Can you post a complete script that reproduces your problem?
Sergey Slizovskiy wrote:
I get the following suspicious message: The size of the file /home/sergey/.local/lib/python3.6/site-packages/kwant/operator.cpython-36m-x86_64-linux-gnu.so is 2734 KB. Do you really want to load it?
On my amd64 Linux system the operator*.so files are also of the order of 2-3 MB, so this is not unusual. However, I've never seen the message "Do you really want to load it?" when importing a package.
Are you sure that the installation of Kwant went well? You can run all tests using
python3 -c 'import kwant; kwant.test(verbose=False)'
Since you are on Linux, it could be easier to use binary packages for Kwant that exist for Debian, Ubuntu and Arch. There exist also conda packages, if you like to use that Python distribution.
Installing Kwant with pip is like compiling it from source locally. For good performance, you must make sure that Kwant is linked against a decent BLAS + LAPACK and also against MUMPS.