Table of Contents
Analysis
(Note: The following lines can be added to ~/.bashrc to automatically load the environment when logging in.)
- Source Maloja conda installation (Python 3.9):
source /sf/maloja/applications/miniconda3/etc/profile.d/conda.sh
- Activate Maloja Analysis conda environment:
conda activate mana
Currently, the environment contains the following packages (and their dependencies):
- sf_datafiles
- jungfrau_utils
- OpenCV
as well as numpy, scipy, matplotlib, jupyter, etc.
Setup on Ra/Jupytera
Automatic Way
A script that automates the setup on Ra can be found in /sf/maloja/bin/. It expects a pgroup as argument:
/sf/maloja/bin/ra_setup.sh p12345
(Replace p12345 with the correct pgroup.)
Manual Way
In order to access the above environment on jupytera run
conda config --add envs_dirs /sf/maloja/applications/miniconda3/envs
in a terminal within jupytera.
The top-most directory you can see in jupytera is your home folder. To be able to see the data folders, you can create a symlink:
cd && ln -s /sf/maloja/data/p12345
(Replace p12345 with the correct pgroup.)
DAQ
- As
gac-maloja, the Maloja DAQ environment can be activated via:
conda activate mdaq
Currently, the environment contains the following packages (and their dependencies):
Jupytera via hop
To create an ssh tunnel from your local computer to jupytera, insert your user name here
user="familyname_initial"; ssh -J $user@hop.psi.ch $user@ra.psi.ch -L 5000:jupytera.psi.ch:443
then run the command. You will be asked your password twice (once for hop, once for Ra). Afterwards, connect to https://localhost:5000/hub/login in your local browser. You will see a certificate warning due to the address now being localhost.
Instead of the command above, you can also download and use this script.
Setup:
curl https://gitlab.psi.ch/maloja/docs/-/wikis/uploads/fbf870b995bff343f14e429c21f4925d/tunnel2jupytera.sh
chmod +x tunnel2jupytera.sh
Run:
./tunnel2jupytera.sh -u familyname_initial
Usage:
Check for the available options via
tunnel2jupytera.sh -h