diff --git a/docs/hpc/07_containers/03_singularity_with_conda.md b/docs/hpc/07_containers/03_singularity_with_conda.md index 51182ced6e..2b22c55cec 100644 --- a/docs/hpc/07_containers/03_singularity_with_conda.md +++ b/docs/hpc/07_containers/03_singularity_with_conda.md @@ -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 @@ -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