Peregrine

Here are the instructions to use Nalu and these examples on NREL’s HPC system Peregrine.

Initial Setup

These steps need to be completed only once to setup the appropriate Nalu environment on the Peregrine system.

1. Create the conda environment:

   module load conda
   conda create -n nalu_python -c conda-forge python=3.6 numpy ruamel.yaml netCDF4 matplotlib scipy pandas
   

2. Set the Nalu environment. This is the same environment used to compile Nalu. If this has not been set, then it can be done by adding the following function to ${HOME}/.bash_profile:

   function nalu_env {
        module purge
        # Load the python environment
        module load conda
        source activate nalu_python
   
        local mod_dir=/nopt/nrel/ecom/ecp/base/modules/
        module use ${mod_dir}/gcc-6.2.0
        module load gcc/6.2.0
   
        compiler=${1:-gcc}
   
        case ${compiler} in
           gcc)
               module unuse ${mod_dir}/intel-18.1.163
               module load binutils openmpi/3.1.1 netlib-lapack cmake
               ;;
           intel)
               module load intel-parallel-studio/cluster.2018.1
               module use ${mod_dir}/intel-18.1.163
               module load binutils intel-mpi intel-mkl cmake
               ;;
        esac
    }
   

   Source the new ${HOME}/.bash_profile:

   source ${HOME}/.bash_profile
   

3. Clone the Nalu repository by:

   git clone https://github.com/Exawind/nalu-wind.git
   

Now the environment is ready to run the examples. To get started, go to: Atmospheric Boundary Layer - Neutral.

Running Every Case

Every time the user logs into Peregrine and wants to run a case, these steps need to be completed:

1. Load the nalu environment:

   nalu_env
   

2. Copy the executables from the public location to the directory where the case is:

   cp /projects/windsim/nalu-wind-executables/* .
   

The system is now ready to compile and use Nalu.