ADCIRC Installation for HPC Cluster

This repository helps to install ADCIRC software on Pantarhei and UAHPC cluster at a user-defined location.

Getting Started

There are three following phases in order to run ADCIRC on the HPC cluster.

• In the first phase, we install the ADCIRC on a user-defined location in their UAHPC account using the install.sh file.
• In the second phase, we activate the installed environment using create_environment.sh file.
• In the third phase, we submit a job script or run an interactive job.

Installation

• Step 1: Clone this repository at your desired location on the HPC cluster

  git clone https://github.com/TrupeshKumarPatel/ADCIRC_UAHPC.git

  [!NOTE]
  All the packages of ADCIRC will be installed in the cloned directory. So, you'll need to run the clone command at your desired file location.

• Step 2: Change your current directory

  cd ADCIRC_UAHPC

• Step 3: Run the installation file

  ./install.sh

  [!WARNING]
  The installation process is very long, due to the package's dependency on previously compiled packages. Therefore, take a cup of coffee and watch for any error message, if there is any.

Setup Environment

• Step 1: Since the ADCIRC is installed on your desired directory, we will need to activate the installed environment every time you log in to HPC or submit any job script to the cluster

  source create_environment.sh

  [!NOTE]
  To run the create_environment.sh file, you must be in the ADCIRC_UAHPC directory.

Submit Job Script

• Step 1: Create a bash script to submit in Slurm Workload Manager at HPC

  #!/bin/bash
  #
  #SBATCH --job-name=ADCIRC_JOB
  #SBATCH --ntasks=<number>
  #SBATCH --output=ADCIRC-run-%J.log
  #SBATCH --qos main
  #SBATCH --mail-type=ALL
  #SBATCH --mail-user=<CRIMSON_ID>@crimson.ua.edu
  
  export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
  
  #~~~~~~ Printing Job Specifications ~~~~~~#
  echo "==============================================================="
  echo "                        JOB INFORMATION                        "
  echo "==============================================================="
  echo "Cluster Name                       : " $SLURM_CLUSTER_NAME
  echo "# of Nodes requested               : " $SLURM_NNODES
  echo "# of tasks per each node           : " $SLURM_TASKS_PER_NODE
  echo "# of CPUs  per task                : " $SLURM_CPUS_PER_TASK
  echo "# of CPUs on the allocated node    : " $SLURM_CPUS_ON_NODE
  echo "# of Processes in the current job  : " $SLURM_NTASKS
  echo "List of nodes allocated to the job : " $SLURM_NODELIST
  echo ""
  echo ""
  
  #~~~~~~ Source and Module for UAHPC Cluster ~~~~~~#
  export CC=/share/apps/intel/2018/bin/icc
  export CXX=/share/apps/intel/2018/bin/icpc
  module load compilers/intel/2018
  module load compilers/intel/util
  module load cmake/3.20.1
  module load mpi/mpich/3.3.2-intel
  module load zlib/1.2.11
  module load hdf5/intel/1.10.6-mpich
  module load netcdf/intel/4.7.3-mpich
  
  cd <PATH_TO_ADCIRC_UAHPC_DIRECTORY>
  
  source create_environment.sh
  
  echo "==============================================================="
  echo "                        MODULE LIST                            "
  echo "==============================================================="
  module list