bootstrap: docker

from: nvidia/cuda:12.8.1-devel-ubuntu20.04

%help

IDI jupyterhub (Cuda 12)

%environment

CUDA_ROOT=/usr/local/cuda

export CUDA_ROOT

SINGULARITY_SHELL=/bin/zsh

export SINGULARITY_SHELL

PATH=$PATH:/opt/anaconda3/bin:/usr/local/cuda/bin

export PATH

LD_PRELOAD=/usr/local/lib/mklpatch.so

export LD_PRELOAD

SHELL=/usr/bin/zsh

export SHELL

MKL_THREADING_LAYER=gnu

export MKL_THREADING_LAYER

CONDA_PKGS_DIRS=/tmp

export CONDA_PKGS_DIRS

%post

apt-get update && DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends aria2 curl git gzip lz4 p7zip-full p7zip-rar \

rsync unzip wget xz-utils zip openssl bzip2 axel binutils cmake diffutils \

elfutils file build-essential gdb htop less libstdc++6 ltrace make mc mosh \

openmpi-bin libopenmpi-dev openssh-client patch patchutils linux-tools-common \

linux-tools-generic psmisc screen strace tmux vim zsh libssl-dev munge \

imagemagick slurm-wlm \

&& rm -rf /var/lib/apt/lists/*

echo "installing conda"

wget -O /tmp/Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"

cd /tmp/ && bash /tmp/Miniforge3.sh -b -p /opt/conda

rm /tmp/Miniforge3.sh

ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh

PATH=$PATH:/usr/local/cuda/bin:/opt/conda/bin

. /etc/profile.d/conda.sh

echo "installing conda extensions"

conda activate

mamba install -q -y "python=3.11" "numexpr>=2.7.2" "numpy>=1.17" h5py scipy numba "mkl>=2020" cython "jupyterlab" jupyter scikit-image scikit-learn seaborn pandas line_profiler black ninja memory_profiler isort "mkl-include>=2020" cmake sympy pytest lmfit pytest-flake8 ruff "numpy<2.2" matplotlib tqdm cython mkl-devel mkl-service "setuptools<60" einops uv joblib

conda clean -a -y &

echo 'installing pnumpy from pip' && pip install pnumpy

echo "installing pycuda from pip" && CFLAGS=-std=c++11 CXXFLAGS=-std=c++11 LIBRARY_PATH=/usr/local/cuda/lib64/stubs CPATH=/usr/local/cuda/include CUDA_ROOT=/usr/local/cuda pip install pycuda

echo 'installing cupy from pip' && pip install cupy-cuda12x &

conda config --file /opt/conda/.condarc --set changeps1 False

conda config --file /opt/conda/.condarc --set auto_activate_base true

cat > /etc/profile.d/zconda.sh << "EOF1"

conda activate

EOF1

cat > /opt/runscript.sh << "EOF2"

. /etc/profile.d/conda.sh

conda activate

exec "$@"

EOF2

chmod +x /opt/runscript.sh

echo 'compiling mkl patch'

cat > /tmp/mklpatch.c << "EOF4"

//https://danieldk.eu/Posts/2020-08-31-MKL-Zen.html

int mkl_serv_intel_cpu_true() {

return 1;

}

EOF4

gcc -shared -fPIC -o /tmp/mklpatch.so /tmp/mklpatch.c

cp /tmp/mklpatch.so /usr/local/lib/mklpatch.so && chmod 775 /usr/local/lib/mklpatch.so && echo 'done'

wait

echo 'install idi' && pip install git+https://github.com/fzimmermann89/idi

wait

conda clean -a -y -f

pip cache purge

jupyter lab clean

rm -rf /root/.conda | true

rm -rf /root/.npm | true

rm -rf /root/.cache | true

rm -rf /tmp/npm* | true

rm -rf /tmp/yarn* | true

rm -rf /var/cache/* | true

touch /INSIDE_SINGULARITY_IDI_IMAGE

echo '####ALL DONE####'

%labels

Maintainer zimmf

Version 0.2

%runscript

exec /opt/runscript.sh python "$@"

%startscript

exec /opt/runscript.sh jupyter lab "$@"

%apprun jupyter

exec /opt/runscript.sh jupyter "$@"

%apprun ipython

exec /opt/runscript.sh ipython "$@"