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Update 07_jupyter_with_conda_singularity.mdx #234

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32 changes: 26 additions & 6 deletions docs/hpc/09_ood/07_jupyter_with_conda_singularity.mdx
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# Jupyter Notebook with Conda/Singularity in OOD
Please note that Greene and Torch organize overlay files and Singularity images in different directories.

## Greene Directories
Overlay Files:
```
/scratch/work/public/overlay-fs-ext3/
```
Singularity Files:
```
/scratch/work/public/singularity/
```

## Torch Directories
Overlay Files:
```
/share/apps/overlay-fs-ext3
```
Singularity Files:
```
/share/apps/images/
```
## OOD + Singularity + conda
This page describes how to use your Singularity with conda environment in OOD GUI at Torch.

Expand Down Expand Up @@ -38,16 +58,16 @@ The above code automatically makes your environment look for the default shared
```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]$ cp -rp /share/apps/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).

### Launch Singularity Environment for Installation
```bash
[NetID@log-1 ~]$ singularity exec --overlay /scratch/$USER/my_env/overlay-15GB-500K.ext3:rw /scratch/work/public/singularity/cuda12.3.2-cudnn9.0.0-ubuntu-22.04.4.sif /bin/bash
[NetID@log-1 ~]$ singularity exec --overlay /scratch/$USER/my_env/overlay-15GB-500K.ext3:rw /share/apps/images/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 `/share/apps/images`

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.

Expand Down Expand Up @@ -125,7 +145,7 @@ Singularity> exit

# wait to be assigned a node

[NetID@cm001 my_env]$ singularity exec --overlay /scratch/$USER/my_env/overlay-15GB-500K.ext3:rw /scratch/work/public/singularity/cuda12.3.2-cudnn9.0.0-ubuntu-22.04.4.sif /bin/bash
[NetID@cm001 my_env]$ singularity exec --overlay /scratch/$USER/my_env/overlay-15GB-500K.ext3:rw /share/apps/images/cuda12.3.2-cudnn9.0.0-ubuntu-22.04.4.sif /bin/bash

Singularity> source /ext3/env.sh
# activate the environment
Expand Down Expand Up @@ -153,11 +173,11 @@ At the bottom of the file we have the template singularity command.
```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 \
/share/apps/images/cuda12.3.2-cudnn9.0.0-ubuntu-22.04.4.sif \
/bin/bash -c "source /ext3/env.sh; $cmd $args"
```
:::warning
If you used a different overlay (/scratch/$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.
If you used a different overlay (/scratch/$USER/my_env/overlay-15GB-500K.ext3 shown above) or .sif file (/share/apps/images/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.
Expand Down
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