The FFTW3 build system makes use of Autotools, so that you can not use it directly with the Android NDK.
A good blog post dealing with this issue is here.
The idea is to generate a proper config.h file offline and to create Android Makefiles, which replace the missing ones normally generated by the Autotools.
To achieve a modular layout for the different native modules you might use, I'd recommend the following:
In your top jni/ directory put these two files:
Application.mk:
APP_OPTIM := release
APP_ABI := armeabi armeabi-v7a
APP_MODULES := fftw3
Android.mk:
TOP_DIR := $(call my-dir)
include $(TOP_DIR)/fftw3/project/jni/Android.mk
This way you can easily add a new module by creating a jni/new_module_name directory and then adding new_module_name to the APP_MODULES list.
Then create a new jni/fftw3 directory and put another Application.mk there:
Application.mk:
APP_PROJECT_PATH := $(call my-dir)/project
APP_MODULES += fftw3
APP_OPTIM := release
APP_ABI := armeabi armeabi-v7a
Then put the original FFTW3 package under jni/fftw3/project/jni.
At this point you need to generate a config.h. You can do this by using a small shell script like this.
The last step is to create the needed Android Makefile. In jni/fftw3/project/jni put a top Android.mk:
LOCAL_PATH := $(call my-dir)
include $(CLEAR_VARS)
include $(LOCAL_PATH)/api/sources.mk
include $(LOCAL_PATH)/dft/sources.mk
include $(LOCAL_PATH)/dft/scalar/sources.mk
include $(LOCAL_PATH)/dft/scalar/codelets/sources.mk
include $(LOCAL_PATH)/kernel/sources.mk
include $(LOCAL_PATH)/rdft/sources.mk
include $(LOCAL_PATH)/rdft/scalar/sources.mk
include $(LOCAL_PATH)/rdft/scalar/r2cb/sources.mk
include $(LOCAL_PATH)/rdft/scalar/r2cf/sources.mk
include $(LOCAL_PATH)/rdft/scalar/r2r/sources.mk
include $(LOCAL_PATH)/reodft/sources.mk
LOCAL_MODULE := fftw3
LOCAL_C_INCLUDES := $(LOCAL_PATH) \
$(LOCAL_PATH)/api \
$(LOCAL_PATH)/dft \
$(LOCAL_PATH)/dft/scalar \
$(LOCAL_PATH)/dft/scalar/codelets \
$(LOCAL_PATH)/kernel \
$(LOCAL_PATH)/rdft \
$(LOCAL_PATH)/rdft/scalar \
$(LOCAL_PATH)/rdft/scalar/r2cb \
$(LOCAL_PATH)/rdft/scalar/r2cf \
$(LOCAL_PATH)/rdft/scalar/r2r \
$(LOCAL_PATH)/reodft
# Use APP_OPTIM in Application.mk
LOCAL_CFLAGS := -g
include $(BUILD_SHARED_LIBRARY)
Frow now on you have to create all these sources.mk files.
E.g. a typical sources.mk looks like this:
rdft/sources.mk:
sources = buffered2.c \
buffered.c \
vrank-geq1.c \
vrank-geq1-rdft2.c
LOCAL_SRC_FILES += $(sources:%=rdft/%)
Call the ndk-build script in the top directory of your app and you should end up with two ready-to-use FFTW3 libraries:
libs/armeabi-v7a/libfftw3.so
libs/armeabi/libfftw3.so