I try to spawn a python3 shell from houdini 16.5 win64 to do things I cant do with python2.7.
but I get the following error :

Fatal Python error: Py_Initialize: unable to load the file system codec
File “Croot/sidefx/H16_5_295/python27\lib\encodings\__init__.py”, line 123

Also If i try to spawn another python2.7 installation with popen ( not the houdini one ) it starts, but is all messed up with its packages.

I guess it has something to do with the environment inherited from the houdini host process but how can I spawn another python installation in a clean way from houdini. No matter if its python3 or python2, which ever works.

try os.system
spawn
and are other old methods that you can try beside popen make sure you pass the argument shell=True, that will open a new shell in the background, instead using the same one where the current python script is running.