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43 changes: 43 additions & 0 deletions kilosort4/Dockerfile_cuda13
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FROM nvidia/cuda:13.3.0-base-ubuntu22.04

LABEL maintainer="Alessio Buccino <alessiop.buccino@gmail.com>"

ENV KILOSORT4_VERSION=4.1.7


# USER root
# Ubuntu package installs
RUN apt update && \
apt install -y --no-install-recommends \
libfftw3-dev \
git \
wget && \
apt clean && \
rm -rf /var/lib/apt/lists/*

# install miniconda
ENV MINICONDA_VERSION=25.5.1-0
ENV PYTHON_VERSION=py312
ENV CONDA_DIR=/home/miniconda3
ENV LATEST_CONDA_SCRIPT="Miniconda3-${PYTHON_VERSION}_${MINICONDA_VERSION}-Linux-x86_64.sh"

RUN wget --quiet https://repo.anaconda.com/miniconda/$LATEST_CONDA_SCRIPT -O ~/miniconda.sh && \
bash ~/miniconda.sh -b -p $CONDA_DIR && \
rm ~/miniconda.sh
ENV PATH=$CONDA_DIR/bin:$PATH
RUN conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main && \
conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r && \
conda update conda && \
conda install conda-build

# make conda activate command available from /bin/bash --login shells
RUN echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> /root/.profile
# make conda activate command available from /bin/bash --interactive shells
RUN conda init bash

# install torch
# RUN conda install -y pytorch pytorch-cuda=11.8 -c pytorch -c nvidia
RUN pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118

# install kilosort4
RUN pip install kilosort==$KILOSORT4_VERSION
7 changes: 7 additions & 0 deletions kilosort4/build_cuda13.sh
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#!/bin/bash

# Extract the KILOSORT4_VERSION from the Dockerfile
KILOSORT4_VERSION=$(grep -E '^ENV KILOSORT4_VERSION=' "Dockerfile" | awk -F= '{print $2}' | tr -d '[:space:]')
echo "Building kilosort4-base:$KILOSORT4_VERSION"

docker build -t spikeinterface/kilosort4-base:latest -t spikeinterface/kilosort4-base:${KILOSORT4_VERSION}_cuda-13.3.0 .