added lang spec to code blocks except julia which needs to be installed

Author: RobJY

docs/hpc/08_ood/open_on_demand.md

@@ -9,9 +9,13 @@ This page describes how to use your Singularity with conda environment in Open O
 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.md). 
 
 ### Preinstallation Warning
-If you have initialized Conda in your base environment (your prompt on Greene may show something like `(base) [NETID@log-1 ~]$)` then you must first comment out or remove this portion of your ~/.bashrc file:
-
+If you have initialized Conda in your base environment, your prompt on Greene may show something like:
+```sh
+(base) [NETID@log-1 ~]$
 ```
+then you must first comment out or remove this portion of your `~/.bashrc` file:
+
+```bash
 # >>> conda initialize >>>
 # !! Contents within this block are managed by 'conda init' !!
 __conda_setup="$('/share/apps/anaconda3/2020.07/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
@@ -31,7 +35,7 @@ unset __conda_setup
 The above code automatically makes your environment look for the default shared installation of Conda on the cluster and will sabotage  any attempts to install packages to a Singularity environment. Once removed or commented out, log out and back into the cluster for a fresh environment.
 
 ### 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 .
@@ -40,26 +44,26 @@ 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](./singularity_with_conda.md), [Squash File System and Singularity](./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
 ```
 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:
-```
+```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
 ```
 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
@@ -68,7 +72,7 @@ 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:
-```
+```bash
 #!/bin/bash
    unset -f which
 source /ext3/miniforge3/etc/profile.d/conda.sh
@@ -78,21 +82,21 @@ 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
 ```
 
 ### 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
 ```
 To confirm that your environment is appropriately referencing your Miniforge installation, try out the following:
-```
+```sh
 unset which
 which conda
 # output: /ext3/miniforge3/bin/conda
@@ -110,7 +114,7 @@ which pip
 Now use either conda install 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
 
 # wait to be assigned a node
@@ -125,7 +129,7 @@ After it is running, you’ll be redirected to a compute node. From there, run s
 
 ### 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
@@ -140,7 +144,7 @@ To set the conda environment, edit the file named 'python' in /.local/share/jupy
 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
 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 \
@@ -149,7 +153,7 @@ singularity exec $nv \
 ***WARNING:*** If you used a different overlay (/scratch/$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.
-```
+```json
 {
  "argv": [
   "PYTHON_LOCATION",
@@ -163,7 +167,7 @@ Edit the default kernel.json file by setting PYTHON_LOCATION and KERNEL_DISPLAY_
 }
 ```
 to
-```
+```json
 {
  "argv": [
   "/home/<Your NetID>/.local/share/jupyter/kernels/my_env/python",