Benny K J added the comment:

Thank you for the response.

I'm not too sure how to set the root directory for arm headers and libraries in 
the configure command line.

So I've tried the below, but still not all of the extensions modules was not 
build (e.g math, socket, select)

export 
CROSS_PATH=/home/benny/workspace/projects/webshield/src/dntl_ws/sw/toolchain/gcc-linaro-4.9-2016.02-x86_64_arm-linux-gnueabihf/bin/../arm-linux-gnueabihf/libc


CONFIG_SITE=config.site CC=arm-linux-gnueabihf-gcc CXX=arm-linux-gnueabihf-g++ 
AR=arm-linux-gnueabihf-ar RANLIB=arm-linux-gnueabihf-ranlib 
READELF=arm-linux-gnueabihf-readelf CFLAGS="-I${CROSS_PATH}/usr/include" 
LDFLAGS="-L${CROSS_PATH}/usr/lib" CPPFLAGS="-I${CROSS_PATH}/usr/include" 
./configure --enable-shared --host=arm-linux --build=x86_64-linux-gnu 
--disable-ipv6 --prefix=/opt/python3

Attached please find the build log

----------
Added file: http://bugs.python.org/file45098/python3.5.2_x86_host_arm_target.log

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