I have installed Jupyter Notebook on ubuntu 16.04 using pip3. I can execute jupyter notebook command. It opens and shows a list of current path directories.
I had the very same issue running Jupyter. After chasing my tail on permissions, I found that everything cleared up after I changed ownership on the directory where I was trying to run/store my notebooks. Ex.: I was running my files out of my ~/bash dir. That was root:root; when I changed it to jim:jim....no more errors.