Documentation for GEOS GCM v10: Difference between revisions

Line 14:

= Changelog =

== [10.12.4] - 2020-05-15 ==

=== Zero-diff to previous release: YES ===

=== Restart Changes: NO ===

Major changes are:

# Brings RRTMGP code up to date with recent Pincus Master changes as of 3 May 2020

# Add ability to run setup scripts in another's install directory

# Support for new surface parameter resource file for land

# Fixes issues with the scm_setup

# Update CircleCI to use Baselibs 6.0.12

# Use different ALLREDUCE algorithm for Intel MPI

# Change Intel MPI GATHERV algorithm so GEOSgcm does not lock up on skylakes at checkpoint

# Add a commented out setenv for the FOR_IGNORE_EXCEPTIONS in MPT

# Add option to symlink GEOSgcm.x in experiment directory

# FSEGMENT bug fix in gcm_forecast.setup

== [10.12.3] - 2020-04-21 ==

=== Zero-diff to previous release: YES ===

=== Restart Changes: NO ===

Major changes are:

* Update to MAPL 2.1 which includes both fixes from [https://github.com/GEOS-ESM/MAPL/releases/tag/v2.1.0 MAPL v2.1.0] and [https://github.com/GEOS-ESM/MAPL/releases/tag/v2.1.1 MAPL v2.1.1]

** With this is included updating to latest releases of [https://github.com/GEOS-ESM/ESMA_env/releases ESMA_env] and [https://github.com/GEOS-ESM/ESMA_cmake/blob/master/CHANGELOG.md ESMA_cmake] needed by MAPL 2.1

** Add monthly mean features

** Add optional equation of time correction to solar position used to calculate solar zenith angle.

== [10.12.2] - 2020-04-16 ==

=== Zero-diff to previous release: YES ===

=== Restart Changes: NO except moist_import has an additional field: FRACI ===

Major changes are:

# Added connectivity from MOIST to CHEM for 2 fields (RI and RL).

# Updates to the obio component which was in the CVS Icarus-2.0 tag.

# Bugfix for coupled mode renaming TSKINI to TSKINICE.

# Bugfix for DTDT_moist which was initially set to temperature but never updated to provide tendency.

# Compute the lightning flash rate (LFR) online following the approach used by GEOSCHEMchem_GridComp. The LFR is calculated in MOIST and then made available to other components as a new export field (LFR_GCC).

# Modified the mk_Restarts script to run on SLES-12.

# Update RRTMGP to Pincus 2020-Feb-12.

# New Surface parameter resource file (GEOSsurface_GridComp/Shared/GEOS_SurfaceGridComp.rc) to avoid having to add new parameters into AGCM.rc.tmpl and prepare for further science development.

# Correcting the following issues with the single column model: (1) GF imports from DYN were not filled; (2) scm_setup incompletely adjusted for L132; (3) SST file for cfmip_s11 case was incorrect.

# Allows regrid.pl to run on SLES-12

# Enabled compilation of convert_aerosols.x as R8

== [10.12.1] - 2020-03-27 ==

=== Zero-diff to previous release: YES ===

=== Restart Changes: NO except moist_internal has an additional 3 fields: NGRAUPEL, NRAIN, NSNOW ===

Major changes are:

# Broader support for various computing environments including SLES12. Adds a new question to gcm_setup (and other setup scripts) that asks a user what type of processor to run on. It then uses the "default" number of cores per those processors to better figure out how to handle the IOserver nodes.

# Changes that enable MAPL2 GEOS to work with MPT at NCCS.

# Changed REPLAY_Shutoff alarm from NON-STICKY to STICKY, and used it in GAAS to stop updates in forecasts during REPLAY mode.

# Updates to moist and GOCART using 2MOMENT microphysics and MG3. These are 0-diff when running the default 1MOMENT microphysics.

# Modified gcmpost.script to only operate on pressure-level collections.

# Fixes issues where systems do not have either ImageMagick or F2Py. If F2Py is not found, then F2Py targets are not built.

# Changes to GMAO_hermes:

#* Split off the independent sections of module m_topo_remap used by FV core into shared_topo_remap

#* write_eta.F90 added to prepare for a config file which eventually will replace m_set_eta module

#* Add option to build HERMES_LIGHT

== [10.12.0] - 2020-03-09 ==

=== Zero-diff to previous release: NO ===

=== Restart Changes: NO ===

Major changes are:

# Fixed "zero-diff" issue related to GF evaporation vs total rain, fixed GF cloud-mass-flux scaling issue.

# Move ShallowCu contribution to mass flux and add scale-dependent stochastics to convection.

== [10.11.0] - 2020-03-04 ==

=== Zero-diff to previous release: NO ===

=== Restart Changes: NO ===

Major changes are:

# RRTMG_SW: Updates RRTMG_SW in GEOS to be equivalent to RRTMG_SW v4.10. This fix increases the heating rates near the stratospause region and is a non zero-diff change.

# RAS_NO_NEG: Provides an optional flag that ensures RAS results are non-negative. This is an important fix for chemical species that was extremely useful in the Icarus but did not make it into Jason. The fix is "off" by default and therefore zero-diff.

# Plots:

* Enable additional upper levels for forecast stats plots.

* Add QITOT & QLTOT to horizontal plots.

* Add aerosols to time series plots.

Other updates:

* Remove #PBS pragmas at NCCS to use #SBATCH.

* Brought the chem setup scripts in line with gcm_setup.

* Bug fixes for gcm_run and gcm_forecast scripts.

== [10.10.0] - 2020-02-20 ==

=== Zero-diff to previous release: NO ===

=== Restart Changes: NO ===

This release is equivalent to the [https://github.com/NOAA-GFDL/FMS/releases/tag/2019.01.01 NOAA 2019.01.01 Release] but with the addition of GEOS constants controlled by <code>-DMAPL_MODE</code>. Additional changes allow building with CMake.

== [10.9.0] - 2020-02-13 ==

=== Zero-diff to previous release: NO ===

=== Restart Changes: NO ===

This release is equivalent in physics to v10.8.0 but now uses [https://github.com/GEOS-ESM/MAPL/releases/tag/v2.0.0 MAPL 2.0]. The release is non-zero-diff due to the use of ESMF regridding for History and ExtData.

Also, this version of GEOSgcm now uses the new PFIO IO server to handle History and ExtData file access and writing. By default, these IO servers run on the same resources (i.e., nodes) as the application. However, <code>gcm_setup</code> and <code>gcm_run.j</code> have been altered so that, by default, at high-resolution (C180+) the IO servers are on separate nodes for performance and memory reasons.

== [10.8.0] - 2020-02-06 ==

=== Zero-diff to previous release: NO ===

=== Restart Changes: NO (only if AOIL_COMP_SWITCH=ON) ===

Recoded atmosphere-ocean interface layer (AOIL). Provides an option to exercise old/new versions of the AOIL.

# Old version (AOIL_COMP_SWITCH = ON): Default. Using the old interface is still non-zero diff to x0039, however, shown to be statistically insignificant in terms of forecast skill scores. Restarts with old interface can be used as is.

# New version (AOIL_COMP_SWITCH = OFF): If the new interface is turned on, then the user must provide additional fields in the internal state. Contact Santha Akella for a utility to do that.

== [10.7.0] - 2020-02-04 ==

=== Zero-diff to previous release: NO ===

=== Zero-diff to CVS tag Jason-3_5_aoil ===

=== Restart Changes: NO ===

# Correction to RRTMG Shortwave 'layreffr' variable to reduce stratospheric cold bias.

# Stats plots updates to produce stratospheric forecast statistics up to 1mb.

# Correction to gcm_run.j & gcm_forecast.tmpl related to REPLAY with GAAS aod files.

== [10.6.0] - 2020-01-31 ==

=== Zero-diff to previous release: NO ===

=== Restart Changes: NO ===

# Atmospheric constituents (aersols, co, co2, etc) are now transported through moist/GF. This is equivalent to the way transport is handled in f525land_fpp/f525_fp.

# Added exports for nitrate tendency and other fluxes related to GF convection.

# Added nitrate tendency to history templates.

# Upgraded to GEOSchem_GridComp to v1.1.0.

# Set the default k_split = 2.

# Fixed gcm_convert.j to work consistent with how gcm_setup and gcm_run.j interact.

== [10.5.0] - 2020-01-24 ==

=== Zero-diff to previous release: YES (but user must setup experiment differently) ===

=== Restart Changes: NO ===

<ol>

<li>Hotfixed a bug to enable regridding of catchement restarts from MERRA2</li>

<li>REPLAY updates:

The REPLAY algorithm within the GEOSagcm has been modified to enable a 4DIAU methodology consistent with that used in DAS mode. Prior to this release, REPLAY could only incorporate one analysis increment within the CORRECTOR_DURATION window (nominally 6-hours). The 4DIAU update allows for multiple analysis increments to be used within the CORRECTOR window. The number of increments that wiil be used is determined by the settings of the REPLAY_FILE_FREQUENCY (in nnnnnn seconds format) and the REPLAY_FILE_REFERENCE_TIME (in HHMMSS format). Based on these two settings, the code will determine how many analysis increments will properly fit within the CORRECTOR window. Note: the previous setting of PREDICTOR_DURATION is no longer needed since the code computes the required length automatically.

The updated algorthm allows for 2 types of REPLAY:

<ol>

<li>Exact (Uses Archived Increment Files)

Exact REPLAYs identically reproduce (bit-for-bit) a previous GEOS DAS experiment by simply using the archived IAU forcing from the DAS experiment. For these cases, only the CORRECTOR step is employed and is, therefore, as efficient as a stand-alone model run.</li>

<li>Regular (Uses Archived Analysis/Assimilation Files)

Regular REPLAYs are used to mimic the original IAU methodology, i.e., both the PREDICTOR and the CORRECTOR steps are employed. The key difference being that the Analysis is based on archived datasets. These Analyses may be from the GEOS DAS system, or from any other source that is written using the appropriate GEOS DAS ana.eta data format.</li></ol>

For more detailed information, please see the comments within the AGCM.rc.tmpl file.</li></ol>

== [10.4.0] - 2020-01-13 ==

=== Zero-diff to previous release: YES (with defaults and without regridding) ===

=== Restart Changes: YES (land regridding) ===

* Non-zero-diff updates for:

*# Regridding land restarts

*# Running Chou-Suarez longwave radiation.

# Update FV3 to latest version v1.0.9 which fixed UH25 diagnostic to build in both R4 and R8.

# Land Updates:

## Clarified LONG_NAME of "snow depth" variable.

## Added wemin wemout options.

## Add PEATMAP data processing (disabled by default).

## GEOSsurface_GridComp changed values of pi to MAPL_PI.

## Added 8 more climatological (fPAR, VISDF, NIRDF stats for CATCHCN) data files and new clsm/country_and _state_code.data file.

## Extra column on soil_param.* files.

# Non-zero-diif bug fix in Chou-Suarez for erroneous cloud contamination in OLR-OLRNA (aerosol forcing).

# Fixed MAPL bug with vector regridding of winds in CTM.

# Workaround fix building FMS on macOS.

== [10.3.6] - 2020-01-02 ==

=== Zero-diff to previous release: YES ===

=== Restart Changes: NO ===

# Compute decomposition in MKIAU GridComp

# Use esma_set_this in GCs

# Allows GEOS-Chem (v12.4.0) chemistry to be setup and run "out of the box".

# INTERNAL and IMPORT restarts for GEOS-Chem are now in AGCM.rc.tmpl.

# GEOS-Chem timestep is set to be 2 x HEARTBEAT by default.

# Enforces GOCART_DT==HEARTBEAT_DT so all species work correctly.

# Bug fix for comments using GNU compilers with Ninja.

== [10.3.5] - 2019-11-07 ==

@@ Line 14: / Line 14: @@
 = Changelog =
+== [10.12.4] - 2020-05-15 ==
+=== Zero-diff to previous release: YES ===
+=== Restart Changes: NO ===
+Major changes are:
+# Brings RRTMGP code up to date with recent Pincus Master changes as of 3 May 2020
+# Add ability to run setup scripts in another's install directory
+# Support for new surface parameter resource file for land
+# Fixes issues with the scm_setup
+# Update CircleCI to use Baselibs 6.0.12
+# Use different ALLREDUCE algorithm for Intel MPI
+# Change Intel MPI GATHERV algorithm so GEOSgcm does not lock up on skylakes at checkpoint
+# Add a commented out setenv for the FOR_IGNORE_EXCEPTIONS in MPT
+# Add option to symlink GEOSgcm.x in experiment directory
+# FSEGMENT bug fix in gcm_forecast.setup
+== [10.12.3] - 2020-04-21 ==
+=== Zero-diff to previous release: YES ===
+=== Restart Changes: NO ===
+Major changes are:
+* Update to MAPL 2.1 which includes both fixes from [https://github.com/GEOS-ESM/MAPL/releases/tag/v2.1.0 MAPL v2.1.0] and [https://github.com/GEOS-ESM/MAPL/releases/tag/v2.1.1 MAPL v2.1.1]
+** With this is included updating to latest releases of [https://github.com/GEOS-ESM/ESMA_env/releases ESMA_env] and [https://github.com/GEOS-ESM/ESMA_cmake/blob/master/CHANGELOG.md ESMA_cmake] needed by MAPL 2.1
+** Add monthly mean features
+** Add optional equation of time correction to solar position used to calculate solar zenith angle.
+== [10.12.2] - 2020-04-16 ==
+=== Zero-diff to previous release: YES ===
+=== Restart Changes: NO except moist_import has an additional field: FRACI ===
+Major changes are:
+# Added connectivity from MOIST to CHEM for 2 fields (RI and RL).
+# Updates to the obio component which was in the CVS Icarus-2.0 tag.
+# Bugfix for coupled mode renaming TSKINI to TSKINICE.
+# Bugfix for DTDT_moist which was initially set to temperature but never updated to provide tendency.
+# Compute the lightning flash rate (LFR) online following the approach used by GEOSCHEMchem_GridComp. The LFR is calculated in MOIST and then made available to other components as a new export field (LFR_GCC).
+# Modified the mk_Restarts script to run on SLES-12.
+# Update RRTMGP to Pincus 2020-Feb-12.
+# New Surface parameter resource file (GEOSsurface_GridComp/Shared/GEOS_SurfaceGridComp.rc) to avoid having to add new parameters into AGCM.rc.tmpl and prepare for further science development.
+# Correcting the following issues with the single column model: (1) GF imports from DYN were not filled; (2) scm_setup incompletely adjusted for L132; (3) SST file for cfmip_s11 case was incorrect.
+# Allows regrid.pl to run on SLES-12
+# Enabled compilation of convert_aerosols.x as R8
+== [10.12.1] - 2020-03-27 ==
+=== Zero-diff to previous release: YES ===
+=== Restart Changes: NO except moist_internal has an additional 3 fields: NGRAUPEL, NRAIN, NSNOW ===
+Major changes are:
+# Broader support for various computing environments including SLES12. Adds a new question to gcm_setup (and other setup scripts) that asks a user what type of processor to run on. It then uses the &quot;default&quot; number of cores per those processors to better figure out how to handle the IOserver nodes.
+# Changes that enable MAPL2 GEOS to work with MPT at NCCS.
+# Changed REPLAY_Shutoff alarm from NON-STICKY to STICKY, and used it in GAAS to stop updates in forecasts during REPLAY mode.
+# Updates to moist and GOCART using 2MOMENT microphysics and MG3. These are 0-diff when running the default 1MOMENT microphysics.
+# Modified gcmpost.script to only operate on pressure-level collections.
+# Fixes issues where systems do not have either ImageMagick or F2Py. If F2Py is not found, then F2Py targets are not built.
+# Changes to GMAO_hermes:
+#* Split off the independent sections of module m_topo_remap used by FV core into shared_topo_remap
+#* write_eta.F90 added to prepare for a config file which eventually will replace m_set_eta module
+#* Add option to build HERMES_LIGHT
+== [10.12.0] - 2020-03-09 ==
+=== Zero-diff to previous release: NO ===
+=== Restart Changes: NO ===
+Major changes are:
+# Fixed &quot;zero-diff&quot; issue related to GF evaporation vs total rain, fixed GF cloud-mass-flux scaling issue.
+# Move ShallowCu contribution to mass flux and add scale-dependent stochastics to convection.
+== [10.11.0] - 2020-03-04 ==
+=== Zero-diff to previous release: NO ===
+=== Restart Changes: NO ===
+Major changes are:
+# RRTMG_SW: Updates RRTMG_SW in GEOS to be equivalent to RRTMG_SW v4.10. This fix increases the heating rates near the stratospause region and is a non zero-diff change.
+# RAS_NO_NEG: Provides an optional flag that ensures RAS results are non-negative. This is an important fix for chemical species that was extremely useful in the Icarus but did not make it into Jason. The fix is &quot;off&quot; by default and therefore zero-diff.
+# Plots:
+* Enable additional upper levels for forecast stats plots.
+* Add QITOT &amp; QLTOT to horizontal plots.
+* Add aerosols to time series plots.
+Other updates:
+* Remove #PBS pragmas at NCCS to use #SBATCH.
+* Brought the chem setup scripts in line with gcm_setup.
+* Bug fixes for gcm_run and gcm_forecast scripts.
+== [10.10.0] - 2020-02-20 ==
+=== Zero-diff to previous release: NO ===
+=== Restart Changes: NO ===
+This release is equivalent to the [https://github.com/NOAA-GFDL/FMS/releases/tag/2019.01.01 NOAA 2019.01.01 Release] but with the addition of GEOS constants controlled by <code>-DMAPL_MODE</code>. Additional changes allow building with CMake.
+== [10.9.0] - 2020-02-13 ==
+=== Zero-diff to previous release: NO ===
+=== Restart Changes: NO ===
+This release is equivalent in physics to v10.8.0 but now uses [https://github.com/GEOS-ESM/MAPL/releases/tag/v2.0.0 MAPL 2.0]. The release is non-zero-diff due to the use of ESMF regridding for History and ExtData.
+Also, this version of GEOSgcm now uses the new PFIO IO server to handle History and ExtData file access and writing. By default, these IO servers run on the same resources (i.e., nodes) as the application. However, <code>gcm_setup</code> and <code>gcm_run.j</code> have been altered so that, by default, at high-resolution (C180+) the IO servers are on separate nodes for performance and memory reasons.
+== [10.8.0] - 2020-02-06 ==
+=== Zero-diff to previous release: NO ===
+=== Restart Changes: NO (only if AOIL_COMP_SWITCH=ON) ===
+Recoded atmosphere-ocean interface layer (AOIL). Provides an option to exercise old/new versions of the AOIL.
+# Old version (AOIL_COMP_SWITCH = ON): Default. Using the old interface is still non-zero diff to x0039, however, shown to be statistically insignificant in terms of forecast skill scores. Restarts with old interface can be used as is.
+# New version (AOIL_COMP_SWITCH = OFF): If the new interface is turned on, then the user must provide additional fields in the internal state. Contact Santha Akella for a utility to do that.
+== [10.7.0] - 2020-02-04 ==
+=== Zero-diff to previous release: NO ===
+=== Zero-diff to CVS tag Jason-3_5_aoil ===
+=== Restart Changes: NO ===
+# Correction to RRTMG Shortwave 'layreffr' variable to reduce stratospheric cold bias.
+# Stats plots updates to produce stratospheric forecast statistics up to 1mb.
+# Correction to gcm_run.j &amp; gcm_forecast.tmpl related to REPLAY with GAAS aod files.
+== [10.6.0] - 2020-01-31 ==
+=== Zero-diff to previous release: NO ===
+=== Restart Changes: NO ===
+# Atmospheric constituents (aersols, co, co2, etc) are now transported through moist/GF. This is equivalent to the way transport is handled in f525land_fpp/f525_fp.
+# Added exports for nitrate tendency and other fluxes related to GF convection.
+# Added nitrate tendency to history templates.
+# Upgraded to GEOSchem_GridComp to v1.1.0.
+# Set the default k_split = 2.
+# Fixed gcm_convert.j to work consistent with how gcm_setup and gcm_run.j interact.
+== [10.5.0] - 2020-01-24 ==
+=== Zero-diff to previous release: YES (but user must setup experiment differently) ===
+=== Restart Changes: NO ===
+<ol>
+<li><p>Hotfixed a bug to enable regridding of catchement restarts from MERRA2</p></li>
+<li><p>REPLAY updates:</p>
+<p>The REPLAY algorithm within the GEOSagcm has been modified to enable a 4DIAU methodology consistent with that used in DAS mode. Prior to this release, REPLAY could only incorporate one analysis increment within the CORRECTOR_DURATION window (nominally 6-hours). The 4DIAU update allows for multiple analysis increments to be used within the CORRECTOR window. The number of increments that wiil be used is determined by the settings of the REPLAY_FILE_FREQUENCY (in nnnnnn seconds format) and the REPLAY_FILE_REFERENCE_TIME (in HHMMSS format). Based on these two settings, the code will determine how many analysis increments will properly fit within the CORRECTOR window. Note: the previous setting of PREDICTOR_DURATION is no longer needed since the code computes the required length automatically.</p>
+<p>The updated algorthm allows for 2 types of REPLAY:</p>
+<ol>
+<li><p>Exact (Uses Archived Increment Files)</p>
+<p>Exact REPLAYs identically reproduce (bit-for-bit) a previous GEOS DAS experiment by simply using the archived IAU forcing from the DAS experiment. For these cases, only the CORRECTOR step is employed and is, therefore, as efficient as a stand-alone model run.</p></li>
+<li><p>Regular (Uses Archived Analysis/Assimilation Files)</p>
+<p>Regular REPLAYs are used to mimic the original IAU methodology, i.e., both the PREDICTOR and the CORRECTOR steps are employed. The key difference being that the Analysis is based on archived datasets. These Analyses may be from the GEOS DAS system, or from any other source that is written using the appropriate GEOS DAS ana.eta data format.</p></li></ol>
+<p>For more detailed information, please see the comments within the AGCM.rc.tmpl file.</p></li></ol>
+== [10.4.0] - 2020-01-13 ==
+=== Zero-diff to previous release: YES (with defaults and without regridding) ===
+=== Restart Changes: YES (land regridding) ===
+* Non-zero-diff updates for:
+*# Regridding land restarts
+*# Running Chou-Suarez longwave radiation.
+# Update FV3 to latest version v1.0.9 which fixed UH25 diagnostic to build in both R4 and R8.
+# Land Updates:
+## Clarified LONG_NAME of &quot;snow depth&quot; variable.
+## Added wemin wemout options.
+## Add PEATMAP data processing (disabled by default).
+## GEOSsurface_GridComp changed values of pi to MAPL_PI.
+## Added 8 more climatological (fPAR, VISDF, NIRDF stats for CATCHCN) data files and new clsm/country_and _state_code.data file.
+## Extra column on soil_param.* files.
+# Non-zero-diif bug fix in Chou-Suarez for erroneous cloud contamination in OLR-OLRNA (aerosol forcing).
+# Fixed MAPL bug with vector regridding of winds in CTM.
+# Workaround fix building FMS on macOS.
+== [10.3.6] - 2020-01-02 ==
+=== Zero-diff to previous release: YES ===
+=== Restart Changes: NO ===
+# Compute decomposition in MKIAU GridComp
+# Use esma_set_this in GCs
+# Allows GEOS-Chem (v12.4.0) chemistry to be setup and run &quot;out of the box&quot;.
+# INTERNAL and IMPORT restarts for GEOS-Chem are now in AGCM.rc.tmpl.
+# GEOS-Chem timestep is set to be 2 x HEARTBEAT by default.
+# Enforces GOCART_DT==HEARTBEAT_DT so all species work correctly.
+# Bug fix for comments using GNU compilers with Ninja.
 == [10.3.5] - 2019-11-07 ==