diff --git a/Chapter10/Readme.md b/Chapter10/Readme.md index fb4f7e1171dbeb7842b6d8f3fb62fd86e6e9fc77..e88273afab8322c43aa2cf792ad7b39f57586b99 100644 --- a/Chapter10/Readme.md +++ b/Chapter10/Readme.md @@ -3,30 +3,50 @@ The notebook for the exercise in Chapter 10 is available from here: [Notebook for mini U-net](https://github.com/vedranaa/teaching-notebooks/blob/main/02506_week10_MiniUnet.ipynb) -You can also open it directly in Google Colab from here: +Training the network may take long time, especially without GPU. We therefore sketch several ways of running the notebook with GPU support. + +## Run the notebook on Google Colab + +You can open the notebook in Google Colab from here, and enable GPU : [](https://colab.research.google.com/github/vedranaa/teaching-notebooks/blob/main/02506_week10_MiniUnet.ipynb) ## Run the notebook on DTU Gbar -It is possible to run the notebook on Gbar on an interactive note. This is done by setting up a Python environment. First you should log onto an interactive GPU node such as `voltash` by running the following command on the command line: +You can run the notebook on Gbar on an interactive GPU node. + +First get to a terminal on the cluster, either with ssh, ThinLinc client, or a browser-based ThinLinc [thinlinc.gbar.dtu.dk](thinlinc.gbar.dtu.dk). Open the terminal (command line). + +Log onto an interactive GPU node such as `voltash` by running the following command on the command line: `voltash -X` -To set up a Python environment, you can use the script `env02506.sh`. You should place the file `env02506.sh` in a folder on the Gbar and then run the command line: +To set up a Python environment, you can use the script `env02506.sh` which we provided for you. You should place the file `env02506.sh` in a folder on the Gbar and then run the command: `source env02506.sh` The first time you run this, the script will create a new python environment called `env02506` and activate it. -Then you should install the packages needed which include: +Then you should install the packages: -`pip install torch torchvision` - -`pip install Pillow` - -`pip install notebook` +``` +pip install torch torchvision +pip install Pillow +pip install notebook +``` Now you are good to go. You can navigate to the folder that you wish to store the code, download the notebook from the link above, and open a jupyter notebook by typing the following in the command line: `jupyter-notebook` + +## Use QIM platform to access GBar + +We are working on establishing an easier way of using Gbar functionality which does the steps described above automatically. This is still experimental. + +First go to QIM platform [https://platform.qim.dk/](https://platform.qim.dk/) and log on using your DTU credentials. + +Under Tools menu, choose Jupyter launcher. In the new window yype in your DTU credentials (needs to be done twice). Under basic config QIM environment choose `qim3d` (it has the largest number of packages installed). Under advanced config choose HPC queue called `gpuqim`. Tick the checkbox Reset SSH tunnel. Click the button `Start jupyter server`. + +The platform shold launch your job and a button with `Open Jupyter` should appear, leading you to a jupyter server running in your home directory on the Gbar. + +