Jupyter notebook using wrong PATH (using Miniconda instead of Anaconda)

Question

I've tried uninstalling Miniconda and reinstalling Anaconda. Running Python in terminal finds the right libraries and PATH but jupyter will say that numpy is not installed because it doesn't find the conda packages.

This is what I get from echo $PATH

/home/clu/anaconda3/bin:/home/clu/anaconda3/bin:/home/clu/anaconda3/bin:/home/clu/anaconda3/bin:/home/clu/anaconda3/bin:/home/clu/bin:/home/clu/.local/bin:/home/clu/anaconda3/bin:/home/clu/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/local/cuda/bin:/usr/local/caffe/bin:/snap/bin:/home/clu/anaconda3/bin

This is the error starting up a new kernel in jupyter

Traceback (most recent call last):
  File "/home/clu/anaconda3/lib/python3.6/site-packages/notebook/base/handlers.py", line 516, in wrapper
    result = yield gen.maybe_future(method(self, *args, **kwargs))
  File "/home/clu/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 1055, in run
    value = future.result()
  File "/home/clu/anaconda3/lib/python3.6/site-packages/tornado/concurrent.py", line 238, in result
    raise_exc_info(self._exc_info)
  File "<string>", line 4, in raise_exc_info
  File "/home/clu/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 1063, in run
    yielded = self.gen.throw(*exc_info)
  File "/home/clu/anaconda3/lib/python3.6/site-packages/notebook/services/sessions/handlers.py", line 75, in post
    type=mtype))
  File "/home/clu/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 1055, in run
    value = future.result()
  File "/home/clu/anaconda3/lib/python3.6/site-packages/tornado/concurrent.py", line 238, in result
    raise_exc_info(self._exc_info)
  File "<string>", line 4, in raise_exc_info
  File "/home/clu/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 1063, in run
    yielded = self.gen.throw(*exc_info)
  File "/home/clu/anaconda3/lib/python3.6/site-packages/notebook/services/sessions/sessionmanager.py", line 79, in create_session
    kernel_id = yield self.start_kernel_for_session(session_id, path, name, type, kernel_name)
  File "/home/clu/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 1055, in run
    value = future.result()
  File "/home/clu/anaconda3/lib/python3.6/site-packages/tornado/concurrent.py", line 238, in result
    raise_exc_info(self._exc_info)
  File "<string>", line 4, in raise_exc_info
  File "/home/clu/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 1063, in run
    yielded = self.gen.throw(*exc_info)
  File "/home/clu/anaconda3/lib/python3.6/site-packages/notebook/services/sessions/sessionmanager.py", line 92, in start_kernel_for_session
    self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_name)
  File "/home/clu/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 1055, in run
    value = future.result()
  File "/home/clu/anaconda3/lib/python3.6/site-packages/tornado/concurrent.py", line 238, in result
    raise_exc_info(self._exc_info)
  File "<string>", line 4, in raise_exc_info
  File "/home/clu/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 307, in wrapper
    yielded = next(result)
  File "/home/clu/anaconda3/lib/python3.6/site-packages/notebook/services/kernels/kernelmanager.py", line 94, in start_kernel
    super(MappingKernelManager, self).start_kernel(**kwargs)
  File "/home/clu/anaconda3/lib/python3.6/site-packages/jupyter_client/multikernelmanager.py", line 110, in start_kernel
    km.start_kernel(**kwargs)
  File "/home/clu/anaconda3/lib/python3.6/site-packages/jupyter_client/manager.py", line 257, in start_kernel
    **kw)
  File "/home/clu/anaconda3/lib/python3.6/site-packages/jupyter_client/manager.py", line 203, in _launch_kernel
    return launch_kernel(kernel_cmd, **kw)
  File "/home/clu/anaconda3/lib/python3.6/site-packages/jupyter_client/launcher.py", line 128, in launch_kernel
    proc = Popen(cmd, **kwargs)
  File "/home/clu/anaconda3/lib/python3.6/subprocess.py", line 707, in __init__
    restore_signals, start_new_session)
  File "/home/clu/anaconda3/lib/python3.6/subprocess.py", line 1326, in _execute_child
    raise child_exception_type(errno_num, err_msg)
FileNotFoundError: [Errno 2] No such file or directory: '/home/clu/miniconda3/bin/python3'

`/home/clu/miniconda3/bin` doesn't contain the `python3` executable. Does the directory even exist? — Jean-François Fabre, Aug 07 '17 at 21:11
check `PYTHONHOME` env. variable. I think it shouldn't exist, or point to the correct location. — Jean-François Fabre, Aug 07 '17 at 21:20
ok, last chance maybe set it to your anaconda distro; `/home/clu/anaconda3`. — Jean-François Fabre, Aug 07 '17 at 21:27
Thanks! That gets rid of the import errors. Is there any downside to using `PYTHONHOME` instead of the default path? — Char, Aug 07 '17 at 21:32

score 1 · Accepted Answer · answered Aug 07 '17 at 21:39

Workaround found (also advised by https://github.com/lmmx/devnotes/wiki/Install-Python-3-and-Python-2-kernels-for-Jupyter-notebook)

Set PYTHONHOME to /home/clu/anaconda3: that forces Jupyter launcher to use this existing python distribution.

Related: Python (Windows) - ImportError: No module named site

Jupyter notebook using wrong PATH (using Miniconda instead of Anaconda)

1 Answers1