How to Use: ViDaL Linux

Step 1: Being on a secure network

• You must be on a campus network (either TAMU or TAMHSC)

• See following link for details as well as general instructions for using ViDaL

  • https://docs.google.com/document/d/1YX8XtTxmA-RqXiBI4GJ4pnYIjxB1Gzcc1TivM8mWRzs/edit#heading=h.v6pn12s8qfwb

Step 2: Getting to ViDaL

• How to access

  1. Go to webpage: go.vidal.tamu.edu

  2. Click Access ViDaL VMs ( or click icon): See link above for details on what node to log into

Step 3: Setting up on ViDaL

• Linux setup (only needs to be setup once for the first login to each Windows node)

  1. Creating a shortcut to your project folder

     1. ln -s /gpfs/des linkname

        • EXAMPLE: ln -s /gpfs/proj1/pinfo_hck pinfo_hck

        • This will setup a symbolic link (short cut) to go straight to where you want to work.

        • /gpfs/des : where des is where you want to go. E.g., /gpfs/proj1/pinfo_hck

        • Linkname: name of the link you want to use. Often same as des (e.g. pinfo_hck)

     2. Root Folder: \\gpfs (You should see subfolders like home, proj1, proj2, proj3)

     3. IMPORTANT: You MUST use the project folder to store any data from the project. This is so that we can track all data including derived data that must be monitored. We recommend you create a personal folder INSIDE the your project folder for all your work

        • E.g. /gpfs/proj2/waiver_hck/uc_hck

Setting up environment to use Python

• In the ViDal GPU node, Python 2 and Python 3 are installed in the system

• To use pip, you will have to create an virtual environment:

  1. virtualenv -p python3 $HOME/venv/pytorch

  2. source $HOME/venv/pytorch/bin/activate

  3. pip install torch torchvision

  4. pip list

• If you would like to share the virtualenv with your group members:

  1. change $HOME/venv to /gpfs/proj1/nil_ysc/venv

Using jupyter notebooks for Python

1. Python3 and venv should already be installed on the Linux node.

2. Open the terminal in your folder.

3. create and activate a Python environment:

   1. python3 -m venv [your env name]

   2. Source [your env name]/bin/activate

4. Install all the packages you need with pip. (ex: pip install pandas)

5. Install jupyter notebook:

   1. Pip install jupyter notebook

6. Run jupyter notebook to start coding:

   1. Jupyter notebook

You should read the general How to doc (for windows) for more details on 

• https://docs.google.com/document/d/1YX8XtTxmA-RqXiBI4GJ4pnYIjxB1Gzcc1TivM8mWRzs/edit#heading=h.v6pn12s8qfwb

• Setting up environment for R

• Which folders to use for your files and backup

• Uploading & Downloading Files on ViDaL