diff --git a/Singularity.v0.1.def b/Singularity.v0.1.def deleted file mode 100644 index 41aa1eb..0000000 --- a/Singularity.v0.1.def +++ /dev/null @@ -1,33 +0,0 @@ -Bootstrap: oras -From: ghcr.io/sinzlab/pytorch-singularity:v3.9-torch1.10.2-dj0.12.7.def - -%labels -MAINTAINER Arne Nix - -%post - # install third-party libraries - # needed for vim extension in jupyter and tex export in matplotlib: - apt update && apt install -y \ - texlive-latex-extra \ - texlive-fonts-recommended \ - texlive-base \ - dvipng \ - zsh \ - python3-venv - - python3.9 -m pip --no-cache-dir install \ - checkout_code \ - requests \ - imageio \ - scikit-image \ - einops \ - vit-pytorch - -%environment - export SHELL=/usr/bin/zsh - -%startscript - exec "$@" - -%runscript - exec "$@" diff --git a/Singularity.v0.2.def b/Singularity.v0.2.def new file mode 100644 index 0000000..f8d26b4 --- /dev/null +++ b/Singularity.v0.2.def @@ -0,0 +1,55 @@ +Bootstrap: docker + +From: continuumio/miniconda3 + +%files + environment.yml + +%post + apt update && apt install -y \ + build-essential \ + git \ + wget \ + vim \ + curl \ + zip \ + zlib1g-dev \ + unzip \ + pkg-config \ + libblas-dev \ + liblapack-dev \ + python3-tk \ + python3-wheel \ + graphviz \ + libhdf5-dev \ + python3.9 \ + python3.9-dev \ + python3.9-distutils \ + python3-testresources \ + software-properties-common \ + swig \ + ffmpeg \ + texlive-latex-extra \ + texlive-fonts-recommended \ + texlive-base \ + dvipng + #zsh + apt-get clean + + ln -s /usr/bin/python3.9 /usr/local/bin/python + ln -s /usr/bin/python3.9 /usr/local/bin/python3 + + + /opt/conda/bin/conda env create -f environment.yml + + /opt/conda/bin/conda run -n $(head -n 1 environment.yml | cut -f 2 -d ' ') pip install ffcv \ + vit-pytorch \ + torch==1.10.2+cu113 \ + torchvision==0.11.3+cu113 \ + torchaudio==0.10.2+cu113 \ + -f https://download.pytorch.org/whl/cu113/torch_stable.html + +%runscript + exec /opt/conda/envs/$(head -n 1 environment.yml | cut -f 2 -d ' ')/bin/"$@" + + diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..c9ae0df --- /dev/null +++ b/environment.yml @@ -0,0 +1,35 @@ +name: nntransfer_env +channels: + - pytorch + - conda-forge +dependencies: + - cupy + - pkg-config + - compilers + - libjpeg-turbo + - opencv + - cudatoolkit=11.3 + - numba + - blackcellmagic + - pytest + - pytest-cov + - numpy + - matplotlib + - scipy + - pandas + - jupyter + - scikit-learn + - scikit-image + - seaborn + - graphviz + - gpustat + - h5py + - gitpython + - Pillow==8.0.1 + - jupyterlab + - datajoint==0.12.7 + - ipykernel + - requests + - imageio + - scikit-image + - einops \ No newline at end of file