
 	rm -f ${PREFIX}/bin/$(FPD); cp $(FPD) ${PREFIX}/bin/
 	mkdir -p ${PREFIX}/include/unifrac