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mdweisner merged 7 commits into from
Dec 12, 2025
Merged

Updating DTN info #239

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45f958c
Merge pull request #235 from NYU-RTS/mdweisner-patch-1
mdweisner Dec 12, 2025
8fd89b6
Update 03_singularity_with_conda.md
mdweisner Dec 12, 2025
da9d676
Merge pull request #236 from NYU-RTS/mdweisner-patch-4
mdweisner Dec 12, 2025
13db630
Update 03_singularity_with_conda.md
mdweisner Dec 12, 2025
f3e0141
Merge pull request #237 from NYU-RTS/mdweisner-patch-4
mdweisner Dec 12, 2025
7bc539d
Update 07_jupyter_with_conda_singularity.mdx
mdweisner Dec 12, 2025
4064b43
Merge pull request #238 from NYU-RTS/mdweisner-patch-5
mdweisner Dec 12, 2025
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10 changes: 7 additions & 3 deletions docs/hpc/07_containers/03_singularity_with_conda.md
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Expand Up @@ -83,10 +83,14 @@ For the most recent supported versions of PyTorch, please check the [PyTorch web

Launch the appropriate Singularity container in read/write mode (with the :rw flag):
```sh
singularity exec --overlay overlay-15GB-500K.ext3:rw /share/apps/images/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif /bin/bash
singularity exec --fakeroot --overlay overlay-15GB-500K.ext3:rw /share/apps/images/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif /bin/bash
```

The above starts a bash shell inside the referenced Singularity Container overlaid with the 15GB 500K you set up earlier. This creates the functional illusion of having a writable filesystem inside the typically read-only Singularity container.
The above starts a bash shell inside the referenced Singularity Container overlaid with the 15GB 500K you set up earlier. This creates the functional illusion of having a writable filesystem inside the typically read-only Singularity container.

:::note
Please note that the default Singularity on Torch is now Apptainer, which requires the --fakeroot option to load overlay files in read/write mode.
:::

Now, inside the container, download and install miniforge to `/ext3/miniforge3`:
```bash
Expand Down Expand Up @@ -164,7 +168,7 @@ The login nodes restrict memory to 2GB per user, which may cause some large pack
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:

```sh
[NetID@cm001 pytorch-example]$ singularity exec --overlay overlay-15GB-500K.ext3:rw /share/apps/images/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif /bin/bash
[NetID@cm001 pytorch-example]$ singularity exec --fakeroot --overlay overlay-15GB-500K.ext3:rw /share/apps/images/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif /bin/bash

Singularity> source /ext3/env.sh
# activate the environment
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6 changes: 4 additions & 2 deletions docs/hpc/09_ood/07_jupyter_with_conda_singularity.mdx
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Expand Up @@ -65,7 +65,7 @@ Above we used the overlay file `overlay-15GB-500K.ext3.gz` which will contain al

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

Expand Down Expand Up @@ -137,6 +137,8 @@ Singularity> which pip

Now use either conda or pip to install your required python packages to the Miniforge environment.

:::note If using Apptainer (the default Singularity installation on Torch) be sure to use the --fakeroot flag when launching overlay files in read-write mode (:rw).

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.
```bash
Singularity> exit
Expand All @@ -145,7 +147,7 @@ Singularity> exit

# wait to be assigned a node

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