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Nextflow pipeline for creating and then launching MOOSE UQ jobs

This repository currently builds on the example1 from UQ-toolkit.

A current caveat for running on Scafell Pike is that the meshing script must be run offline and uploaded to the basedir, since the GCLIB version required by gmsh is not available on Scafell Pike.

Usage

Below we detail the steps for running a Nextflow+MOOSE pipeline. To enable getting started easier, we will assume the user has a suitable directory set as $MYWORKDIR which could be any of the following: $HOME, $LUSTRE, $SCRATCH or another desired path.

Prerequisities

We assume the user has a python3 installation with commonly-used modules such as numpy, matplotlib and scipy. Load your environment and install the following additional modules (if not already), which UQ-toolkit depends on:

pip install hjson UQpy

Nextflow can be installed as shown below, note that it depends on Java >= 11.0.

cd $MYWORKDIR 
mkdir nextflow-build && cd nextflow-build
curl -s https://get.nextflow.io | bash
export PATH=$PWD:$PATH

when running in offline mode, as is typical of interactive sessions on compute nodes of many HPCs (such as Scafell Pike), you will be prompted to download the following file to the home directory of your compute node (not login node)

mkdir $MYWORKDIR/.nextflow/framework/24.04.4/ -p
cd $MYWORKDIR/.nextflow/framework/24.04.4/
wget https://www.nextflow.io/releases/v24.04.4/nextflow-24.04.4-one.jar

One should also have a MOOSE executable installed and copied to bin/ (in the same directory as your workflow file):

git clone https://github.com/farscape-project/nextflow-moose.git $MYWORKDIR/nextflow-moose
cd $MYWORKDIR/nextflow-moose
mkdir bin
cp $MYWORKDIR/moose/module/combined/combined-opt bin/ # can be replaced with another MOOSE executable
cd -

and a python installation with dependencies for UQ-toolkit installed, as well as UQ-toolkit itself downloaded.

# download and set path to UQ-toolkit
git clone https://github.com/farscape-project/uq-toolkit.git $MYWORKDIR/uq-toolkit
export UQKITPATH=$MYWORKDIR/uq-toolkit

For the examples, you can use the following paths in uq-toolkit

export pipelineBasedirPATH=$UQKITPATH/run_case1_thermomechanicalcube/basedir/
export uqConfigPATH=$pipelineBasedirPATH/config_thermomech.jsonc

Running nextflow workflow

Once all prerequisites are installed, the nextflow pipeline can be launched like so:

nextflow run moose-cube.nf \
    -profile sfpSKLoffline \
    --uqpath $UQKITPATH \
    --basedirpath $pipelineBasedirPATH \
    --uqconfigpath $uqConfigPATH \
    --numsamples 5 \
    -bg > my_log_file.txt