Container for Full Binary Pursuit

full-binary-pursuit/Dockerfile

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+FROM nvidia/cuda:11.7.1-base-ubuntu22.04
+
+LABEL maintainer="Vincent Prevosto <[email protected]>"
+
+# USER root
+# Ubuntu package installs
+RUN apt update && \
+    apt install -y --no-install-recommends \
+    build-essential \
+    libaio1 \
+    opencl-headers \
+    ocl-icd-libopencl1 \
+    # nvidia-opencl-icd \ this is a virtual package - do not install. Instead install the actual package that matches your host's driver version
+    libnvidia-compute-535 \
+    clinfo \
+    git \
+    wget && \
+    apt clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# install miniconda
+ENV MINICONDA_VERSION 23.3.1-0
+ENV PY_VERSION py39
+ENV CONDA_DIR /home/miniconda3
+ENV LATEST_CONDA_SCRIPT "Miniconda3-${PY_VERSION}_${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:$PATH
+ENV PYTHONPATH=$CONDA_DIR/bin:$CONDA_DIR/lib/python3.9/site-packages
+RUN conda update conda && \
+    conda install conda-build && \
+    conda install conda-forge::ocl-icd-system
+    # See pyopencl docs: 
+    # https://documen.tician.de/pyopencl/misc.html#using-vendor-supplied-opencl-drivers-mainly-on-linux
+
+# 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 IBL python port of pykilosort
+RUN git clone https://github.com/njh27/spikesorting_fullpursuit.git /src/fullpursuit
+WORKDIR /src/fullpursuit
+
+# Install conda environment
+SHELL ["conda","run","-n","base","/bin/bash","-c"]
+RUN conda install -c intel mkl mkl-service
+RUN conda install -c defaults numpy matplotlib
+RUN conda install -c conda-forge pyopencl scipy scikit-learn
+RUN pip install Cython 
+
+# Install full binary pursuit
+RUN conda install --quiet --yes -c defaults ipykernel && \
+    python -m ipykernel install --user --display-name "fullpursuit" && \ 
+    pip install -e .   
+
+WORKDIR /

full-binary-pursuit/README.md

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+### Run container
+docker run --rm -it -v <host-data-folder>:<docker-data-folder> --gpus all fullpursuit:latest
+flags:
+--rm: removes container once it's stopped
+-it: for interactive session (-d for detached)
+-v: mounted volumes (directories)
+--gpus: enables GPU use within container 
+
+### Build this image
+Build default image: 
+docker build -t fullpursuit-base:latest .
+
+Note: Full binary pursuit relies on opencl. Installation varies by OS and CPU / GPU type. 
+For Intel CPUs, see https://www.intel.com/content/www/us/en/developer/articles/tool/opencl-drivers.html. 
+For configuration on Ubuntu and Docker, see also https://linuxhandbook.com/setup-opencl-linux-docker/.  On Ubuntu, you may need to add your user to the `video` and `render` groups to access the GPU. 
+```
+sudo gpasswd -a $USER render
+sudo gpasswd -a $USER video
+```
+Then log out and back in to apply the changes: `su - $USER`
+
+Check fullpursuit version:
+docker run --rm -it spikeinterface/fullpursuit-base:latest bash -c "python -c 'import spikesorting_fullpursuit; print(spikesorting_fullpursuit.__version__)'"
+
+Check that pyopencl can detect your graphics card:
+docker run --rm -it --gpus all  spikeinterface/fullpursuit-base:latest bash -c "python -c 'import pyopencl as cl; platforms = cl.get_platforms(); print(platforms[0].get_devices(cl.device_type.GPU))'"
+
+### Test
+Adapted from the readme file's instructions.
+
+First make the voltage data and save ground truth (mounting the host data folder to the docker data folder):  
+```bash
+docker run --rm -it -v <host-data-folder>:<docker-data-folder> --gpus all spikeinterface/fullpursuit-base:latest bash -c "python /src/fullpursuit/demos/make_and_save_voltage.py <docker-data-folder>/test_voltage.npy <docker-data-folder>/test_ground_truth.pickle"
+```
+e.g.:  
+Create the data folder: `mkdir -p /home/$USER/data/fullpursuit_data`
+Then create the groundtruth data: `docker run --rm -it -v /home/$USER/data/fullpursuit_data:/data --gpus all spikeinterface/fullpursuit-base:latest bash -c "python /src/fullpursuit/demos/make_and_save_voltage.py /data/test_voltage.npy /data/test_ground_truth.pickle"`
+
+Then run the sorting algorithm on the generated synthetic data:  
+```bash
+docker run --rm -it -v <host-data-folder>:<docker-data-folder> --gpus all spikeinterface/fullpursuit-base:latest bash -c "python /src/fullpursuit/demos/test_demo_run_sort.py <docker-data-folder>/test_voltage.npy <docker-data-folder>/sorted_demo.pickle"
+```
+e.g.:  
+`docker run --rm -it -v /home/$USER/data/fullpursuit_data:/data --gpus all spikeinterface/fullpursuit-base:latest bash -c "python /src/fullpursuit/demos/test_demo_run_sort.py /data/test_voltage.npy /data/sorted_demo.pickle"`
+
+Run automated postprocessing to place sorter output into a dictionary sorted neurons:  
+```bash
+docker run --rm -it -v <host-data-folder>:<docker-data-folder> --gpus all spikeinterface/fullpursuit-base:latest bash -c "python /src/fullpursuit/demos/test_demo_postprocessing.py <docker-data-folder>/sorted_demo.pickle <docker-data-folder>/sorted_neurons.pickle"
+```
+e.g.:  
+`docker run --rm -it -v /home/$USER/data/fullpursuit_data:/data --gpus all spikeinterface/fullpursuit-base:latest bash -c "python /src/fullpursuit/demos/test_demo_postprocessing.py /data/sorted_demo.pickle /data/sorted_neurons.pickle"`
+
+Finally run a quick script that compares sorted results to the ground truth generated data and make a couple figures:  
+```bash
+docker run --rm -it -v <host-data-folder>:<docker-data-folder> --gpus all spikeinterface/fullpursuit-base:latest bash -c "python /src/fullpursuit/demos/test_demo_results.py <docker-data-folder>/sorted_neurons.pickle <docker-data-folder>/test_ground_truth.pickle"
+```
+e.g.:  
+`docker run --rm -it -v /home/$USER/data/fullpursuit_data:/data --gpus all spikeinterface/fullpursuit-base:latest bash -c "python /src/fullpursuit/demos/test_demo_results.py /data/sorted_neurons.pickle /data/test_ground_truth.pickle"`

full-binary-pursuit/build.sh

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+#!/bin/bash
+
+docker build -t spikeinterface/fullpursuit-base:latest -t spikeinterface/fullpursuit-base:1.1.0_cuda-11.7.1 .
+
+# version info
+# 01/31/2024 - FBP 1.1.0 CUDA 11.7.1 Ubuntu 22.04

full-binary-pursuit/push.sh

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+#!/bin/bash
+
+docker push --all-tags spikeinterface/fullpursuit-base