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SDS_bwVisu_setup.md

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Joining the SDS

  • you need to be invited to join SDS with acronym and password. Please provide your uni-id to your supervisor
  • access SDS management via this link: https://sds-hd.urz.uni-heidelberg.de/management/
    • unter Mitarbeit Speichervorhaben bei einem existierenden SV beitreten.
    • chose Uni-Heidelberg in dropdown menu and login with normal credentials
      • sign up using SV-credentials and personal data; accept terms of use
    • Check E-mail for Registration.
      • first E-mail (should arrive immediatly) indicates that membership of SDS was succesfully processed![[Pasted image 20220211091845.png]]
      • second E-mail (arrived 25 min later) confirmed registration![[Pasted image 20220211092136.png]]

(optional) Mount SDS-storage to computer

WINDOWS:

- add file-path directly into the file-path of windows explorer ![[Pasted image 20220211092751.png]]
- might take some time for login-windows to appear

LINUX

  • sd22a004 is the name of the SV
  • create the folder/s you want to mount at, with root privileges and
  • chown it afterwards with your 'normal' user --> replace %USERID% with your local userid

sudo mkdir /mnt/sds-stud
sudo chown -R %USERID% /mnt/sds-stud

Map the sds to this created folder

sshfs -o reconnect [email protected]:/sd22a004 /mnt/sds-stud -o idmap=user -o uid=$(id -u) -o gid=$(id -g)

bwservices

set up bwVisu

  • Log in to the bwVisu web frontend at https://bwvisu-web.urz.uni-heidelberg.de. Your username will be _, e.g. hd_ab123 for a user from Heidelberg.
  • The password will be your bwVisu service password set at bwservices.uni-heidelberg.de, and your registered device will be used as second factor.
  • scroll down application window and click on "latest" for jupyter ![image info](./attachments/Pasted image 20220211093328.png)
  • Click on green button "Start new job"
  • Setup Job settings (you might want to increase the runtime, but make sure to properly shut down the job afterwards to free up ressources)
  • click on your running job (blue button)
  • click on your jupyter-connection-link.
  • verify that you are able to see the sds-hd drive mounted

Installing env and packages

  • Note: it's normal if the import of libraries takes long in bwVisu, so please be patient
  • load miniconda modules and the cuda modules available by clicking on the hexagon icon on the left panel
  • Open a terminal from Jupyter. This can be done by clicking the + button from the top left and selecting Terminal, and then type the following commands:

conda create --name wft_endo
conda activate wft_endo
pip install -r /mnt/sds-hd/sd22a004/guest/setup/requirements.txt
pip install ipykernel
python3 -m ipykernel install --user --name=wft_endo

  • hint: if 'conda activate wft_endo' doesn't work, try 'source activate wft_endo' !
  • try to run the cells in endo_data_quickstart and pytorch_quickstart notebooks
  • once successful, please go back to the job tab and cancel the job to free up the resource for other users