This is likely the netcdf4 memory leak issue. The solution is to convert EQUATES netcdf4 files to netcdf3-classic files using nccopy.
Please see:
Example instruction to convert EQUATES input data from nc4 to nc3
This ncopy conversion requires using the netCDF version built to support netCDF-4 compression.
Then [use the I/O API and netCDF libraries that were built to disable netCDF-4 compression](./configure --prefix=$cwd/…/netcdf --disable-netcdf-4 --disable-dap) to run CMAQ using the netcdf3-classic input files.
To manage multiple versions of netCDF builds, please consider building and using custom Environment Modules.