Hello and thank you for the feedback,
Let me clarify the challenge we are facing with OOD by dividing the discussion into two parts: the CentOs setup and the Ubuntu setup. Note that both setups are using v3.0.
CentOs Setup: Although the OOD setup was successful, our primary issue arises with maintaining user identity across the two systems when executing Slurm commands.
- In our current configuration, all users logged into OOD on CentOS are funneled through a single user account on the Ubuntu Slurm server (an account called oodadmin). This is facilitated by SSH keys set up for passwordless access.
While this allows us to remotely execute Slurm commands, it does not preserve the individual user’s identity when interacting with the Slurm server. Instead, every job submitted through OOD appears under the oodadmin account on Ubuntu. This connection was using a static account and id-rsa key.
deally, each user would access the system with their own username, as the email authentication using dex is already functioning correctly in both setups
As for the option submit_host, I was not able to find it listed as per the cluster configuration for slurm, I am now attempting to change it to match the Linux Host cluster configuration. I have created the following settings file:
# /etc/ood/config/clusters.d/clusterbio.yml
---
v2:
metadata:
title: "clusterbio"
url: "https://ood.vhio.net" # Same url as the one serving ood.
hidden: false
login:
host: "172.27.0.66" # HPC master node
job:
adapter: "linux_host" # The host uses SLURM internally
submit_host: "172.27.0.66" # Setting submit_host as suggested
ssh_hosts: # Actual login nodes
- "172.27.0.35"
- "172.27.0.225"
- "172.27.0.184"
- "172.27.0.117"
site_timeout: 7200
debug: true
singularity_bin: "/usr/bin/singularity" # Verified the path is correct
singularity_bindpath: "/etc,/media,/mnt,/opt,/run,/srv,/usr,/var,/users"
# The singularity image has been created at CentOs 7.9 and moved to Ubuntu
singularity_image: "/opt/ood/linuxhost_adapter/centos_7.sif" # Located at login host
strict_host_checking: false
tmux_bin: "/usr/bin/tmux" # Verified the path is correct at the login host
acls:
- adapter: "group"
groups:
- "gsg_bioinformatica"
type: "allowlist"
batch_connect:
basic:
script_wrapper: "module restore\n%s"
set_host: "host=$(hostname -A | awk '{print $2}')"
Ubuntu setup: Using Ubuntu 22.04, the user mapping would have been correct, since it’s using the same OS as the computing nodes; however, the installation failed
2.- Thanks for pointing out the issue with bundler. I was attempting to follow the steps from a message on a resolved issue that had a similar error where the gems were not found. I have a similar symptom, the issue is installed but not found. I am attaching a screenshot for reference:
3.- As for the missing gems warning, as shown in the previous screenshot, that would also happen for other parts of the application, for instance the error I am getting at the web browser would also show it.
The previous screenshot shows the message displayed on the webpage after login (the login works correctly with dex), indicating an error 404 (request not found). I did validate the gems were installed, also executed gem pristine as suggest and the passenger validation was correct, which was validated with the apache configuration as well using passenger-config validate-install :
However, the issue still persists, and I am seeking further insights or recommendations that might help us resolve these ongoing challenges with user identity management and installation errors.
Please let me know if there is anything else I can do to fix the OOD setup. Many thanks!