Problems building ICON and BCON in v5.3


I have been trying to install the v5.3 beta. However I’m running into problems when I try to build the ICON or BCON executables. I’m attaching the log files, but essentially the cgrid_spcs.f routine is tyring to use a module that isn’t available. Further, as I’ve looked into the issue it seems to me that icon and bcon haven’t been fully updated for the v5.3 of CMAQ. For example, in bldit_icon.csh there are a number of options that you can set the Mechanism variable to, yet most of those options are no longer mechanisms available to the CCTM or ICON. Anyway, are there deeper problems with ICON and BCON in v5.3 that I should know about? If not, does anyone have a fix for these problems?

Thanks to anyone who can help

bldit_icon.txt (13.2 KB)
bldit_bcon.txt (11.5 KB)

There are significant updates to ICON and BCON in the final release of CMAQv5.3. These updates were not included with CMAQv5.3beta because they were still under development. Species mapping has been removed from ICON and BCON in v5.3 to make these programs more independent from CCTM source code.

Apologies for the frustration that this has caused in your testing of the v5.3beta.

I can share the new ICON/BCON programs with you next month when development is complete if you are interested in testing them.

Here is additional information on the updates to ICON and BCON in v5.3:

Several bug fixes have been addressed in the ICON and BCON updates. This includes: (1) compiler info issues in the scripts for ICON/BCON; and (2) ICON/BCON compilation problems in v5.3 resulting from changes in files symbolicly linked to the CCTM/src.

Several enhancements are also included in the ICON/BCON updates: support for nesting from polar stereographic projection grids; support for nesting from time independent gridded files; support vertical interpolation by sigma, Z, and PRES; support for time interpolation from gridded files with coarse time resolution.

The preprocessors have also been simplified to: (1) enable selection of IC/BC type (regrid, profile, patterns) as a runtime option instead of the previous compile-time option; (2) removal of the species mapping - users will need to use the combine utility for species mapping; and (3) removal of parallel processing code from ICON (feature no longer used/needed).

The updates also include a new profile dataset, developed from an annual average Hemispheric CMAQ (HCMAQ) simulation for a marine remote grid cell over the Pacific Ocean (latitude 37oN, longitude -157oW) from a 2016 HCMAQ CMAQv5.3 CB6R3_AE7NVPOA_AQ simulation.

Significance and Impact of v5.3 updates:
ICON and BCON can now be used to generate ICs/BCs from HCMAQ simulations, using vertical and horizontal interpolation methods available in ICON and BCON.

The profile data being release with CMAQv5.3 is different from previous model releases. The profile data included in this release is based on a HCMAQ simulation that used chemical mechanism CB6R3_AE6NVPOA_AQ. ICON and BCON will no longer map profile data species to different chemical mechanisms. Users will need to use the combine utility on ICON/BCON output for species mapping to a different mechanism. Examples will be provided for using the combine utility to map to SAPRC07t and RACM2.

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Thank you for your response. That is very helpful to know. I am very interested in testing those programs if that is possible. Do you also know whether or not the current version of MCIP included with CMAQv5.3beta has been updated or not?

MCIP was not updated in CMAQv5.3beta. MCIPv5.0 will be released with the final release of CMAQv5.3. I will let you know when the new code is available on GitHub.

For your reference, here is a summary of updates that will be included in MCIPv5.0:

  • Enabled the use of WRFv4.0+ and the hybrid vertical coordinate in WRF with the CMAQ system.
  • Added 7 new variables to the output if the Pleim-Xiu land-surface model was used in internal versions of WRFv4.0.2 or in WRFv4.1+; these variables can enhance the dust simulation in the CCTM. This option replaces the 2D time-varying leaf-area index (LAI) with an analogous field from the Pleim-Xiu land-surface model, and adds 6 2D time-varying fields to the output.
  • Added an option to write MCIP output in netCDF.
  • Updated the units of most output fields to conform to CF compliance.
  • Removed support for using files from MM5.
  • Removed the option for layer collapsing.
  • Changed the fill value for convective rainfall (output variable RC) with “no cumulus parameterization” in WRF from -1 to a large negative number to prevent inadvertent use in CCTM and post-processing.
  • Changed default output wind components to the “face” points (UWINDC and VWINDC" from the “dot” points (UWIND and VWIND). The “face” points are on the Arakawa C staggered grid that is used by both WRF and CCTM. The “dot” points are on the Arakawa B staggered grid that is used by MM5. The UWIND and VWIND fields can be omitted from the output with a runtime switch in the MCIP script.
  • Corrected minor bugs that are associated with configuration options that are typically not used with the retrospective WRF simulations.
  • Added an option to process additional cloud-related fields from the Kain-Fritsch convective parameterization scheme with radiative feedbacks (KF-rad). These additional 3D fields are not usually included in the WRF output, and they would need to be deliberately added to the output files. These fields can be used in developmental work to improve the coupling of cloud processes between WRF and CCTM. If present, 4 additional 3D time-varying fields are written.

Dear Dr. Foley,

I was interested in CMAQv5.3 and got trouble with the same issues on the compilation, have you got the updated version of ICON and BCON modules?

Be well,


Please obtain the latest release of CMAQ and the updated ICON and BCON available in the following release announcement: