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CMAQ-ISAM Benchmark Tutorial

Procedure to build and run the CMAQ-ISAM model using gnu compiler:

Step 1: Download and run the CMAQv5.3.2 benchmark case (without ISAM) to confirm that your model run is consistent with the provided benchmark output.

If you encounter any errors, try running the model in debug mode and refer to the CMAS User Forum to determine if any issues have been reported.

https://forum.cmascenter.org/

Step 2: Read the User Guide Chapter on Integrated Source Apportionment Method.

Note: This benchmark is intended to demonstrate how to build and run CMAQ-ISAM with the provided input files:

The following isam control file is provided in the CCTM/scripts directory when you obtain the CMAQv5.3.2 code from github (step 5 below):

isam_control.txt

The following gridmask file is provided with the benchmark inputs in the CMAQv5.3.2_Benchmark_2Day_Input/2016_12SE1 directory (see step 10 below)

GRIDMASK_STATES_12SE1.nc

The instructions require the user to edit the emissions control namelist file in the BLD directory (see step 9 below).

EmissCtrl_cb6r3_ae7_aq.nml

Step 3 (optional): choose your compiler, and load it using the module command if it is available on your system

module avail

module load openmpi_4.0.1/gcc_9.1.0

Step 4 (optional): Install I/O API (note, this assumes you have already installed netCDF C and Fortran Libraries)

I/O APIv3.2 supports up to MXFILE3=256 open files, each with up to MXVARS3=2048. ISAM applications configured to calculate source attribution of a large number of sources may exceed this upper limit of model variables, leading to a model crash. To avoid this issue, users may use I/O API version 3.2 "large" that increases MXFILE3 to 512 and MXVARS3 to 16384. Instructions to build this version are found in Chapter 3. Note, using this ioapi-large version is NOT REQUIRED for the CMAQ-ISAM Benchmark Case. If a user needs to use these larger setting for MXFILE3 and MXVAR3 to support their application, the memory requirements will be increased. If needed, this version is available as a zip file from the following address:

https://www.cmascenter.org/ioapi/download/ioapi-3.2-large-20200828.tar.gz

Otherwise, use the I/O API version available here: https://www.cmascenter.org/ioapi/download/ioapi-3.2-20200828.tar.gz

Step 5: Install CMAQ with ISAM

git clone -b master https://github.com/USEPA/CMAQ.git CMAQ_REPO

Build and run in a user-specified directory outside of the repository

In the top level of CMAQ_REPO, the bldit_project.csh script will automatically replicate the CMAQ folder structure and copy every build and run script out of the repository so that you may modify them freely without version control.

Edit bldit_project.csh, to modify the variable $CMAQ_HOME to identify the folder that you would like to install the CMAQ package under. For example:

set CMAQ_HOME = /work/your_username/CMAQ_v5.3.2

Now execute the script.

./bldit_project.csh

Change directories to the CMAQ_HOME directory

cd /work/your_username/CMAQ_v5.3.2

Step 6. Edit the config_cmaq.csh to specify the paths of the ioapi and netCDF libraries

Step 7: Modify the bldit_cctm.csh

Change directory to CCTM/scripts

cd CCTM/scripts

Comment out the following option to compile CCTM with ISAM:

#> Integrated Source Apportionment Method (ISAM)
set ISAM_CCTM                         #> uncomment to compile CCTM with ISAM activated

Step 8: Run the bldit_cctm.csh script

./bldit_cctm.csh gcc |& tee bldit_cctm_isam.log

Step 9: Edit the Emission Control Namelist to recognize the CMAQ_REGIONS file

Change directories to the build directory

cd BLD_CCTM_v532_ISAM_gcc

edit the emissions namelist file

gedit EmissCtrl_cb6r3_ae7_aq.nml

Uncomment the line that contains ISAM_REGIONS as the File Label

&RegionsRegistry
 RGN_NML  =
 !          | Region Label   | File_Label  | Variable on File
 !<Default>    'EVERYWHERE'  ,'N/A'        ,'N/A',
 !<Example>    'WATER'       ,'CMAQ_MASKS' ,'OPEN',
 !<Example>    'ALL'         ,'CMAQ_MASKS' ,'ALL',
               'ALL'         ,'ISAM_REGIONS','ALL',

Step 10: Download the benchmark input data

Link to CMAQv5.3.2_Benchmark_2Day_Input.tar.gz input data on the following Google Drive Folder

  • You can see a list of the files in the Benchmark dataset: by clicking on CMAQv5.3.2_Benchmark_2Day_Input.tar.gz.list
  • Use the gdrive command to download the dataset.
  • If this is the first time that you are using gdrive, or if you have an issue with your token, please read the following instructions
  • Tips to download data from CMAS Data Warehouse
gdrive download 1ex6Wr4dX6a0fgaDfhO0VEJNaCKqOflI5

Step 11: Edit the CMAQ-ISAM runscript

gedit run_cctm_Bench_2016_12SE1.csh

Set General Parameters for Configuring the Simulation

set VRSN = v532_ISAM

Turn on ISAM and uncomment ISAM regions file

setenv CTM_ISAM Y
setenv ISAM_REGIONS $INPDIR/GRIDMASK_STATES_12SE1.nc

Run or Submit the script to the batch queueing system

./run_cctm_Bench_2016_12SE1.csh

OR (If using SLRUM)

sbatch run_cctm_Bench_2016_12SE1.csh

Step 12: Verify that the run was successful

  • look for the output directory
cd ../../data/output_CCTM_v532_ISAM_gcc_Bench_2016_12SE1

If the run was successful you will see the following output

tail ./LOGS/CTM_LOG_000.v532_ISAM_gcc_Bench_2016_12SE1_20160701

|>--- PROGRAM COMPLETED SUCCESSFULLY ---<|

Step 13: Compare output with the 2 day benchmark outputs provided on the google drive

https://drive.google.com/drive/u/1/folders/1jAKw1EeEzxLSsmalMplNwYtUv08pwUYk

Note, the following ISAM output files are generated in addition to the standard CMAQ output files.

    CCTM_SA_CONC_v532_ISAM_gcc_Bench_2016_12SE1_20160701.nc
    CCTM_SA_WETDEP_v532_ISAM_gcc_Bench_2016_12SE1_20160701.nc
    CCTM_SA_DRYDEP_v532_ISAM_gcc_Bench_2016_12SE1_20160701.nc
    CCTM_SA_ACONC_v532_ISAM_gcc_Bench_2016_12SE1_20160701.nc
    CCTM_SA_CGRID_v532_ISAM_gcc_Bench_2016_12SE1_20160701.nc