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
- not source the config.cmaq file
- 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 .
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. You will want to pay attention to the M3HOME and EXEC_ID variables but those should both be reset in the config.cmaq file used for building.