CMAQ

CMAQ-5.1 is installed on the Argon HPC system. CMAQ is typically used with full read and write access to the entire CMAQ distribution. This is not possible on a shared installation so working with CMAQ on the cluster system will be a little different than what people might be used to. We can consider two aspects of working with the CMAQ installation, read access and write access. CMAQ was installed with all source code into /opt/apps/CMAQ so there is full read access to everything. The binaries are located in the distribution tree and loading the environment module will set the M3HOME variable to point to the shared installation. The run scripts were modified to

1. not source the config.cmaq file
2. not set the working directory to $BASE

This means that you must obtain the appropriate data sets and set your M3DATA environment variable to point to a directory of your choice containing the data. For example

tar xzvf DATA.CMAQv5.1.Nov2015.tar.gz
export M3DATA=CMAQv5.1/data

Then you can run CMAQ as follows.

module load CMAQ
$M3HOME/scripts/bcon/run.bcon

If you need to customize the script simply download and edit.

cp $M3HOME/scripts/cctm/run.cctm .

Then run that script. It will use the binaries located in the distribution but with whatever model changes were set in the script. Of course, computations should be run on compute nodes so the module loading, setting MM3DATA, and running the CMAQ script would all be entered into an SGE job script. 

Since there is no write access to the CMAQ distribution, if you need to recompile some components, you can copy the parts of the distribution, or the entire distribution, and compile with the build scripts. In this case, you will need to pay attention to the value of $M3HOME as that will be different from what is set in the environment module. You will also need to set the value of M3HOME in the config.cmaq script to point to where you copied the source to. Using this method you will still be using the patched scripts to build with the same tools as the central distribution. Note that even if you copy the distribution and compile you will still want to load the CMAQ environment module to set up all of the dependencies. The M3HOME variable in the config.cmaq script will be used for building but you will need to set its value appropriately for your local copy.

To reiterate, if you do not need to recompile code, you can just edit run scripts to change settings for computations. Settings can either point to data in the shared installation or local data. All of the parameter and profile data that is part of CMAQ is in the CMAQ installation tree.