Step 1: Download and run the CMAQv5.4 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.
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 CMAQv5.4 code from github (step 5 below):
isam_control.txt
The following gridmask file is provided with the benchmark inputs in the 2018_12NE3_BENCH/2018_12NE3 directory (see step 10 below)
GRIDMASK_STATES_12NE3.nc
The instructions require the user to edit the DESID emissions control namelist file in the BLD directory (see step 9 below).
CMAQ_Control_DESID.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
git clone -b main 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 = [your_install_path]/CMAQ_v5.4
Now execute the script.
./bldit_project.csh
Change directories to the CMAQ_HOME directory
cd [your_install_path]/CMAQ_v5.4
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
./bldit_cctm.csh gcc |& tee bldit_cctm_isam.log
Change directories to the build directory
cd BLD_CCTM_v54_ISAM_gcc
edit the DESID emissions namelist file
gedit CMAQ_Control_DESID.nml
Uncomment the line that contains ISAM_REGIONS as the File Label
&Desid_RegionDef
Desid_Reg_nml =
! Region Label | File_Label | Variable on File
'EVERYWHERE' ,'N/A' ,'N/A',
'NY' ,'CMAQ_MASKS', 'NY',
!<Example> 'WATER' ,'CMAQ_MASKS' ,'OPEN',
!<Example> 'ALL' ,'CMAQ_MASKS' ,'ALL',
!<Example> 'ALL' ,'ISAM_REGIONS','ALL',
Download the CMAQ two day reference input and output data from the [CMAS Center Data Warehouse Google Drive](https://drive.google.com/file/d/1AFUB-4kzIXXoZr4hOHNBqRvy9JQ9_MDp/view?usp=sharing. The CMAQ benchmark test case is a two day simulation for July 1-2 2018 on a 100 column x 105 row x 35 layer 12-km resolution domain over the northeast U.S.
- 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
- Text files are included that provide a list of the files in the benchmark input and output datasets.
The benchmark data is also available from the CMAS Center Data Warehouse Amazon Web Services S3 Bucket.
Copy the data to $CMAQ_DATA. Navigate to the $CMAQ_DATA directory, unzip and untar the two day benchmark input and output files:
cd $CMAQ_DATA
tar xvzf CMAQv5.4_2018_12NE3_Benchmark_2Day_Input.tar.gz
tar xvzf CMAQv5.4_2018_12NE3_Benchmark_2Day_Output.tar.gz
The input files for the CMAQv5.4 ISAM benchmark case are the same as the benchmark inputs for the base model. Output source apportionment files associated with the sample isam_control.txt provided in this release package are included in the benchmark outputs for the base model.
cp run_cctm_Bench_2018_12NE3.csh run_cctm_Bench_2018_12NE3.ISAM.csh
gedit run_cctm_Bench_2018_12NE3.ISAM.csh
Set General Parameters for Configuring the Simulation
set VRSN = v54_ISAM
Turn on ISAM and uncomment the SA_IOLIST file and uncomment the ISAM regions file
setenv CTM_ISAM Y
setenv SA_IOLIST ${WORKDIR}/isam_control.2018_12NE3.txt
setenv ISAM_REGIONS $INPDIR/GRIDMASK_STATES_12NE3.nc
Run or Submit the script to the batch queueing system
./run_cctm_Bench_2018_12NE3.ISAM.csh
OR (If using SLRUM)
sbatch run_cctm_Bench_2018_12NE3.ISAM.csh
- look for the output directory
cd ../../data/output_CCTM_v54_ISAM_gcc_Bench_2018_12NE3_2day_ISAM
If the run was successful you will see the following output
tail ./LOGS/CTM_LOG_000.v532_ISAM_gcc_Bench_2016_12SE1_20160702
|>--- PROGRAM COMPLETED SUCCESSFULLY ---<|
The following ISAM output files are generated in addition to the standard CMAQ output files.
CCTM_SA_DRYDEP_v54_ISAM_gcc_Bench_2018_12NE3_2day_ISAM_20180702.nc
CCTM_SA_WETDEP_v54_ISAM_gcc_Bench_2018_12NE3_2day_ISAM_20180702.nc
CCTM_SA_CONC_v54_ISAM_gcc_Bench_2018_12NE3_2day_ISAM_20180702.nc
CCTM_SA_ACONC_v54_ISAM_gcc_Bench_2018_12NE3_2day_ISAM_20180702.nc
CCTM_SA_CGRID_v54_ISAM_gcc_Bench_2018_12NE3_2day_ISAM_20180702.nc