setup-cirrus.md

Set up Cirrus environment

Get source code repository

Run:

git clone https://github.com/marangiop/unet.git

This will clone the source code repository into a unet directory.

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Set up Python environment

First, follow instructions to install miniconda on Cirrus: https://cirrus.readthedocs.io/en/master/user-guide/python.html?highlight=miniconda

Create unet environment:

conda create -n unet

Proceed ([y]/n)? y

Activate environment:

conda activate unet

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Install dependencies

cd unet
conda install -c anaconda --file requirements_conda.txt
pip install -r requirements_pip.txt

Build Tensorflow-gpu using Singularity image (required for running on GPUs)

module load singularity
singularity build tfgpu.simg docker://tensorflow/tensorflow:1.12.0-gpu-py3

Install packages inside Tensorflow-gpu image

module load singularity
singularity shell tfgpu.simg
conda install -c anaconda --file requirements_conda.txt
pip install -r requirements_pip.txt