HPC Command Line Interfaceļƒ

Usage on a High Performance Computing Cluster (HPC) is slightly different from the other methods. This system uses Singularity instead of Docker due to security requirements on an HPC. As HPCs may differ, these commands are meant to serve as a general template but may not reflect the exact usage you will require. These commands and scripts are build for a SLURM queue managment system.

HPC Setup Commandsļƒ

Setup

module load singularity
module load python/3.7.0
sudo yum install git
git clone https://github.com/PNNL-CompBio/ion-mob-ms.git
cd ion-mob-ms
pip3 install -r requirements_py3.7_CLI.txt
cd singularity_dev

Run Instructions:

First edit the sample.json file to include absolute paths to your current directory, then choose your run option:

Note: SLURM options in IMD_hpc_in_background.sh will also have to be modified to allow it to run on your own account.

Note: A minumium of 4 cores is required, and using more is highly recommended. This can be specified with the SLURM ā€œ-nā€ command.

Run Test Data on Current Node

python3 CLI_hpc.py --json sample.json

Run Test Data using SLURM Queue

bash IMD_hpc_in_background.sh

To run your own data view General Command Line Usage <https://ionmobility.readthedocs.io/en/latest/getting_started/AWS.html/>`__.