Hi,
Forgive me for this very basic question! I am trying to get started with GROMACS. I followed the installation as given in the instruction page for Windows users (using ubuntu app). I run my jupyter notebook from my “ubuntu” terminal in the following matter:
(base) root@MSI:~# ls
Miniconda3-latest-Linux-x86_64.sh md-intro-tutorial md-intro-tutorial-main md-intro-tutorial-main.zip miniconda3
(base) root@MSI:~# cd md-intro-tutorial-main
(base) root@MSI:~/md-intro-tutorial-main# ls
LICENSE README.md data environment.yml environment_withoutgmx.yml images src tutorial.ipynb
(base) root@MSI:~/md-intro-tutorial-main# conda activate md-intro-tutorial-main
WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or
- Make your system-wide implementation visible by installing ocl-icd-system conda package.
(md-intro-tutorial-main) root@MSI:~/md-intro-tutorial-main# jupyter-notebook tutorial.ipynb
[W 2024-02-16 03:05:41.573 ServerApp] A `_jupyter_server_extension_points` function was not found in notebook_shim. Instead, a `_jupyter_server_extension_paths` function was found and will be used for now. This function name will be deprecated in future releases of Jupyter Server.
[I 2024-02-16 03:05:41.573 ServerApp] jupyter_lsp | extension was successfully linked.
[I 2024-02-16 03:05:41.577 ServerApp] jupyter_server_terminals | extension was successfully linked.
[I 2024-02-16 03:05:41.581 ServerApp] jupyterlab | extension was successfully linked.
[I 2024-02-16 03:05:41.585 ServerApp] notebook | extension was successfully linked.
[I 2024-02-16 03:05:41.922 ServerApp] notebook_shim | extension was successfully linked.
[I 2024-02-16 03:05:41.942 ServerApp] notebook_shim | extension was successfully loaded.
[I 2024-02-16 03:05:41.943 ServerApp] jupyter_lsp | extension was successfully loaded.
[I 2024-02-16 03:05:41.944 ServerApp] jupyter_server_terminals | extension was successfully loaded.
[I 2024-02-16 03:05:41.947 LabApp] JupyterLab extension loaded from /root/miniconda3/envs/md-intro-tutorial-main/lib/python3.12/site-packages/jupyterlab
[I 2024-02-16 03:05:41.947 LabApp] JupyterLab application directory is /root/miniconda3/envs/md-intro-tutorial-main/share/jupyter/lab
[I 2024-02-16 03:05:41.948 LabApp] Extension Manager is 'pypi'.
[I 2024-02-16 03:05:41.962 ServerApp] jupyterlab | extension was successfully loaded.
[I 2024-02-16 03:05:41.964 ServerApp] notebook | extension was successfully loaded.
[C 2024-02-16 03:05:41.964 ServerApp] Running as root is not recommended. Use --allow-root to bypass.
My problem is that, when I execute the first cell of tutorial.ipynb:
# Execute this first
#
# * trigger notebook styling
# * check if notebook had been modified since its distribution
#
# Note: executing any cells before this modifies the notebook.
#
%run src/init_notebooks.py
hide_toggle()
check_notebook()
I get the following error:
/root/md-intro-tutorial-main/src/init_notebooks.py:1: DeprecationWarning: Importing display from IPython.core.display is deprecated since IPython 7.14, please import from IPython display
from IPython.core.display import display, HTML
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
File ~/md-intro-tutorial-main/src/init_notebooks.py:46
43 import requests
45 from requests.compat import urljoin
---> 46 from notebook.notebookapp import list_running_servers
48 def get_notebook_name():
49 """
50 Return the full path of the jupyter notebook.
51 """
ModuleNotFoundError: No module named 'notebook.notebookapp'
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[2], line 10
8 get_ipython().run_line_magic('run', 'src/init_notebooks.py')
9 hide_toggle()
---> 10 check_notebook()
NameError: name 'check_notebook' is not defined
I am not really sure what I am doing wrong. Am i missing something? I am not really sure why I get such an error. Any help trying to solve the issue will be very appreciated!!