4. Advanced Tutorial

• Learn how to install CMAQ software and underlying libraries, copy input data, and run CMAQ.

• 4.1. Create Cyclecloud CMAQ Cluster
  • 4.1.1. Configure the Cycle Cloud Application Host using the Azure Portal
  • 4.1.2. Customize your Host Virtual Machine for the CycleCloud Application
    • Create Storage Account
  • 4.1.3. Connect to Cyclecloud Web Interface
  • 4.1.4. Instructions to upgrade the number of processors available to the Cycle Cloud Cluster (only needed if you want to modify the number of nodes in the HPC queue)
• 4.2. Modify Cyclecloud CMAQ Cluster
  • 4.2.1. If you make changes to the nodes you must run the following commands
• 4.3. Install CMAQv533 and pre-requisite libraries on linux
  • 4.3.1. Login to updated cluster
  • 4.3.2. Change shell to use .tcsh
  • 4.3.3. Log out and then log back in to activate the tcsh shell
  • 4.3.4. Optional Step to allow multiple users to run on the CycleCloud Cluster
  • 4.3.5. Check to see if the group is added to your user ID
  • 4.3.6. Make the /shared/build directory
  • 4.3.7. Change ownership to your username
  • 4.3.8. Make the /shared/cyclecloud-cmaq directory
  • 4.3.9. Change ownership to your username
  • 4.3.10. Install git
    • Install the cluster-cmaq git repo to the /shared directory
    • Optional - Change the group to cmaq recursively for the /shared directory/build
    • Check what modules are available on the cluster
    • Load the openmpi module
    • Load the gcc copiler - note, this may have been automatically loaded by the openmpi module
    • Verify the gcc compiler version is greater than 8.0
    • Change directories to install and build the libraries and CMAQ
    • Build netcdf C and netcdf F libraries - these scripts work for the gcc 8+ compiler
    • A .cshrc script with LD_LIBRARY_PATH was copied to your home directory, enter the shell again and check environment variables that were set using
    • If the .cshrc wasn’t created use the following command to create it
    • Execute the shell to activate it
    • Verify that you see the following setting
    • Build I/O API library
    • Build CMAQ
• 4.4. Configuring selected storage and obtaining input data
  • 4.4.1. Install AWS CLI to obtain data from AWS S3 Bucket
  • 4.4.2. edit .cshrc file to add /usr/local/bin to path
    • Verify you can run the aws command
  • 4.4.3. Azure Cyclecloud install input on the /shared/data directory
  • 4.4.4. Change ownership
  • 4.4.5. Use the S3 script to copy the CONUS input data from the CMAS s3 bucket
• 4.5. Copy the run scripts from the CycleCloud repo
• 4.6. Run the CONUS Domain on 180 pes
• 4.7. Check the status in the queue
• 4.8. check the timings while the job is still running using the following command
• 4.9. When the job has completed, use tail to view the timing from the log file.
• 4.10. Check whether the scheduler thinks there are cpus or vcpus