diff --git a/docs/hpc/07_containers/03_singularity_with_conda.md b/docs/hpc/07_containers/03_singularity_with_conda.md index 01aeb0f80..6333dfc65 100644 --- a/docs/hpc/07_containers/03_singularity_with_conda.md +++ b/docs/hpc/07_containers/03_singularity_with_conda.md @@ -92,7 +92,12 @@ The above starts a bash shell inside the referenced Singularity Container overla 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`: +Now, inside the container, download and install miniforge to `/ext3/miniforge3`. + +:::note +Please note your prompt should indicate you're in singularity with the `Singularity>` prompt +::: + ```bash wget --no-check-certificate https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh bash Miniforge3-Linux-x86_64.sh -b -p /ext3/miniforge3 @@ -167,6 +172,11 @@ srun --cpus-per-task=2 --mem=10GB --time=04:00:00 --pty /bin/bash 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. Your prompt should look similar to this: ```sh +# Your prompt should now look something like this once your jobs starts: [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 + +source /ext3/env.sh [NetID@cm001 pytorch-example]$ ``` Then you can activate your environment: @@ -509,6 +519,7 @@ Building on the previous Julia example, this will demonstrate how to set up a si Copy overlay image: ```sh +cd ~/julia cp -rp /share/apps/overlay-fs-ext3/overlay-2GB-100K.ext3.gz . gunzip overlay-2GB-100K.ext3.gz mv overlay-2GB-100K.ext3 julia-pkgs.ext3 @@ -566,6 +577,9 @@ julia --version Run Julia to install packages: ```julia julia +julia> using Pkg +julia> Pkg.add("KNITRO") +julia> Pkg.add("JuMP") # Your prompt should now be julia> using Pkg Pkg.add("KNITRO")