Unable to start servers

[ThomasLudwig]

Hi,

I just installed plasmabio on a fresh machine : virtualbox with ubuntu server 24.04

I used the machine where i wish to install as the ansible controller.

I scratched the whole machine and started over several times, with the same results.

Here is what I have done, with my notes.

Any help would be useful.

Cheers.

Install conda

mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm ~/miniconda3/miniconda.sh
source ~/miniconda3/bin/activate
conda init --all

Install mamba

conda config --add channels conda-forge
conda config --set channel_priority strict
conda install mamba

Adding public key

ssh-keygen -t ed25519 -f ~/.ssh/id_ed25519
ssh-copy-id -i ~/.ssh/id_ed25519.pub tludwig@127.0.0.1

Installing Ansible

eval "$(mamba shell hook --shell bash)"
mamba create -n ansibleplasma -c conda-forge python nodejs
mamba activate ansibleplasma

python -m pip install ansible 
python -m pip install passlib #needed to encrypted passwords
python -m pip install ansible
git clone https://github.com/plasmabio/plasma
cd plasma/ansible

Playbooks

Edit hosts

[codeine]
127.0.0.1 ansible_user=tludwig ansible_become=true

[codeine:vars]
ansible_python_interpreter=/usr/bin/python3

Run playbooks

ansible-playbook site.yml -i hosts -u tludwig --ask-become-pass

### installing cockpit
ansible-playbook cockpit.yml -i hosts -u tludwig --ask-become-pass -e "name_server=127.0.0.1"
### => fail1, replace cockpit-docker with cockpit-podman
### => fail2, added  -e "name_server=127.0.0.1" but really not sure about that

Users

Edit user-config.yml

plasma_groups:
  - teacher
  - student

users:
  - name: admin
    password: plasmadmin
    groups:
      - teacher
      - student
    admin: true
    
  - name: teacher1
    password: TEACHER1
    groups:
      - teacher
      - student
    admin: true
    
  - name: alice
    password: ALICE
    groups:
      - student

Run

ansible-playbook include-groups.yml -i hosts -u tludwig --ask-become-pass -e @user-config.yml
ansible-playbook users.yml -i hosts -u tludwig --ask-become-pass -e @user-config.yml

Errors

Cockpit Errors

• cockpit package does not exist anymore msg: No package matching 'cockpit-docker' is available, replaced with cockpit-podman
• The task includes an option with an undefined variable.. 'name_server' is undefined

Error when logging to cockpit

juil. 04 07:57:21 codeine systemd[1]: Starting cockpit.service - Cockpit Web Service...
juil. 04 07:57:21 codeine cockpit-certificate-ensure[18890]: /usr/lib/cockpit/cockpit-certificate-helper: line 25: sscg: command not fo>
juil. 04 07:57:21 codeine cockpit-certificate-ensure[18891]: .+.....+.+...+..+.......+.....+............+..........+...+...........+.+.>
juil. 04 07:57:22 codeine cockpit-certificate-ensure[18891]: ..+.+...+..+...+....+.....+.+..............+..........+...+........+......>
juil. 04 07:57:22 codeine cockpit-certificate-ensure[18891]: -----
juil. 04 07:57:22 codeine systemd[1]: Started cockpit.service - Cockpit Web Service.

Errors in Jupyther hub

• Some of the users are not showing (alice), I had to add manually

Errors while spawning

Spawn failed: Server at http://127.0.0.1:32768/user/admin/ didn't respond in 30 seconds

Results of sudo journalctl -u jupyterhub -f -n 1000

juil. 04 08:21:37 codeine python3[20866]: [I 2025-07-04 08:21:37.502 JupyterHub provider:660] Creating oauth client jupyterhub-user-admin
juil. 04 08:21:37 codeine python3[20866]: [W 2025-07-04 08:21:37.667 JupyterHub dockerspawner:972] Removing container that should have been cleaned up: jupyter-admin- (id: 39b7553)
juil. 04 08:21:37 codeine python3[20866]: [I 2025-07-04 08:21:37.667 JupyterHub dockerspawner:815] Removing container 39b75530abdc723427167288e821939e64ebe5f6f06dc651e430f16fe97b295d
juil. 04 08:21:37 codeine python3[20866]: [I 2025-07-04 08:21:37.815 JupyterHub dockerspawner:985] Created container jupyter-admin- (id: bbc196c) from image biobash:HEAD
juil. 04 08:21:37 codeine python3[20866]: [I 2025-07-04 08:21:37.815 JupyterHub dockerspawner:1009] Starting container jupyter-admin- (id: bbc196c)
juil. 04 08:21:38 codeine python3[20866]: [I 2025-07-04 08:21:38.494 JupyterHub log:192] 302 POST /hub/spawn?_xsrf=[secret] -> /hub/spawn-pending/admin?_xsrf=[secret] (admin@10.0.2.2) 1017.35ms
juil. 04 08:21:38 codeine python3[20866]: [I 2025-07-04 08:21:38.547 JupyterHub pages:399] admin is pending spawn
juil. 04 08:21:47 codeine python3[20866]: Task exception was never retrieved
juil. 04 08:21:47 codeine python3[20866]: future: <Task finished name='Task-1211' coro=<BaseHandler.spawn_single_user() done, defined at /opt/tljh/hub/lib/python3.12/site-packages/jupyterhub/handlers/base.py:971> exception=HTTPError()>
juil. 04 08:21:47 codeine python3[20866]: Traceback (most recent call last):
juil. 04 08:21:47 codeine python3[20866]:   File "/opt/tljh/hub/lib/python3.12/site-packages/jupyterhub/handlers/base.py", line 1178, in spawn_single_user
juil. 04 08:21:47 codeine python3[20866]:     await gen.with_timeout(
juil. 04 08:21:47 codeine python3[20866]: TimeoutError: Timeout
juil. 04 08:21:47 codeine python3[20866]: During handling of the above exception, another exception occurred:
juil. 04 08:21:47 codeine python3[20866]: Traceback (most recent call last):
juil. 04 08:21:47 codeine python3[20866]:   File "/opt/tljh/hub/lib/python3.12/site-packages/jupyterhub/handlers/base.py", line 1212, in spawn_single_user
juil. 04 08:21:47 codeine python3[20866]:     raise web.HTTPError(
juil. 04 08:21:47 codeine python3[20866]: tornado.web.HTTPError: HTTP 500: Internal Server Error (Spawner failed to start [status=ExitCode=127, Error='', FinishedAt=2025-07-04T08:21:39.594198407Z]. The logs for admin may contain details.)

Conda log

Tricky to get, as the container lives for about 1s

Activating profile: /srv/conda/etc/profile.d/conda.sh
su: ignoring --preserve-environment, it's mutually exclusive with --login
Activating profile: /etc/profile.d/conda.sh
--root-prefix: 1 required TEXT missing
Run with --help for more information.