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mdweisner merged 1 commit into from
Dec 12, 2025
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Update 07_jupyter_with_conda_singularity.mdx #238

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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
Expand Down
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