made another pass on OOD

Author: RobJY

docs/hpc/09_ood/01_open_on_demand.md

@@ -10,13 +10,13 @@ If you're not on the NYU network, you may need to connect via NYU's Virtual Priv
 This page describes how to use your Singularity with conda environment in Open OnDemand (OOD) GUI at Greene. 
 
 ### Log Into Greene via the Terminal
-The following commands must be run from the terminal. Information on accessing via the terminal can be found at the [Connecting to the HPC page](../02_connecting_to_hpc/01_connecting_to_hpc.mdx). 
+The following commands must be run from the terminal. Information on accessing via the terminal can be found at [Connecting to the HPC](../02_connecting_to_hpc/01_connecting_to_hpc.mdx). 
 
 ### Preinstallation Warning
 :::warning
 If you have initialized Conda in your base environment, your prompt on Greene may show something like:
 ```sh
-(base) [NETID@log-1 ~]$
+(base) [NetID@log-1 ~]$
 ```
 then you must first comment out or remove this portion of your `~/.bashrc` file:
 
@@ -41,116 +41,122 @@ The above code automatically makes your environment look for the default shared
 :::
 
 ### Prepare Overlay File 
-```sh
-mkdir /scratch/$USER/my_env
-cd /scratch/$USER/my_env
-cp -rp /scratch/work/public/overlay-fs-ext3/overlay-15GB-500K.ext3.gz .
-gunzip overlay-15GB-500K.ext3.gz
+```bash
+[NetID@log-1 ~]$ mkdir /scratch/$USER/my_env
+[NetID@log-1 ~]$ cd /scratch/$USER/my_env
+[NetID@log-1 my_env]$ cp -rp /scratch/work/public/overlay-fs-ext3/overlay-15GB-500K.ext3.gz .
+[NetID@log-1 my_env]$ gunzip overlay-15GB-500K.ext3.gz
 ```
-Above we used the overlay file "overlay-15GB-500K.ext3.gz" which will contain all of the installed packages. There are more optional overlay files. You can find instructions on the following pages: [Singularity with Conda](../07_containers/03_singularity_with_conda.md), [Squash File System and Singularity](../07_containers/04_squash_file_system_and_singularity.md). 
+Above we used the overlay file `overlay-15GB-500K.ext3.gz` which will contain all of the installed packages. There are more optional overlay files. You can find instructions on the following pages: [Singularity with Conda](../07_containers/03_singularity_with_conda.md), [Squash File System and Singularity](../07_containers/04_squash_file_system_and_singularity.md). 
 
 ### Launch Singularity Environment for Installation
-```sh
-singularity exec --overlay /scratch/$USER/my_env/overlay-15GB-500K.ext3:rw /scratch/work/public/singularity/cuda12.3.2-cudnn9.0.0-ubuntu-22.04.4.sif /bin/bash
+```bash
+[NetID@log-1 ~]$ singularity exec --overlay /scratch/$USER/my_env/overlay-15GB-500K.ext3:rw /scratch/work/public/singularity/cuda12.3.2-cudnn9.0.0-ubuntu-22.04.4.sif /bin/bash
 ```
-Above we used the Singularity OS image "cuda12.3.2-cudnn9.0.0-ubuntu-22.04.4.sif " which provides the base operating system environment for the conda environment. There are other Singularity OS images available at `/scratch/work/public/singularity`
+Above we used the Singularity OS image `cuda12.3.2-cudnn9.0.0-ubuntu-22.04.4.sif` which provides the base operating system environment for the conda environment. There are other Singularity OS images available at `/scratch/work/public/singularity`
 
-Launching Singularity with the --overlay flag mounts the overlay file to a new directory: /ext3 - you will notice that when not using Singularity /ext3 is not available. Be sure that you have the Singularity prompt (Singularity>) and that /ext3 is available before the next step:
+Launching Singularity with the `--overlay` flag mounts the overlay file to a new directory: `/ext3` - you will notice that when not using Singularity `/ext3` is not available.
+
+:::warning
+Be sure that you have the Singularity prompt (`Singularity>`) and that `/ext3` is available before the next step.
 ```sh
 Singularity> ls -lah /ext3
 total 8.5K
 drwxrwxr-x.  2 root root 4.0K Oct 19 10:01 .
 drwx------. 29 root root 8.0K Oct 19 10:01 ..
 ```
+:::
 
 ### Install Miniforge to Overlay File
-```sh
-wget --no-check-certificate https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
-sh Miniforge3-Linux-x86_64.sh -b -p /ext3/miniforge3
+```bash
+Singularity> wget --no-check-certificate https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
+Singularity> sh Miniforge3-Linux-x86_64.sh -b -p /ext3/miniforge3
 ```
-Next, create a wrapper script at /ext3/env.sh
-```sh
-touch /ext3/env.sh
-echo '#!/bin/bash' >> /ext3/env.sh
-echo 'unset -f which' >> /ext3/env.sh
-echo 'source /ext3/miniforge3/etc/profile.d/conda.sh' >> /ext3/env.sh
-echo 'export PATH=/ext3/miniforge3/bin:$PATH'         >> /ext3/env.sh
-echo 'export PYTHONPATH=/ext3/miniforge3/bin:$PATH'   >> /ext3/env.sh
-```
-Your /ext3/env.sh file should now contain  the following:
+Next, create a wrapper script at `/ext3/env.sh`:
+```bash
+Singularity> touch /ext3/env.sh
+Singularity> echo '#!/bin/bash' >> /ext3/env.sh
+Singularity> echo 'unset -f which' >> /ext3/env.sh
+Singularity> echo 'source /ext3/miniforge3/etc/profile.d/conda.sh' >> /ext3/env.sh
+Singularity> echo 'export PATH=/ext3/miniforge3/bin:$PATH'         >> /ext3/env.sh
+Singularity> echo 'export PYTHONPATH=/ext3/miniforge3/bin:$PATH'   >> /ext3/env.sh
+```
+Your `/ext3/env.sh` file should now contain the following:
 ```bash
 #!/bin/bash
-   unset -f which
+unset -f which
 source /ext3/miniforge3/etc/profile.d/conda.sh
 export PATH=/ext3/miniforge3/bin:$PATH
 export PYTHONPATH=/ext3/miniforge3/bin:$PATH
 ```
 The wrapper script will activate your conda environment, to which you will be installing your packages and dependencies. 
 
 Next, activate your conda environment with the following:
-```sh
-source /ext3/env.sh
+```bash
+Singularity> source /ext3/env.sh
 ```
 
 ### Install Packages to Miniforge Environment
-Now that your environment is activated, you can update and install packages
-```sh
-conda config --remove channels defaults
-conda update -n base conda -y
-conda clean --all --yes
-conda install pip --yes
-conda install ipykernel --yes # Note: ipykernel is required to run as a kernel in the Open OnDemand Jupyter Notebooks
+Now that your environment is activated, you can update and install packages:
+```bash
+Singularity> conda config --remove channels defaults
+Singularity> conda update -n base conda -y
+Singularity> conda clean --all --yes
+Singularity> conda install pip --yes
+Singularity> conda install ipykernel --yes # Note: ipykernel is required to run as a kernel in the Open OnDemand Jupyter Notebooks
 ```
 To confirm that your environment is appropriately referencing your Miniforge installation, try out the following:
-```sh
-unset which
-which conda
+```bash
+Singularity> unset which
+Singularity> which conda
 # output: /ext3/miniforge3/bin/conda
 
-which python
+Singularity> which python
 # output: /ext3/miniforge3/bin/python
 
-python --version
-# output: Python 3.8.5
+Singularity> python --version
+# output: Python 3.12.9
 
-which pip
+Singularity> which pip
 # output: /ext3/miniforge3/bin/pip
 ```
 
-Now use either conda install or pip to install your required python packages to the Miniforge environment.
+Now use either conda or pip to install your required python packages to the Miniforge environment.
 
 To install larger packages, like Tensorflow, you must first start an interactive job with adequate compute and memory resources to install packages. The login nodes restrict memory to 2GB per user, which may cause some large packages to crash.
-```sh
-srun --cpus-per-task=2 --mem=10GB --time=04:00:00 --pty /bin/bash
+```bash
+Singularity> exit
+
+[NetID@log-1 my_env]$ srun --cpus-per-task=2 --mem=10GB --time=04:00:00 --pty /bin/bash
 
 # wait to be assigned a node
 
-singularity exec --overlay /scratch/$USER/my_env/overlay-15GB-500K.ext3:rw /scratch/work/public/singularity/cuda12.3.2-cudnn9.0.0-ubuntu-22.04.4.sif /bin/bash
+[NetID@cm001 my_env]$ singularity exec --overlay /scratch/$USER/my_env/overlay-15GB-500K.ext3:rw /scratch/work/public/singularity/cuda12.3.2-cudnn9.0.0-ubuntu-22.04.4.sif /bin/bash
 
-source /ext3/env.sh
+Singularity> source /ext3/env.sh
 # activate the environment
 ```
 
 After it is running, you’ll be redirected to a compute node. From there, run singularity to setup on conda environment, same as you were doing on login node.
 
 ### Configure iPython Kernels
 To create a kernel named my_env copy the template files to your home directory.
-```sh
-mkdir -p ~/.local/share/jupyter/kernels
-cd ~/.local/share/jupyter/kernels
-cp -R /share/apps/mypy/src/kernel_template ./my_env # this should be the name of your Singularity env
-cd ./my_env 
+```bash sh
+Singularity> mkdir -p ~/.local/share/jupyter/kernels
+Singularity> cd ~/.local/share/jupyter/kernels
+Singularity> cp -R /share/apps/mypy/src/kernel_template ./my_env # this should be the name of your Singularity env
+Singularity> cd ./my_env 
 
-ls
+Singularity> ls
 #kernel.json  logo-32x32.png  logo-64x64.png  python # files in the ~/.local/share/jupyter/kernels directory
 ```
 
-To set the conda environment, edit the file named 'python' in /.local/share/jupyter/kernels/my_env/. 
+To set the conda environment, edit the file named `python` in `/.local/share/jupyter/kernels/my_env/`. 
 
 The python file is a wrapper script that the Jupyter notebook will use to launch your Singularity container and attach it to the notebook.
 
 At the bottom of the file we have the template singularity command.
-```sh
+```bash
 singularity exec $nv \
   --overlay /scratch/$USER/my_env/overlay-15GB-500K.ext3:ro \
   /scratch/work/public/singularity/cuda12.3.2-cudnn9.0.0-ubuntu-22.04.4.sif \
@@ -160,7 +166,7 @@ singularity exec $nv \
 If you used a different overlay (/scratch/$USER/my_env/overlay-15GB-500K.ext3 shown above) or .sif file (/scratch/work/public/singularity/cuda12.3.2-cudnn9.0.0-ubuntu-22.04.4.sif shown above), you MUST change those lines in the command above to the files you used.
 :::
 
-Edit the default kernel.json file by setting PYTHON_LOCATION and KERNEL_DISPLAY_NAME using a text editor like nano/vim.
+Edit the default `kernel.json` file by setting PYTHON_LOCATION and KERNEL_DISPLAY_NAME using a text editor like nano/vim.
 ```json
 {
  "argv": [
@@ -194,3 +200,12 @@ Update the `"<Your NetID>"` to your own NetID without the `"<>"` symbols.
 [https://ood.hpc.nyu.edu](https://ood.hpc.nyu.edu)
 
 ![OOD Launch](./static/OOD_launch.png)
+
+### Configure and Launch your Notebook
+
+![Configure Notebook](./static/configure_notebook.png)
+
+### Select kernel
+Once configured and launched, kernels can be selected in the "New" dropdown or within the notebook under the kernel menu. Please note that your notebook view may look slightly different depending on available directories and environments, as well as if you choose the lab or traditional notebook view.
+
+![Select Kernel](./static/select_kernel.png)