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DAS-5 cluster

Account creation

Ask for an account by sending an email to das-account@cs.vu.nl. Use your @uva.nl email address.
It should normally take 1-2 days.

Hostname

fs4.das5.science.uva.nl to access GPU nodes.

Useful things to have in your .bashrc

module load gcc
module load slurm
module load cuda80
module load cuDNN
alias mywatch='/home/koelma/bin/mywatch'

Other modules are also available, full list is avaible with module avail.

Pick the version you want for CUDA by looking at what's available module avail cuda.

Get a node with slurm

srun -u --pty bash -i Get an interactive session on a CPU node
srun -u --pty --gres=gpu:1 bash -i Get an interactive session on a GPU node
srun -u --pty -w node404 bash -i Get an interactive session on node404
srun -u --pty -p fatq bash -i Get an interactive session on the fatq node (more RAM)

Ideally you should submit a job instead of using an interactive session:

srun --gres=gpu:1 python myscript.py --myargument=foo

srun --gres=gpu:4 bash mybashscript.sh

slurm will provide a job id. Use that id if you want to remove yourself from the queue with scancel [job id].

Jupyter notebook on a node

For those who want to play with jupyter notebook on a node, here is the procedure.

  1. Get an interective session on a CPU or GPU node
  2. Record which node you got (e.g. node401)
  3. On the obtained node, run jupyter notebook --no-browser --port=8888
  4. From your local machine, run ssh -t -t username@fs4.das5.science.uva.nl -L 8888:localhost:8888 ssh node401 -L 8888:localhost:8888
  5. Open a browser on your local machine and go to http://localhost:8888
  6. You should now have access to a jupyter notebook that is running on a node on das5
  7. Do NOT forget to kill both sessions once you are done

Note: if you run into issues to launch jupyter notebook on the GPU node, you might want to remove the following environment variable unset XDG_RUNTIME_DIR

Monitor node usage

Either use squeue or mywatch (see last line of .bashrc)

Data storage

Your homefolder space is quite limited. Only use it for scripts.

Install your own python or other stuff on /var/scratch/ (there is already a directory for each user). Also store your data on /var/scratch/. If you run out of space, ask Dennis.

Check your current quota with quota -sv.

More info

Read more on the das-5 website.