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During this chapter the user will learn about how to obtain the CMAQ source codes and how to set-up their CMAQ environment to complete a CMAQ simulation. It should be noted that before you can configure your CMAQ Environment, consult the chapter "Preparing to run" to see you have the minimum requirement of hardware and software on your system.
CMAQ source code can be installed either using git or from tarballs downloaded from the git repository hosted by GitHub. Both options are described here.
In the directory where you would like to install CMAQ, issue the following command to clone the official EPA GitHub repository for CMAQv5.5:
git clone -b main https://github.com/USEPA/CMAQ CMAQ_REPO
Using the git clone option, CMAQ will install into the following directories:
CMAQ_REPO/CCTM
CMAQ_REPO/PREP
CMAQ_REPO/POST
CMAQ_REPO/UTIL
CMAQ_REPO/PYTOOLS
CMAQ_REPO/DOCS
Zip files of the CMAQ source code are available from the public GitHub repository. Click the button "Clone or download" from https://github.com/USEPA/CMAQ and select "Download ZIP" to download a Zip file of the CMAQ repository. Alternatively, you may download the Zip file from the EPA CMAQ website.
Reference input/output data for testing the installation of the software are available from the CMAS Center; data are not available through GitHub. You must register/login to access the source codes and data from the CMAS Center.
In the directory where you would like to install CMAQ, unzip the model distribution file:
unzip CMAQ-main.zip
The following directories will be created:
CMAQ-main/CCTM
CMAQ-main/PREP
CMAQ-main/POST
CMAQ-main/UTIL
CMAQ-main/PYTOOLS
CMAQ-main/DOCS
The Git and Zip file installation options will produce slightly different subdirectories on your Linux system. The base installation directory using the git clone command will be CMAQ_REPO; the directory from the Zip file will be CMAQ-main. The subsequent instructions in this guide will be based on the git clone installation. For Zip file installations, replace CMAQ_REPO with CMAQ-main in the instructions that follow. The differences in the directory names highlights the difference in functionality between the two options. Cloning the repository gives the user access to the full repository and its history, while downloading the Zip file will only give access to version 5.4.
After downloading the source codes the user is encouraged to look through the repository to familiarize themselves with the structure. A summarized image of the repository is shown below:
Figure 5‑1. CMAQ repository structure
In this image it can be seen that there are six main sub folders within the CMAQ repository. The first folder, CCTM, houses all the source codes (i.e. Fortran/C programs) and scripts that drive the CMAQ Chemistry Transport Model (CCTM).
The second folder, DOCS, contains the CMAQ User's Guide and a Developers Guide for a general description of CMAQ's open-source collaboration workflow and step-by-step instructions for how to make code contributions through GitHub.
The third folder in the repository is the POST folder which contains several very useful tools for post-processing of the input/output data files. Each tool within the folder comes wth the source code, scripts and a README used to run the tool. A technical description of the tools within this folder can be found in Chapter 8.
The fourth folder in the repository is the PREP folder which contains several pre-processing programs that can be run before the CCTM to prepare meteorology, initial conditions and boundary conditions inputs. Similar to the POST tools, documentation on compiling and running the programs is provided within each subfolder under PREP.
The fifth folder in the repository is the PYTOOLS folder. This folder holds python tools relating to OCEAN file augmentation and tools relating to PREP and POST processing of inputs for CMAQ. Similar to the PREP and POST tools, documentation on how to run these tools is provided within each subfolder under PYTOOLS.
The last folder within the repository is the UTIL folder which contains useful utilities relating to the CMAQ program suite. An example is the bldmake utility which is used to compile the source code into executables when you use any of the build scripts in the CMAQ repository. Also included in this repository is a top-level README file with an overview of the contents of the release and two additional C-Shell scripts, bldit_project.csh and config_cmaq.csh. bldit_project.csh allows the user to extract the build and run scripts and compile the model outside of the repository, while config_cmaq.csh helps enforce consistent environment setting for the CMAQ project. Both these scripts will be discussed in the following sections.
When cloning the repository or unpacking the tar file of the CMAQ distribution, the top-level directory is recognized by the default build and run scripts as CMAQ_HOME (formerly M3HOME prior to CMAQv5.2). This directory is an arbitrary base location of the CMAQ installation on your Linux system for a specific application. If the user will build and run CMAQ within the repository folder structure, then CMAQ_HOME does not need to be set explicitly in the bldit_project.csh script. If, on the other hand, the user wishes to extract the build and run scripts and compile the model outside of the repository, then CMAQ_HOME will need to be specified in bldit_project.csh. Executing bldit_project.csh will automatically perform this extraction and create a CMAQ folder structure under the location now specified by CMAQ_HOME. To perform this operation, modify the variable CMAQ_HOME in the bldit_project.csh script to identify the folder that you would like to install the CMAQ package under. For example:
set CMAQ_HOME = /home/username/CMAQ_v5.5
Now execute the script:
./bldit_project.csh
It should be noted that from now on, the other CMAQ directories are referenced relative to CMAQ_HOME and it is where your CMAQ project will be run from. While this directory structure is convenient for the benchmark case and most CMAQ applications, other configurations are possible.
Consistency of configuration variables is critical for building CMAQ itself, not just its libraries. Accordingly CMAQ includes the configuration script config_cmaq.csh to help enforce consistent environment settings for CMAQ and its associated libraries. Appendix A lists the config_cmaq.csh variables defined for the build process and suggests values to which to set those variables.
Note that for multiprocessor applications it is recommended that the Fortran MPI wrapper script mpiifort (for Intel compiler; for GNU and PGI fortran compiler, use mpifort) be specified for the Fortran compiler (myFC). Using this script, instead of a direct call to the Fortran compiler, will ensure that the full suite of MPI components (libraries and include files) for the compiler are included in the parallel build without anything provided by the user explicitly.
Use the following steps to initialize your CMAQ environment:
source config_cmaq.csh [compiler]
After running the above command, it should be noticed now under CMAQ_HOME, the data file directory has been created and serves as a container for the input and output data for the model, and the lib directory contains links to the compiled binary library files required to build the CMAQ executables. The CMAQ scripts use the following environment variables to alias the locations of these directories:
CMAQ_LIB = $CMAQ_HOME/lib (M3LIB before CMAQv5.2)
CMAQ_DATA = $CMAQ_HOME/data (M3DATA before CMAQv5.2)
If you encounter errors about libraries not being found, check the settings of the config_cmaq.csh script variables IOAPI, NETCDF, or MPI to ensure that they correctly point to the locations of these libraries on your Linux system.
Sourcing the config_cmaq.csh script only needs to be invoked during a new installation of CMAQ to make sure the links to these libraries are working correctly. For every successive session, links to these libraries will automatically be created when you run any of the build or run scripts.
After all required CMAQ inputs are generated using the preprocessors mentioned above the user is now ready to compile CCTM. CMAQ’s current coding structure is based on a modular design principle that seperates CCTM’s main driver, science modules, data estimation modules, and control/utility subroutines. Also distinguished from each other are the science models (including submodels for meteorology, emissions, chemistry-transport modeling) and the analysis and visualization subsystems.
In CCTM, the process modules that affect the pollutant concentration fields are classified as listed below. Each bullet contains a description of the process followed by module name in parentheses. These modules are discussed further in Chapter 6.
Science Modules:
- Horizontal advection (hadv)
- Vertical advection (vadv)
- Horizontal diffusion (hdiff)
- Vertical diffusion (vdiff)
- Emissions (offline and online emissions sources) (emis)
- Dry Deposition/Air Surface Exchange (depv)
- Gas-phase chemical reaction solver (gas)
- Aqueous-phase reactions and cloud mixing (cloud)
- Aerosol dynamics and size distributions (aero)
- Potential vorticity scaling for stratosphere/troposphere exchange (pv_o3)
The user has the ability to configure the model in a multitude of ways by selecting from different options for each scientific process. Model configuration is split into build time options and run time options. To modify any science options during build time, edit the bldit_cctm.csh script. The bldit_cctm.csh script also contains other information, such as the option to run in single or multiprocessor mode as well as debug mode. It should be noted default build time options are alrady set within the bldit_cctm.csh. To modify any run time options, such as turning on in-line biogenic emission calculation or using in-line windblown dust emission, edit the run script, run_cctm.csh, and set the corresponding environment variable. To read more about build and run time configurations for specific scientific processes, see the next chapter (Chapter 6). To see a complete list configuration options reference Appendix A.
Once the bldit_cctm.csh script is configured to the user's preference, the user is ready to run the script to build the CCTM executable. To do this run the following commands:
cd $CMAQ_HOME/CCTM/scripts
source bldit_cctm.csh [compiler] [version] |& tee build_cctm.log
The bldit script invokes the CMAQ utility program bldmake, which extracts source code from your CMAQ GIT repository, constructs a Makefile based on your selected options, and compiles the executable automatically. Following normal termination of the script with the default configuration, the user will notice a BLD directory created. This is the location of the CCTM executable along with the relevant source codes and the Makefile needed to build the model. In this directory a few useful commands can be used to update the executable if any changes are made to the Fortran source codes via the MakeFile. For example, if the user wants to recompile the source codes in debug mode instead of re-running the bldit_cctm.csh script the user can use the following commands:
cd BLD_CCTM_v54_[compiler][version]
make clean
make DEBUG=TRUE
In another example, if the user has made any changes to the source codes in the BLD directory and wanted to update the CCTM executable to reflect these changes the user can use the following commands:
cd BLD_CCTM_v54_[compiler][version]
make
The Make utility only compiles the modified files and all associated file which are defined by the dependency of each source file in the Makefile.
After setting up the CCTM executable the model is ready to be run. Much like the bldit_cctm.csh script, to modify any run time options edit the run_cctm.csh script referencing Appendix A for a complete list of optional settings. After these settings have been configured use the following commands to run the script:
cd $CMAQ_HOME/CCTM/scripts
run_cctm.csh |& tee run_cctm.log
The CCTM simulation will write two types of logfile, a main logfile (e.g. run_cctm.log) and processor-specific logfiles that have the name convention:
CTM_LOG_[ProcessorID].v54_[compiler]_[data_name]/_[RUNDATE].log
The main logfile contains extensive metadata and useful information about the details of your simulation. The following examples describe some of this information:
Start Model Run At Tue Sep 13 14:55:26 EDT 2022
Compiler is set to intel
No compiler version given. Atmos system Detected. Assume Intel 21.0
Working Directory is ...
Build Directory is ...
Output Directory is ...
Log Directory is ...
Executable Name is CCTM_v54.exe
---CMAQ EXECUTION ID: CMAQ_CCTMv54_sha=[git-SHA]_[userID]_YYYYMMDD_hhmmss_nanosecs ---
Set up input and output files for Day YYYY-MM-DD.
Existing Logs and Output Files for Day YYYY-MM-DD Will Be Deleted
/bin/rm: No match.
CMAQ Processing of Day 20170722 Began at Tue Sep 13 14:55:26 EDT 2022
This section documents the folder structure, username, and run date for the simulation, and is meant to aid in maintaining transparency of simulation results after runs have been completed. This section is followed by the CMAQ and I/O API headers, and a record of all environment variables and their values for this simulation.
Next, the program outputs a table describing the domain decomposition breakdown for the run.
-=- MPP Processor-to-Subdomain Map -=-
Number of Processors = 128
____________________________________________________
| |
| PE #Cols Col_Range #Rows Row_Range |
|__________________________________________________|
| |
| 0 12 1: 12 24 1: 24 |
| 1 12 13: 24 24 1: 24 |
| 2 12 25: 36 24 1: 24 |
| 3 12 37: 48 24 1: 24 |
| 4 12 49: 60 24 1: 24 |
| 5 12 61: 72 24 1: 24 |
| 6 12 73: 84 24 1: 24 |
| 7 12 85: 96 24 1: 24 |
| 8 12 97: 108 24 1: 24 |
| 9 12 109: 120 24 1: 24 |
| 10 12 121: 132 24 1: 24 |
| 11 11 133: 143 24 1: 24 |
| 12 11 144: 154 24 1: 24 |
| 13 11 155: 165 24 1: 24 |
| 14 11 166: 176 24 1: 24 |
| 15 11 177: 187 24 1: 24 |
| 16 12 1: 12 24 25: 48 |
| 17 12 13: 24 24 25: 48 |
| 18 12 25: 36 24 25: 48 |
| 19 12 37: 48 24 25: 48 |
| 20 12 49: 60 24 25: 48 |
| 21 12 61: 72 24 25: 48 |
| 22 12 73: 84 24 25: 48 |
| 23 12 85: 96 24 25: 48 |
| 24 12 97: 108 24 25: 48 |
| 25 12 109: 120 24 25: 48 |
| 26 12 121: 132 24 25: 48 |
| 27 11 133: 143 24 25: 48 |
| 28 11 144: 154 24 25: 48 |
| 29 11 155: 165 24 25: 48 |
| 30 11 166: 176 24 25: 48 |
| 31 11 177: 187 24 25: 48 |
| 32 12 1: 12 24 49: 72 |
| 33 12 13: 24 24 49: 72 |
| 34 12 25: 36 24 49: 72 |
| 35 12 37: 48 24 49: 72 |
| 36 12 49: 60 24 49: 72 |
| 37 12 61: 72 24 49: 72 |
| 38 12 73: 84 24 49: 72 |
| 39 12 85: 96 24 49: 72 |
| 40 12 97: 108 24 49: 72 |
| 41 12 109: 120 24 49: 72 |
| 42 12 121: 132 24 49: 72 |
| 43 11 133: 143 24 49: 72 |
| 44 11 144: 154 24 49: 72 |
| 45 11 155: 165 24 49: 72 |
| 46 11 166: 176 24 49: 72 |
| 47 11 177: 187 24 49: 72 |
| 48 12 1: 12 23 73: 95 |
| 49 12 13: 24 23 73: 95 |
| 50 12 25: 36 23 73: 95 |
| 51 12 37: 48 23 73: 95 |
| 52 12 49: 60 23 73: 95 |
| 53 12 61: 72 23 73: 95 |
| 54 12 73: 84 23 73: 95 |
| 55 12 85: 96 23 73: 95 |
| 56 12 97: 108 23 73: 95 |
| 57 12 109: 120 23 73: 95 |
| 58 12 121: 132 23 73: 95 |
| 59 11 133: 143 23 73: 95 |
| 60 11 144: 154 23 73: 95 |
| 61 11 155: 165 23 73: 95 |
| 62 11 166: 176 23 73: 95 |
| 63 11 177: 187 23 73: 95 |
| 64 12 1: 12 23 96: 118 |
| 65 12 13: 24 23 96: 118 |
| 66 12 25: 36 23 96: 118 |
| 67 12 37: 48 23 96: 118 |
| 68 12 49: 60 23 96: 118 |
| 69 12 61: 72 23 96: 118 |
| 70 12 73: 84 23 96: 118 |
| 71 12 85: 96 23 96: 118 |
| 72 12 97: 108 23 96: 118 |
| 73 12 109: 120 23 96: 118 |
| 74 12 121: 132 23 96: 118 |
| 75 11 133: 143 23 96: 118 |
| 76 11 144: 154 23 96: 118 |
| 77 11 155: 165 23 96: 118 |
| 78 11 166: 176 23 96: 118 |
| 79 11 177: 187 23 96: 118 |
| 80 12 1: 12 23 119: 141 |
| 81 12 13: 24 23 119: 141 |
| 82 12 25: 36 23 119: 141 |
| 83 12 37: 48 23 119: 141 |
| 84 12 49: 60 23 119: 141 |
| 85 12 61: 72 23 119: 141 |
| 86 12 73: 84 23 119: 141 |
| 87 12 85: 96 23 119: 141 |
| 88 12 97: 108 23 119: 141 |
| 89 12 109: 120 23 119: 141 |
| 90 12 121: 132 23 119: 141 |
| 91 11 133: 143 23 119: 141 |
| 92 11 144: 154 23 119: 141 |
| 93 11 155: 165 23 119: 141 |
| 94 11 166: 176 23 119: 141 |
| 95 11 177: 187 23 119: 141 |
| 96 12 1: 12 23 142: 164 |
| 97 12 13: 24 23 142: 164 |
| 98 12 25: 36 23 142: 164 |
| 99 12 37: 48 23 142: 164 |
|100 12 49: 60 23 142: 164 |
|101 12 61: 72 23 142: 164 |
|102 12 73: 84 23 142: 164 |
|103 12 85: 96 23 142: 164 |
|104 12 97: 108 23 142: 164 |
|105 12 109: 120 23 142: 164 |
|106 12 121: 132 23 142: 164 |
|107 11 133: 143 23 142: 164 |
|108 11 144: 154 23 142: 164 |
|109 11 155: 165 23 142: 164 |
|110 11 166: 176 23 142: 164 |
|111 11 177: 187 23 142: 164 |
|112 12 1: 12 23 165: 187 |
|113 12 13: 24 23 165: 187 |
|114 12 25: 36 23 165: 187 |
|115 12 37: 48 23 165: 187 |
|116 12 49: 60 23 165: 187 |
|117 12 61: 72 23 165: 187 |
|118 12 73: 84 23 165: 187 |
|119 12 85: 96 23 165: 187 |
|120 12 97: 108 23 165: 187 |
|121 12 109: 120 23 165: 187 |
|122 12 121: 132 23 165: 187 |
|123 11 133: 143 23 165: 187 |
|124 11 144: 154 23 165: 187 |
|125 11 155: 165 23 165: 187 |
|126 11 166: 176 23 165: 187 |
|127 11 177: 187 23 165: 187 |
|__________________________________________________|
With this output, users will be able to trace issues that occur on specific processors to geographic regions of the model domain.
Then, as the time-dependent portion of the model begins, output is provided for every timestep with the following form:
Processing Day/Time [YYYYDDD:HHMMSS]: 2017356:000000
Which is Equivalent to (UTC): 0:00:00 Friday, Dec. 22, 2017
Time-Step Length (HHMMSS): 000500
VDIFF completed... 3.7 seconds
COUPLE completed... 0.1 seconds
HADV completed... 8.4 seconds
ZADV completed... 0.3 seconds
HDIFF completed... 0.3 seconds
DECOUPLE completed... 0.0 seconds
PHOT completed... 1.4 seconds
CLDPROC completed... 0.3 seconds
CHEM completed... 1.5 seconds
AERO completed... 2.5 seconds
Master Time Step
Processing completed... 18.7 seconds
This section documents the date and time the model is currently processing along with the time spent calculating every major sub-process. At the end of each simulation hour, the calculation time is also printed for the output process.
Processing Day/Time [YYYYDDD:HHMMSS]: 2017356:005500
Which is Equivalent to (UTC): 0:55:00 Thursday, Dec. 22, 2017
Time-Step Length (HHMMSS): 000500
VDIFF completed... 31.7 seconds
COUPLE completed... 0.2 seconds
HADV completed... 2.3 seconds
ZADV completed... 0.4 seconds
HDIFF completed... 0.5 seconds
DECOUPLE completed... 0.0 seconds
PHOT completed... 0.6 seconds
CLDPROC completed... 19.1 seconds
CHEM completed... 1.5 seconds
AERO completed... 2.5 seconds
Master Time Step
Processing completed... 58.9 seconds
=--> Data Output completed... 52.2 seconds
This procedure repeats for every hour of the output day until completion of that day.
==============================================
|>--- PROGRAM COMPLETED SUCCESSFULLY ---<|
==============================================
Date and time 0:00:00 Dec. 23, 2017 (2017357:000000)
The elapsed time for this simulation was 6390.3 seconds.
real 6394.83
user 2000938.03
sys 827.71
CMAQ Processing of Day 20171222 Finished at Tue Sep 13 16:42:02 EDT 2022
\\\\\=====\\\\\=====\\\\\=====\\\\\=====/////=====/////=====/////=====/////
After the final day has been completed, summary information is printed for the computation time of every executed day.
==================================
***** CMAQ TIMING REPORT *****
==================================
Start Day: 2017-12-22
End Day: 2018-01-01
Number of Simulation Days: 8
Domain Name: 12US1
Number of Grid Cells: 1538636 (ROW x COL x LAY)
Number of Layers: 44
Number of Processes: 128
All times are in seconds.
Num Day Wall Time
01 2017-12-22 6394.83
02 2017-12-23 6137.89
03 2017-12-24 6039.40
04 2017-12-25 6201.84
05 2017-12-26 6403.34
06 2017-12-27 6108.96
07 2017-12-28 6308.07
08 2017-12-29 6207.25
09 2017-12-30 6306.42
10 2017-12-31 6303.56
11 2018-01-01 6107.77
Total Time = 68519.33
Avg. Time = 6229.03
The processor-specific logfiles provide detailed information on the operation of hundreds of model tasks from mapping variables to opening and reading input files. Warnings that may be important for users to be aware of are printed to these files. To confirm that the model ran to completion view the run.[data].log file. For MPI runs, you may check any of the CTM_LOG_[ProcessorID]*.log files. A successful run will contain the following line at the bottom of the log(s):
>>----> Program completed successfully <----<<
Note: The log file for each processor is also moved from the $CMAQ_HOME/CCTM/scripts directory to the data output directory:
$CMAQ_DATA/output_CCTM_v54_[compiler]/[data_name]
The output results will have been placed in the directory:
$CMAQ_DATA/output_CCTM_v54_[compiler]_[data_name]
and can include the following netCDF-type files: ACONC, AELMO, B3GTS_S, CGRID, CONC, DEPV, DRYDEP, DUSTEMIS, LTNGDIAG1, LTNGDIAG2, MEDIA_CONC, ELMO, RJ_1, RJ_2, RJ_3, SOILOUT, SSEMIS, VDIFF, VSED, WETDEP1, WETDEP2 and VEXT_1. The in-depth description about each of these files is described in Chapter 7.
Common errors in a CCTM simulation include the following:
- Incorrect paths to input files. Look in the CCTM screen output (captured in your log file) for an Error message about an input file not being found.
- Incorrect MPI implementation. A series of MPI errors at the end of the log file often indicate that the MPI job was not submitted correctly.
Check the last few lines of the CCTM output log for messages to help diagnose why the simulation did not complete.
See the CMAQ Installation and Benchmarking Tutorial for step-by-step instructions for running the 2 day benchmark case and links to reference input and output data.
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CMAQv5.5 User's Guide