Hi,
OpenCV is installed with JetPack by default. Just install other dependence and caffe should work fine.
For example,
sudo apt-get install libboost-dev libboost-all-dev libgflags-dev libgoogle-glog-dev liblmdb-dev libatlas-base-dev liblmdb-dev libblas-dev libatlas-base-dev libprotobuf-dev libleveldb-dev libsnappy-dev libhdf5-serial-dev protobuf-compiler
Edit Makefile.config.example
+++ USE_CUDNN := 1
--- INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include
+++ INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include /usr/include/hdf5/serial/
Edit Makefile
--- LIBRARIES += glog gflags protobuf boost_system boost_filesystem m hdf5_hl hdf5
+++ LIBRARIES += glog gflags protobuf boost_system boost_filesystem m hdf5_serial_hl hdf5_serial
Build
cd $CAFFE_ROOT
cp Makefile.config.example Makefile.config
make -j4