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Running PyHealth on the Campus Cluster

Quick Start

git clone https://github.com/Multimodal-PyHealth/PyHealth.git
cd PyHealth
chmod +x setup.sh
./setup.sh

Data Paths

All MIMIC-4 data is under /projects/illinois/eng/cs/jimeng/physionet.org/files/:

| Data | Path | | EHR | /projects/illinois/eng/cs/jimeng/physionet.org/files/mimiciv/2.2 | | Clinical Notes | /projects/illinois/eng/cs/jimeng/physionet.org/files/mimic-note | | Chest X-rays | /projects/illinois/eng/cs/jimeng/physionet.org/files/mimic-cxr-jpg/2.1.0 |

Important: NOTE_ROOT should be .../mimic-note (not .../mimic-note/note). The config YAML appends note/ automatically.

Set CACHE_DIR to your own writable directory: /u/<NetID>/pyhealth_cache

Running on a Compute Node

Run on a compute node: Slurm command example:

srun --account=jimeng-cs-eng --partition=eng-research-gpu --time=00:10:00 --gres=gpu:1 --pty bash

Once on the compute node, re-activate and run:

module load miniconda3/24.9.2
conda activate pyhealth2
cd ~/PyHealth
python examples/mortality_prediction/multimodal_mimic4.py

For a clean install, which reruns the setup proccess by deleting the enviroment packages and conda env and reinstalls them, run: ./setup.sh clean