4.1. Install CMAQv5.4+ on Single Virtual Machine Advanced (optional)

Run CMAQv5.4+ on a single Virtual Machine (VM) using c6a.xlarge (4 CPUs) and Ubuntu 22.04.2 LTS (GNU/Linux 5.15.0-1031-aws x86_64), then upgrade to c6a.48xlarge.

• 4.1.1. Install Software and run CMAQv5.4 on c6a.xlarge for the 12km Listos Training Domain
  • Build CMAQv5.4+ on c6a.xlarge EC2 instance
    • Create a c6a.xlarge Virtual Machine
    • Login to the Virtual Machine
    • Make the /shared directory
    • Change the group and ownership of the shared directory
    • Create subdirectories on /shared
    • Check operating system version
    • Install Environment Modules
    • Logout and then log back in to activate modules command
    • Verify module command works
    • Set up build environment
    • Install Compilers and OpenMPI
    • Change shell to use tcsh
    • Logout and log back in, then check the shell
    • Check available versions of compiler
    • Choose gcc-9 and gfortran-9 as default compilers
    • Check version of gcc
    • Check version of gfortran
    • Check version of OpenMPI
    • Install Parallel Cluster CMAQ Repo
    • Install and build netcdf C, netcdf Fortran, I/O API, and CMAQ
    • Install netcdf-C and netcdf-Fortran
    • Copy a file to set paths
    • Exit cluster and log back in to activate the update shell, or use csh
    • Create Custom Environment Module for Libraries
    • Find path for openmpi libraries
    • Find path for include files for openmpi
    • Edit the config_cmaq_singlevm.csh script to specify the paths for OpenMPI
    • Install Python
    • Install jupyter notebook.
    • Install and Build CMAQ
      • Add compile option to makefile to get beyond a type mismatch error (note, this is only needed if you were using the gcc-11 compiler.
    • Run make again
    • Copy the run scripts from the repo to the run directory
  • Download the Input data from the S3 Bucket
    • Install aws command line
    • Install unzip and unzip file
    • Edit .cshrc
    • Install the input data using the s3 script
    • Link the input data directory to the default location
  • Run CMAQ interactively using the following command:
    • First check to see how many cpus you have available on the machine.
    • If you upgrade this VM from a c6.xlarge to a c6.8xlarge, then you could run CMAQ interactively on 16 pes using the following command:
• 4.1.2. Install Software and run CMAQv5.4 on c7g-hpc7g for the 12km Listos Training Domain
  • Build CMAQv5.4+ on c7g.xlarge EC2 instance
    • Create a c7g.xlarge Virtual Machine
    • Login to the Virtual Machine
    • Make the /shared directory
    • Change the group and ownership of the shared directory
    • Create subdirectories on /shared
    • Check operating system version
    • Install Environment Modules
    • Logout and then log back in to activate modules command
    • Verify module command works
    • Set up build environment
    • Install Compilers and OpenMPI
    • Compiler versions
    • Change shell to use tcsh
    • Logout and log back in, then check the shell
    • Check available versions of compiler
    • Choose gcc-9 and gfortran-9 as default compilers
    • Check version of gcc
    • Check version of gfortran
    • Check version of OpenMPI
    • Install Parallel Cluster CMAQ Repo
    • Install and build netcdf C, netcdf Fortran, I/O API, and CMAQ
    • Install netcdf-C and netcdf-Fortran
    • Copy a file to set paths
    • Exit cluster and log back in to activate the update shell, or use csh
    • Create Custom Environment Module for Libraries
    • Find path for openmpi libraries
    • Find path for include files for openmpi
    • Edit the config_cmaq_singlevm.csh script to specify the paths for OpenMPI
    • Install Python
    • Install jupyter notebook.
    • Install and Build CMAQ
      • Add compile option to makefile to get beyond a type mismatch error (note, this is only needed if you were using the gcc-11 compiler.
    • Run make again
    • Copy the run scripts from the repo to the run directory
  • Download the Input data from the S3 Bucket
    • Install aws command line
    • Install unzip and unzip file
    • Edit .cshrc
    • Install the input data using the s3 script
    • Link the input data directory to the default location
  • Run CMAQ interactively using the following command:
    • First check to see how many cpus you have available on the machine.
    • If you upgrade this VM from a c6.xlarge to a c6.8xlarge, then you could run CMAQ interactively on 16 pes using the following command:
• 4.1.3. Install I/O API libraries that support HDF5
• 4.1.4. Upgrade to run CMAQ on larger EC2 Instance
  • Save the AMI and create a new VM using a larger c6a.8xlarge (with 32 processors)
    • Use the AWS Console to Stop the Image
    • Use the AWS Console to Create a new AMI
    • Use the newly created AMI to launch a new Single VM using a larger EC2 instance.
    • Load the modules
    • Test running the listos domain on 32 processors
  • Run CMAQv5.4 for the full 12US1 Domain on c6a.48xlarge
    • Run utility to uncompress hdf5 *.nc4 files and save as classic *.nc files
    • Increased disk space on /shared to 500 GB