portal_guides:migration

Migration from Newton

Migration from Newton

Consequences of the HPC renovation to be aware of

Home directories have moved from “/home” to “/trinity/home” — old hard-coded absolute paths will no longer work
Operating system changed from Ubuntu 18.04 to Rocky Linux 9.7 — binaries built on Newton may not run reliably
Workflow for running sbatch scripts has changed — jobs are now recommended to be submitted from the web portal rather than from JupyterLab

Steps to migrate

Update hard-coded absolute paths to start with “/trinity/home”. Where possible, avoid fixed paths and use portable alternatives (e.g., “~” in Bash or path utilities such as “os.path.abspath()” in Python)
Fix user-space Conda/pip environments (contact an administrator if shared environments need recreating), for that you can either:
- Use VS Code. It enables a flexible way of finding kernels, so ipykernel reinstallation is not needed
- Fix kernel path inside /trinity/home/<USER>/.conda/envs/<ENV>/share/jupyter/kernels/python3/kernel.json:
  “/home/<USER>/.conda/envs/<ENV>/bin/python” —> “/trinity/home/<USER>/.conda/envs/<ENV>/bin/python”
- Reinstall ipykernel in your environment:
```
conda install -n <ENV> ipykernel -c conda-forge --force-reinstall -y
```
  for all envs:
```
for name in $(ls ~/.conda/envs);
do 
  conda install -n $name ipykernel -c conda-forge --force-reinstall -y; 
done
```
- Recreate environment (if above does not work):
  - Export Conda environment to a file:
```
conda env export -n <OLD_ENV> --no-builds -f environment.yml
```
  - Create a new Conda environment from the file:
```
conda env create -n <NEW_ENV> -f environment.yml
```
  - In case the new environment does not work (e.g., cannot solve the environment/conflicts), repeat the first step, using:
```
conda env export -n <OLD_ENV> --from-history -f environment.yml
```
Rebuild manually compiled software and contact an administrator if centrally installed software needs to be rebuilt

Tips & Bonuses

JupyterLab now has a Python LSP server (jump to definitions and references, make use of dynamic tips)
JupyterLab now supports showing hidden files (can be enabled in JupyterLab settings)
JupyterLab now has a bunch of color themes
It is recommended to try VS Code (codeserver) instead of JupyterLabs. Advantages: a lot of features to be overwhelmed by. Disadvantages: a lot of features to be overwhelmed by

Table of Contents

Migration from Newton

Consequences of the HPC renovation to be aware of

Steps to migrate

Tips & Bonuses