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Update 03_singularity_with_conda.md #232

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36 changes: 18 additions & 18 deletions docs/hpc/07_containers/03_singularity_with_conda.md
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Original file line number Diff line number Diff line change
Expand Up @@ -39,30 +39,30 @@ Create a directory for the environment:
```
Copy an appropriate gzipped overlay images from the overlay directory. You can browse available images to see available options:
```bash
[NetID@log-1 pytorch-example]$ ls /scratch/work/public/overlay-fs-ext3
[NetID@log-1 pytorch-example]$ ls /share/apps/overlay-fs-ext3
```
In this example we use `overlay-15GB-500K.ext3.gz` as it has enough available storage for most conda environments. It has 15GB free space inside and is able to hold 500K files
You can use another size as needed.
```bash
[NetID@log-1 pytorch-example]$ cp -rp /scratch/work/public/overlay-fs-ext3/overlay-15GB-500K.ext3.gz .
[NetID@log-1 pytorch-example]$ cp -rp /share/apps/overlay-fs-ext3/overlay-15GB-500K.ext3.gz .
[NetID@log-1 pytorch-example]$ gunzip overlay-15GB-500K.ext3.gz
```

Choose a corresponding Singularity image. For this example we will use the following image:
```bash
/scratch/work/public/singularity/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif
/share/apps/images/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif
```

For Singularity image available on nyu HPC Torch, please check the singularity images folder:
```sh
[NetID@log-1 pytorch-example]$ ls /scratch/work/public/singularity/
[NetID@log-1 pytorch-example]$ ls /share/apps/images/
```

For the most recent supported versions of PyTorch, please check the [PyTorch website](https://pytorch.org/get-started/locally/).

Launch the appropriate Singularity container in read/write mode (with the :rw flag):
```sh
singularity exec --overlay overlay-15GB-500K.ext3:rw /scratch/work/public/singularity/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif /bin/bash
singularity exec --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.
Expand Down Expand Up @@ -143,7 +143,7 @@ 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 /scratch/work/public/singularity/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif /bin/bash
[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

Singularity> source /ext3/env.sh
# activate the environment
Expand Down Expand Up @@ -174,7 +174,7 @@ Singularity> exit
```
#### Test your PyTorch Singularity Image
```sh
[NetID@cm001 pytorch-example]$ singularity exec --overlay /scratch/<NetID>/pytorch-example/my_pytorch.ext3:ro /scratch/work/public/singularity/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif /bin/bash -c 'source /ext3/env.sh; python -c "import torch; print(torch.__file__); print(torch.__version__)"'
[NetID@cm001 pytorch-example]$ singularity exec --overlay /scratch/<NetID>/pytorch-example/my_pytorch.ext3:ro /share/apps/images/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif /bin/bash -c 'source /ext3/env.sh; python -c "import torch; print(torch.__file__); print(torch.__version__)"'

#output: /ext3/miniforge3/lib/python3.8/site-packages/torch/__init__.py
#output: 2.7.1+cu126
Expand Down Expand Up @@ -223,7 +223,7 @@ module purge

singularity exec --nv \
--overlay /scratch/<NetID>/pytorch-example/my_pytorch.ext3:ro \
/scratch/work/public/singularity/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif\
/share/apps/images/singularity/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif\
/bin/bash -c "source /ext3/env.sh; python torch-test.py"
```

Expand All @@ -249,7 +249,7 @@ Check your SLURM output for results, an example is shown below:
### Optional: Convert ext3 to a compressed, read-only squashfs filesystem
Singularity images can be compressed into read-only squashfs filesystems to conserve space in your environment. Use the following steps to convert your ext3 Singularity image into a smaller squashfs filesystem.
```sh
[NetID@log-1 pytorch-example]$ srun -N1 -c4 singularity exec --overlay my_pytorch.ext3:ro /scratch/work/public/singularity/centos-8.2.2004.sif mksquashfs /ext3 /scratch/<NetID>/pytorch-example/my_pytorch.sqf -keep-as-directory -processors 4 -noappend
[NetID@log-1 pytorch-example]$ srun -N1 -c4 singularity exec --overlay my_pytorch.ext3:ro /share/apps/images/centos-8.2.2004.sif mksquashfs /ext3 /scratch/<NetID>/pytorch-example/my_pytorch.sqf -keep-as-directory -processors 4 -noappend
```

Here is an example of the amount of compression that can be realized by converting:
Expand All @@ -265,7 +265,7 @@ Notice that it saves over 3GB of storage in this case, though your results may v

You can use squashFS images similarly to the ext3 images:
```sh
[NetID@log-1 pytorch-example]$ singularity exec --overlay /scratch/<NetID>/pytorch-example/my_pytorch.sqf:ro /scratch/work/public/singularity/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif /bin/bash -c 'source /ext3/env.sh; python -c "import torch; print(torch.__file__); print(torch.__version__)"'
[NetID@log-1 pytorch-example]$ singularity exec --overlay /scratch/<NetID>/pytorch-example/my_pytorch.sqf:ro /share/apps/images/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif /bin/bash -c 'source /ext3/env.sh; python -c "import torch; print(torch.__file__); print(torch.__version__)"'

#example output: /ext3/miniforge3/lib/python3.12/site-packages/torch/__init__.py
#example output: 2.6.0+cu124
Expand All @@ -277,10 +277,10 @@ If the first ext3 overlay image runs out of space or you are using a squashFS co

Open the first image in read only mode:
```sh
[NetID@log-1 pytorch-example]$ cp -rp /scratch/work/public/overlay-fs-ext3/overlay-2GB-100K.ext3.gz .
[NetID@log-1 pytorch-example]$ cp -rp /share/apps/overlay-fs-ext3/overlay-2GB-100K.ext3.gz .
[NetID@log-1 pytorch-example]$ gunzip overlay-2GB-100K.ext3.gz

[NetID@log-1 pytorch-example]$ singularity exec --overlay overlay-2GB-100K.ext3 --overlay /scratch/<NetID>/pytorch-example/my_pytorch.ext3:ro /scratch/work/public/singularity/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif /bin/bash
[NetID@log-1 pytorch-example]$ singularity exec --overlay overlay-2GB-100K.ext3 --overlay /scratch/<NetID>/pytorch-example/my_pytorch.ext3:ro /share/apps/images/cuda12.1.1-cudnn8.9.0-devel-ubuntu22.04.2.sif /bin/bash
Singularity> source /ext3/env.sh
Singularity> pip install tensorboard
```
Expand All @@ -303,7 +303,7 @@ Create a directory for your Julia work, such as `/scratch/<NetID>/julia`, and th

Copy an overlay image, such as the 2GB 100K overlay, which generally has enough storage for Julia packages. Once copied, unzip to the same folder, rename to julia-pkgs.ext3:
```sh
[NetID@log-1 julia]$ cp -rp /scratch/work/public/overlay-fs-ext3/overlay-2GB-100K.ext3.gz .
[NetID@log-1 julia]$ cp -rp /share/apps/overlay-fs-ext3/overlay-2GB-100K.ext3.gz .
[NetID@log-1 julia]$ gunzip overlay-2GB-100K.ext3.gz
[NetID@log-1 julia]$ mv overlay-2GB-100K.ext3 julia-pkgs.ext3
```
Expand Down Expand Up @@ -478,7 +478,7 @@ Building on the previous Julia example, this will demonstrate how to set up a si

Copy overlay image:
```sh
[NetID@log-1 julia]$ cp -rp /scratch/work/public/overlay-fs-ext3/overlay-2GB-100K.ext3.gz .
[NetID@log-1 julia]$ cp -rp /share/apps/overlay-fs-ext3/overlay-2GB-100K.ext3.gz .
[NetID@log-1 julia]$ gunzip overlay-2GB-100K.ext3.gz
[NetID@log-1 julia]$ mv overlay-2GB-100K.ext3 julia-pkgs.ext3
```
Expand Down Expand Up @@ -507,7 +507,7 @@ Launch Singularity with overlay images in writable mode to install packages:
--bind /share/apps \
--bind /scratch/<NetID>/julia/julia-compiled:/ext3/pkgs/compiled \
--bind /scratch/<NetID>/julia/julia-logs:/ext3/pkgs/logs \
/scratch/work/public/apps/torch/centos-8.2.2004.sif \
/share/apps/images/centos-8.2.2004.sif \
/bin/bash
```

Expand Down Expand Up @@ -569,7 +569,7 @@ singularity exec \
--bind /share/apps \
--bind /scratch/<NetID>/julia/julia-compiled:/ext3/pkgs/compiled \
--bind /scratch/<NetID>/julia/julia-logs:/ext3/pkgs/logs \
/scratch/work/public/apps/torch/centos-8.2.2004.sif \
/share/apps/images/centos-8.2.2004.sif \
/bin/bash -c "
source /ext3/env.sh
julia $args
Expand Down Expand Up @@ -629,7 +629,7 @@ singularity exec \
--bind /share/apps \
--bind /scratch/<NetID>/julia/julia-compiled:/ext3/pkgs/compiled \
--bind /scratch/<NetID>/julia/julia-logs:/ext3/pkgs/logs \
/scratch/work/public/apps/torch/centos-8.2.2004.sif \
/share/apps/images/centos-8.2.2004.sif \
/bin/bash -c "
source /ext3/env.sh
julia $args
Expand All @@ -649,7 +649,7 @@ Install packages to the writable image:

If you do not need host packages installed in `/share/apps`, you can work with Singularity OS image:
```sh
/scratch/work/public/singularity/ubuntu-20.04.1.sif
/share/apps/images/ubuntu-20.04.1.sif
```

Download Julia installation package from [https://julialang-s3.julialang.org/bin/linux/x64/1.5/julia-1.5.3-linux-x86_64.tar.gz](https://julialang-s3.julialang.org/bin/linux/x64/1.5/julia-1.5.3-linux-x86_64.tar.gz)
Expand Down
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