Documentation for GEOS GCM v10

This page lists pages with information on setting up and running GEOS GCM version 10. Earlier and later versions of GEOS may differ in details that, while minor, will require different steps for building and running, so caveat utilitor.

If you have any issues or questions, please email the GMAO SI Team at siteam_AT_gmao.gsfc.nasa.gov

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Running GEOS GCM

• GEOS GCM Quick Start: This page describes the minimum steps required to build and run GEOS GCM v10 on NCCS discover and NAS pleiades. You should successfully complete the steps in these instructions before doing anything more complicated.

• Regridding Restarts for GEOS GCM

• Using the ExtData component

• Running a Suite of Forecasts

• Setting up to create an experiment page on GMAO Intranet

• Using the SatSim Gridded Component in Jason

• GEOS GCM Single Column Model

GEOS GCM Documentation

• GEOS 5 Developer's Guide (pdf)
• List of Export/Import/Internal states, generated with src/Shared/@MAPL/MAPL_Base/mapl_vlist.py
  • Sorted by short name
  • Sorted by component name

• GEOS-5 Run-Time Characteristics

• Hierarchical structure: Below is a (partially folded) view of the Jason 3.0 hierarchy where each node is a GridComp. Some of the nodes are folded (marked with a circle at the end) for clarity - clicking the composite node reveals the sub-nodes.

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Changelog

[10.22.3] - 2022-06-08

Restart Changes: NO

Zero-Diff Changes: * Update CMake in ADAS-only subdirs by @mathomp4 in #262 * Change restart name geocachem_internal_rst to achem_internal_rst in regrid.pl by @weiyuan-jiang in #264 * Fix Emissions Handling: Use copy not link by @mathomp4 in #325 * Use correct EXPID when cloning an experiment by @sdrabenh in #329 * New Files added to support ExtData2G by @bena-nasa in #590 * Upticks to MAPL v2.21.3 and CMAKE v3.16.0

[10.22.2] - 2022-05-03

Restart Changes: NO

Major Zero-Diff Changes: * Hotfix to GOCART and GEOSchem_GridComp to allow proper functioning and regression of 4D-IAU. * Hotfix to GOCART using non-default klid. * Emissions handling now uses experiment RC directory by @mathomp4 in #320 * Set collection’s monthly attribute by default for most collections by @sdrabenh in #316 #259 * Removed connectivities from MOIST to CHEM that are no longer needed by @mmanyin in #572 * Defined replay predictor duration by @lltakacs in #581 * Initialize arrays in mkiau GC by @mathomp4 in #574 * Add fstats customized for screen-level Q and T with “land only” option by @saraqzhang in #246 * Clean up Optics in AGCM.rc.tmpl by @mathomp4 in #319 * Update tags in regrid.pl by @mathomp4 in #257 * Default to 72x36 for c12 mom6 by @mathomp4 in #314 * Updates for Spack Support, Round 2 by @mathomp4 in #568 #312 * Update CI to use v1 orb and job by @mathomp4 in #578 * Minor CMake change for mod file by @mathomp4 in #258 * Upticks in MAPL GEOS_OceanGridComp MOM6 CICE

[10.22.1] - 2022-03-18

Restart Changes: NO

Major Zero-Diff Changes: * tskinice real fix by @rtodling in #547 #297 * Update geosit history by @rtodling in #301 * Add option to read ocean data using ExtData by @sanAkel in #562 * Support for ocean datasets using ExtData by @sanAkel in #245 * Gather memory and detailed timing information for coupled model by @sanAkel in #289 * Reynolds ONLY SST and Ice Concentration with a land-sea mask from @rcullath by @sanAkel in #239 * Remove Ocean Grid Comp by @mathomp4 in #551 #379 * For sea ice development: add CICE6 and SIS2 sea ice models by @sanAkel in #558 #385 * Run History in predictor by @bena-nasa in #546 * Updates for using cubed sphere observed precip files by @lltakacs in #559 * Profiling with pflogger by @tclune in #307 * chckhist.new update to fix plotting for OPS HISTORY.rc, minor 3CH bugfix by @lltakacs in #252 * Updates to support Spack by @mathomp4 in several repositories. * Upticks in MAPL, ESMA_cmake, ESMA_env, and GEOSchem_GridComp.

[10.22.0] - 2022-03-15

Restart Changes: YES

Summary of changes for the refactored GOCART-2G:

• This is the first release of GEOSgcm that includes GOCART-2G, a refactoring of the GOCART component that adopts the ESMF for every child component and refactors the multi-instantiation mechanism. GOCART-2G only includes aerosols; other trace gases are not included by design.
• This release also includes new science, including the inclusion of secondary organic aerosols (SOAs) and Brown Carbon. In this implementation, Brown Carbon is comprise of that portion of Organic Carbon emitted by biomass burning, having absorptive properties.
• This release also introduces the notion of a “Process Library” which replaces what used to be found under Chem_Shared; it also eliminates any dependency on Chem_Base. The @GOCART repository is shared with NOAA and has been implemented in the UFS.
• Several new restarts (achem,cabc,cabr,caoc,du,ni,ss,su) have been added since the gridded components of GOCART-2G have been split out accordingly.
• GOCART-2G required changes in many other sub-repositories. Users are encouraged to look through those individually for a detailed list of changes.

[10.21.1] - 2022-02-14

Restart Changes: NO

Major Zero-Diff Changes: 1. Add CLDXXSW diagnostics and many cosmetic changes to Solar GC by @dr0cloud in #510 2. Add additional radiation RRTMG tau and water path diagnostics by @dr0cloud in #519 3. Simple fix to prevent negative tauaer in RRTMG LW by @dr0cloud in #521 4. Add RRTMGP as a fork in GEOS by @mathomp4 in #528 5. Update RRTMGP file locations and half gpoints by @mathomp4 in #294 6. Cleanup of Catchment model constants by @gmao-rreichle in #525 7. Removed redundant code: DQS calc, QC constraint, RA calc by @gmao-rreichle in #518 8. Fix mk_GEOSldasRestart for catchcnclm45 by @weiyuan-jiang in #516 9. make_bcs clarification of options by @biljanaorescanin in #517 10. Bug fix for RUNSRF units in Catchment by @gmao-rreichle in #535 11. Cleanup of gndtmp[_cn]() by @gmao-jkolassa in #536 12. New peat hydrology (PEATCLSM) by @biljanaorescanin in #524 13. Add LDAS_INCR to AGCM.rc.tmpl for land-atmos coupled das by @saraqzhang in #288 14. Fixes for C12 MOM6 by @mathomp4 in # 15. Updates for handling CS ocean by @mathomp4 in #287 16. Update for NAS Runs by @mathomp4 in #291 17. Compress CircleCI Artifacts by @mathomp4 in #513 18. Use circleci-tools orb for CI by @mathomp4 in #242

[10.21.0] - 2021-12-21

Restart Changes: YES (see below)

Major Non-Zero-Diff Changes: 1. Changed the default config to use new orbit parameters by @sdrabenh in #277 2. Refactored RRTMG long-wave and short-wave radiation by @dr0cloud in #492 3. Adding SHOC+EDMF updates by @narnold1 in #479. All restarts and variables within remain 0-diff except for the following: 1. moist_import * added: EDMF_FRC, HL2, HL3, HLQT, QT2, QT3, W2, W3, WHL, WQT 2. moist_internal * added: PDF_A 3. turb_import * added: PHIS, SH, WTHV2 4. turb_internal * added: QT2, QT3 * removed: BRUNTSHOC, CLD, DQDT_SHC, DQIDT_SHC, DQLDT_SHC, DTDT_SHC, LSHOC, SHEARSHOC, TKEBUOY, TKEDISS, TKESHEAR, TKETRANS, WTHV2 * changed: TKH “lev” coordinate to “edge” coordinate

[10.20.0] - 2021-12-17

Restart Changes: YES for TR

Major Non-Zero-Diff Changes:

1. Uptick to GEOSchem_GridComp v1.7.0
   • Wet deposition for CO, CO2 and CH4 is disabled, while a bug-fix is developed.
   • GMI and TR have cleaner units handling.
2. make_bcs fixes issues with “old land” choices by @smahanam in #438
   • Old land BCS files have the same science but won’t be binary-equivalent due to bug fixes (e.g., “Mali bug”)
3. Adds code to Satsim to choose subcolumns based on horizontal resolution by @mathomp4 in #459
   • This is zero-diff for resolutions C720 and coarser but not for higher resolutions
4. Uptick to ESMA_env v3.8.0 to use Intel 2021.3 which helps alleviate issues with LDAS amd NAS.
5. Uptick to ESMA_cmake v3.8.0 to change default vectorization flag for Intel Fortran.

Major Zero-Diff Changes:

1. Updated regrid.pl for GOCART-2G by @bena-nasa in #231
2. Plot Updates from L. Takacs by @sdrabenh in #235
   • Added supports to plot aerosols from GOCART-2G.
   • Three-Corner-Hat (3CH) analysis tools were added.
   • Enhancements and bugfixes to quickplot and quickstat utilities.
3. Lightning module has been re-located and revamped. #451 #212 #141
4. HEMCO config files for GOCART and GMI have been updated for v2.2 GEOSchem_GridComp v1.7.0
5. Uptick to MAPL v2.14.0
6. Refactoring of interp_restart code necessitated an uptick to fvdycore geos/v1.3.0
7. Regridding fix and read_topo fix code necessitated an uptick to FVdycoreCubed_GridComp v1.4.1

[10.19.6] - 2021-12-09

Restart Changes: NO

Major 0-diff changes:

1. 5deg ocean (MOM6) configuration by @sanAkel in #488
2. Fixed missing verify status of iDUAL_OCEAN in GEOS_OceanGridComp.F90 by @sanAkel in #491
3. Cleaned up CircleCI by @mathomp4 in #493
4. Make big 5-d buffer in Moist optional by @mathomp4 in #496
5. The idcheck.pl script was updated for changes in SemperPy by @gmao-jstassi in #233
6. Update regrid.pl for Ocean Model Questions by @mathomp4 in #222
7. Added HISTORY_GEOSIT.rc.tmpl by @rtodling in #273
8. Uptick to MAPL v2.13.0 full list of changes

[10.19.5] - 2021-11-30

Restart Changes: NO

Possible History changes:

1. Bug fix for MAPL wherein non-default duration in HISTORY.rc was not being correctly handled. For example, if a collection has a duration of 24 hours and a frequency of 12 hours, MAPL now correctly writes a file with two timesteps in it. Before, MAPL was handling this incorrectly. Note that the data is still the same as 10.19.4, but now is contained within one file.

Major 0-diff changes:

1. Fix mom5 mom6 for das by @mathomp4 in #270
2. Allow gcm_setup to run anywhere by @mathomp4 in #261
3. WSUB fix in gmichem_setup by @mmanyin in #263
4. Make runtime and setup variable consistent for GCM by @rtodling in #265
5. Add code to install source tarfile by @mathomp4 in #262
6. Replace _RETURN(_SUCCESS) by @weiyuan-jiang in #484
7. Add error checking in mk_restarts executables by @weiyuan-jiang in #467
8. Support update for MOM6 by @sanAkel in #468
9. Add logic to allow guest oceans to be stubbed by @tclune in #474
10. Add ability to get timing from MOM6 modules by @sanAkel in #477
11. Add in support of quarter degree MOM6 to ADAS by @rtodling in #478
12. Updated pyrob to work with GEOS-IT files by @mathomp4 in #224
13. Add Cascade knob to g5fcst_stats.pl and regrid.pl; revised dyn_blob; make sure echorc.x exits with success code when applicable; by @rtodling in #226
14. Add OpenMP support for fvdycore by @mathomp4 in #44
15. ESMA_env: Update to Baselibs 6.2.8 needed for MAPL and move to use MPT 2.25 at NAS. full list of changes
16. ESMA_cmake: Add ability to create source tarball after install, various cleanup and fixes. full list of changes
17. MAPL: Requires gFTL 1.5.1 (Baselibs 6.2.8), added option to flip vertical orientation of checkpoints, various 0-diff bug fixes for compilers, refactored code. full list of changes

[10.19.4] - 2021-10-07

Restart Changes: NO

Major 0-diff Changes: 1. Restructuring under GEOSocean_GridComp by @yvikhlya in #448 2. Updates to support two versions of Catchment-CN: Catchment-CN.4.0 and Catchment-CN.4.5 by @gmao-jkolassa in #368 3. Compile time choice of CN model by @weiyuan-jiang in #370 4. Runtime choice for clm4.0 and clm4.5 by @weiyuan-jiang in #373 5. mk_GEOSldasRestart can now take restart hour and restart name by @weiyuan-jiang in #449 6. Fixes to enable mepo variant styles by @tclune in #334 7. Updates needed for Cascade Lake at NCCS by @mathomp4 in #335 8. Updates and corrections for the trajectory file created for JEDI. Variables for proper diurnal layer, TS, and CO2 have been added by @rtodling in #257 9. Null out WSUB_NATURE for 1MOM and GFDL physics by @mathomp4 in #251 10. Cleanup gcm_run and sync forecast scripts by @sdrabenh in #256 11. Fixes for SCM Setup on macOS by @mathomp4 in #253 12. Updated suite of PRs for GEOSadas by @mathomp4 in v1.4.10 13. Bug fix for CICE4 segfault by @mathomp4 in #215 14. Add pyrob_CF script by @mathomp4 in #208

[10.19.3] - 2021-07-21

Restart Changes: NO

Potential Non-0-diff Change:

1. Upgrade to MAPL v2.8.0. For the MERRA2 GOCART Emissions, all testing shows it is zero-diff. But for the Ops GOCART Emissions, it there are very small roundoff differences. The results are non-zero-diff due to a bug fix (to a race condition) in this version of MAPL on how grids are handled.

Major 0-diff Changes: 1. Detect MERRA2OX date violation during setup. 2. Make species consistent with emissions choice. 3. Only allow Rome nodes at NAS if built on Rome. 5. Updates for MVAPICH2, enable multigroup by default. 6. Bugfix for correct day when running EMIPs. 7. Update ldas increment alarm setting in CatchGC. 8. Updates to plots package. 9. Update to fvdycore v1.1.7.

[10.19.2] - 2021-06-11

Restart Changes: NO

Changes include:

1. Upgrade to Baselibs 6.2.4 and cmake v3.5.0.
2. Update parallel_build to use GMAO_Shared main if develop.
3. Created a new grid comp GEOS_SeaiceGridComp as a top level container component serving sea ice sub-components to OGCM. This new structure mirrors the existing GuestOcean/MOMPlug relationship for the ocean model hierarchy.
4. Bug fix that makes sure that diagnostics CNV_MFC still works when the UW shallow convection code is disabled.
5. Add changes consistent with what is in GEOSadas 5.28.
6. Addition of variables for analysis in two RC files and correction in IAU reftime consistent with GEOSadas.
7. Fixes for IOSERVER on Rome.

[10.19.1] - 2021-05-25

History Changes: YES

Major changes include:

1. Upgrade to MAPL v2.7.0 which changes how programs set up command line options.
2. Update to FVdycoreCubed_GridComp v1.2.15 and GEOSgcm_App v1.5.1 for compatibility with MAPL v2.7.0.
3. Enable GEOSgcm to output the configuration values in GEOS_SurfaceGridComp.rc.
4. Fixes a bug in the export of SSKINW (an internal state of Openwater) that was being filled incorrectly leading to MAPL_UNDEF. Now there are actual values.
5. Merged changes present in GEOSadas-5_27_1_p3 that never made it into the GIT repo: revised stochastic perturbation tendency exports.
6. A bug fix to prevent a seg-fault during the calculation of the GEOS-Chem lightning flash rate due to an array size mismatch.
7. Add ability to write out energy components to file.
8. Update gitignore for mepo updates.
9. Follow MAPL’s change to add a new MAPL_CapOptions constructor.

[10.19.0] - 2021-05-14

History Changes: YES

Major Non-0-diff changes include: 1. Updates the DEFAULT Land BCs of GEOSgcm to be Icarus-NLv3. Also applies a fix to GEOS_SurfaceGridComp.rc to correctly implement it.

Major 0-diff changes include: 1. Updates GMAO_psas to work with MAPL2. 2. Rename LANL_cice to CICE4 that is located at LANL_Shared/ 3. Remove BULK_SST alias for TS_FOUND in HISTORies used in model (only) simulations. 4. Updates to use Python2 and Python3 at same time. 5. Fixed the -wemin and -wemout options in regrid.pl so that they will accept integer values. 6. Bugfix to detect if saltwater splitting is needed in more files. 7. Add IOSERVER code into gcm_forecast.tmpl. 8. Updates needed for GEOSadas to work with MAPL2. 9. Add GEOS-Chem and HEMCO as separate external repositories. 10. GMI is now set to import RI and RL only when running Cloud-J. This is a work-around for a CTM issue. 11. Uptick of MAPL and FMS repositories.

[10.18.0] - 2021-04-15

History Changes: YES

Major Non-0-diff changes include: 1. Modified PCHEM interpolation that fixes the problem of negative PCHEM tracers. 2. A bug fix to atmOcnIntlayer consistent with what was applied to GEOS-FP GEOS-5.27.1 (02/2021) which mitigates anomalous spikes in TSKINWTR and related fields when the sea ice fraction departs 100%. 3. Changed scaling and cleaned up Henry’s law code in ConvPar_GF_GEOS5 (bug fix, non-zero diff for GOCART). 4. Update to use the 2020 NRL Solar file.

Major 0-diff changes include: 1. Fix DUAL_OCEAN options in coupled model to only work with MOM5 (It does not and can not work with MOM6). 2. Added diagnostic output for NH3, NH4A convective scavenging to GEOS_MoistGridComp used for GOCART evaluation. 3. Revive OceanBioGeoChem. 4. Fixed CMake bugs for DAS build only libraries. 5. Upticks of FVdycoreCubed_GridComp, fvdycore, and cmake repos.

[10.17.6] - 2021-04-06

History Changes: NO

Major changes include:

1. Upgrade to ESMA_env v3.2.0 whose main change is updating to ESMF 8.1.0, which is needed for MAPL development. All testing has shown it zero-diff to GEOSgcm with ESMF 8.0.1. Tests were run from C12 to C720 as well as Replay and MOM6. However, ESMF notes that there are changes in some regridding situations which could produce non-zero-diff results.

[10.17.5] - 2021-04-06

History Changes: NO

Major changes include:

1. parallel_build.csh now accepts a -hydrostatic or -nonhydrostatic argument during building. If no argument is provided the model will build hydrostatically as before. Therefore, setup scripts were modified depending on what -DHYDROSTATIC option was supplied to CMake. If -DHYDROSTATIC=ON then it will assume the user wants to use hydrostatic dynamics options and vice versa.
2. Fixed decomposition regression for nonhydrostatic model.
3. Updates from ADAS 5.27 folded into git GMAO_Shared v1.3.9. This brings the GEOSadas code closer to the current GEOSgcm.
4. Upticks in MOM6, MAPL, env and other repositiories.

[10.17.4] - 2021-03-17

History Changes: NO

Major changes include:

1. Moved GOCART legacy to be sourced from separate GOCART repository.
2. Update to MOM6 geos/v2.0.0 and update to FMS geos/2019.01.02+noaff.6
3. Bug fix for regrid.pl which can cause non-0-diff regridding for agcm_import_rst.
4. Fixed MOM6 diagnostics to use correct netcdf reference year.
5. Fix bug in gustiness calculations.
6. Fixed a bug in rotation angle for surface ocean stress.
7. DSO’s for mom5 and mom6.
8. GAAS Replay fix.
9. Add MOM.res.nc to the list of restarts that are checked in regression testing.
10. Remove OCEAN_PRELOAD since it is not needed with the DSO.
11. Change path names to support “automatic” MERRA-2 Regular Replay at NAS.
12. Remove CMIP_1977_1982 directory in GEOS_Util/pre/NSIDC-OSTIA_SST-ICE_blend.
13. Update binarytile.x for river routing.
14. Bug fix for edge level arrays out-of-bounds in Lighting_mod.
15. Plot updates for stats.

[10.17.3] - 2021-02-12

History Changes: NO

Major changes include:

1. Performance modification for surface rc file in run methods.
2. Relocation of mk_restarts and Raster.
3. Bugfix for running Catchment-CN with constant CO2.
4. Fixed land BCs in coupled mode
5. Added optional PCHEM species file with prod/loss of strat water vapor
6. Added support for the new Rome nodes at NAS named like r201c2t1n4
7. Plots and stats updates.
8. Eliminated references to MAPL_COMM - these are no longer used and will be deleted in future releases of MAPL.
9. Upgrade to MAPL v2.6.0

[10.17.2] - 2021-01-29

History Changes: NO

Major changes include: 1. Upgrade to MAPL 2.5.0 2. Updates to plots and stats package. 3. Updated PBS Batch handling at NAS. 4. Addded CODE_OF_CONDUCT.md

[10.17.1] - 2021-01-12

History Changes: YES - Roundoff differences in TSOIL1 and TSOIL2

Major changes include:

1. Soil temperatures export variables (TP’s) are now in units of Kelvin throughout the Catch and CatchCN. Note: this has introduced roundoff differences in TSOIL1 and TSOIL2 output.
2. New MOM6 configuration (OM4), and a bug fix in MOM6_Plug.
3. Update default coupled model surf collection with a few addition fields.
4. Fix saltwater_internal splitting to work with in AMIP and EMIP mode.
5. Add ASSERTs to RRTMG to test input sanity.
6. Adds a -partition option to mk_restarts so that there can be a -partition option in regrid.pl.
7. Fix gcm_convert.j which was broken.
8. Added flag to regrid_forcing_esmf.x to force a 0 to 1 range when regridding files that should use fractions.
9. Update flags for zonal.f to match CVS and fixed a bug in res/zonal.gs for zonal.x location.
10. Updates to ignores CI if non-essential files are updated (only).
11. Use CONFIGURE_DEPENDS flag to check if any globbed files changed when re-running cmake.
12. Allow use of aggressive flags with GEOS.

[10.17.0] - 2020-11-25

Restart Changes: NO

Major changes include: 1. The way the model is build has changed. Manage externals is no longer supported. Mepo is now the default and replacement manager for multiple repositories. 2. Add dependency to turn on BUILD_SHARED_LIBS for NCEP_Shared. 3. Splits the RRTMG k_g tables into separate files. 4. Bugfix to change Intel Debug flags for MOM6 and FMS. 5. gcm_run.j bugfix for tile_hist running MOM6. 6. Update plots and stats to be consistent with recent CVS tags. 7. Bugfix for C99 compliance on MacOS. 8. Updates to CI and other subrepos.

Previous Versions

For previous changes please see the CHANGELOG.md on the GitHub repository

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