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mdweisner merged 1 commit into from
Dec 12, 2025
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Update 03_singularity_with_conda.md #236

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9 changes: 6 additions & 3 deletions docs/hpc/07_containers/03_singularity_with_conda.md
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Expand Up @@ -83,10 +83,13 @@ 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.

:::information
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 +167,7 @@ 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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