Makefile revamped. See comments:

- Added CUSTOMFLAGS to define flags from Make CLI.
- Separated and re-arranged C object targets.
- Added targets for test binaries.

java/source/infodynamics/measures/continuous/kraskov/cuda/Makefile

@@ -18,25 +18,52 @@ ifdef DEBUG
 	NVCCFLAGS  += -g -G
 endif
 
+ifdef CUSTOMFLAGS
+	CCFLAGS    += ${CUSTOMFLAGS}
+	NVCCFLAGS  += ${CUSTOMFLAGS}
+endif
+
+
 # Common includes and paths for CUDA. This assumes the CUDA toolkit is in PATH
 INCLUDES      := -I. -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux
 LDFLAGS       += -L. -lcuda -lcudart
 
-# Target rules
+# Main target rule
 all:  libKraskov.so
 
+## Compile device code
+#---------------------
 gpuKnnLibrary.o: gpuKnnLibrary.cu helperfunctions.cu gpuKnnBF_kernel.cu
 	${NVCC} ${NVCCFLAGS} ${INCLUDES} -Xcompiler -fPIC -c gpuKnnLibrary.cu
 
 libgpuKnnLibrary.a: gpuKnnLibrary.o
 	${AR} -r libgpuKnnLibrary.a gpuKnnLibrary.o
 
-libKraskov.so: libgpuKnnLibrary.a kraskovCuda.c
-	${NVCC} ${NVCCFLAGS} ${INCLUDES} -Xcompiler -fPIC -shared -o libKraskov.so digamma.c gpuMILibrary.c kraskovCuda.c ${LDFLAGS} -lgpuKnnLibrary
 
-test:	libKraskov.so
-	${GCC} -std=c++11 -o unittest unittests.cpp -L. -lKraskov
+## Compile host code
+#-------------------
+c_objects = digamma.o gpuMILibrary.o kraskovCuda.o
+
+%.o:	%.c
+	${GCC} ${INCLUDES} ${CCFLAGS} -x c -std=c99 -fPIC -c $< -o $@
+
+
+## Final shared library linking
+#------------------------------
+libKraskov.so: libgpuKnnLibrary.a $(c_objects)
+	${NVCC} ${NVCCFLAGS} ${INCLUDES} -Xcompiler -fPIC -shared -o libKraskov.so $(c_objects) ${LDFLAGS} -lgpuKnnLibrary
+
+
+## Test binary targets
+#------------------------------
+test:	unittest perftest
+
+unittest:	libKraskov.so unittest.cpp
+	${GCC} ${CCFLAGS} -std=c++11 unittests.cpp -L. -lKraskov -o $@ 
+
+perftest: libKraskov.so perftest.cpp 
+	${GCC} ${CCFLAGS} -DTIMER -std=c++11 perftest.cpp -L. -lKraskov -o $@ 
 
 clean:
-	rm -f *.o *.so *.a unittest
+	rm -f *.o *.so *.a unittest perftest