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execnotebook

The execnotebook command allows a user to execute a Jupyter notebook for up to 24 hours without staying connected to the cluster. Users are recommended to checkpoint their work to prevent data loss.

Prerequisites

  1. The user must have executed mynotebook prior to running execnotebook
  2. The .ipynb file must not be located in the scratch directory.

Limitations

  1. Each job will be executed for up to 24 hours.
  2. Users should wait for the job to complete before reading or writing to the .ipynb file.

Guide to using execnotebook

  1. On the cluster execute the command execnotebook

  2. You will be prompted for the filename of the ipynb file you would want the program to execute

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    [IS000G3@origami ~]$ execnotebook
You are beta testing Juypter Notebook Running 📔 🏃 v0.2
Issues? Please reach out to me

Checking for existing jupyterlab venv...
Please input the name of your Jupyter notebook
The ipynb notebook must located be within your home directory
Input only the filename of your notebook — e.g project1.ipynb
Enter file name :

  3. Input the ipynb filename and press enter

    Location of ipynb files

    The ipynb files must be located within your home directory.

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    Please input the name of your Jupyter notebook
The ipynb notebook must located be within your home directory
Input only the filename of your notebook — e.g project1.ipynb
Enter file name : testingNotebook.ipynb

  4. Input your email address when prompted

    Provide your SMU email address : testuser@scis.smu.edu.sg

  5. Select the build environment you require

    Modules

    Modules loaded in your Jupyter notebook will not be affected by the options selected here

    Do you require Tensorflow or PyTorch related modules to be loaded?
1) Tensorflow
2) PyTorch
3) Only Python v3.11.7

Please select an option :

  6. Select if you would want to override your existing notebook

    Overwriting files

    If you choose to overwrite the notebook, the output format of the new ipynb file will be nameofnotebook.output.ddmmyyyyHHMMSS.ipynb

    Would you like to overwrite your existing notebook testingNotebook.ipynb ?
1) Yes
2) No (Recommended)
Please select an option :

  7. Select your GPU requirements

    Do you require a GPU?
1) Yes
2) No GPU required
Please select an option :

  8. Displayed screen upon successful job submission

    Submitted batch job 1742
======================= JOB QUEUE =======================
            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
            1742   project ipynbRun  IS000G3  R   11:32:05      1 aloha
======================= JOB QUEUE =======================

===================== Job states ========================
R = RUNNING | PD = PENDING | F = FAILED | CG = COMPLETING
===================== Job states ========================
...output redacted

Troubleshooting & Tips

Job state is pending

Refer to the myinfo command to find out more about entitlement for concurrent jobs.