Merge branch 'main' into feature/mathomp4/gocart-ceds-fix

GEOS-ESM · Jan 14, 2025 · 8ffd714 · 8ffd714
2 parents 618bccb + 1bf10d3
commit 8ffd714
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -15,7 +15,7 @@ parameters:
     default: ""
 
 # Anchors to prevent forgetting to update a version
-os_version: &os_version ubuntu20
+os_version: &os_version ubuntu24
 baselibs_version: &baselibs_version v7.27.0
 bcs_version: &bcs_version v11.6.0
 tag_build_arg_name: &tag_build_arg_name gcmversion

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
@@ -19,7 +19,7 @@ jobs:
     if: "!contains(github.event.pull_request.labels.*.name, '0 diff trivial')"
     runs-on: ubuntu-latest
     container:
-      image: gmao/ubuntu20-geos-env:v7.27.0-intelmpi_2021.13-ifort_2021.13
+      image: gmao/ubuntu24-geos-env:v7.27.0-intelmpi_2021.13-ifort_2021.13
       # Per https://github.com/actions/virtual-environments/issues/1445#issuecomment-713861495
       # It seems like we might not need secrets on GitHub Actions which is good for forked
       # pull requests

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,40 @@
 
 ## Unreleased
 
+## [11.6.3] - 2025-01-10
+
+### Zero-diff to Previous Release: YES
+### Restart Changes: YES (metadata only)
+
+### Major Zero-Diff Changes:
+
+* Added new Gigatraj grid comp to calculate particle trajectories. By default, this feature not built, but can be using the cmake option `-DBUILD_WITH_GIGATRAJ=ON` [#954](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/954) [#820](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/820) [#665](https://github.com/GEOS-ESM/GEOSgcm_App/pull/665)
+* Adding Data Atmosphere from S2S to mainline gcm [#668](https://github.com/GEOS-ESM/GEOSgcm_App/pull/668)
+* Fixed DataAtmosphere with corrections to `SW`, `SH` and `EVAP` etc. [#1040](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/1040)
+* Prevent `SURFSTATE` from terminating when CICE6 is running [#1030](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/1030)
+* Updated refresh method registration: enables CICE6 rewind through MAPL using a new flag [#1022](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/1022)
+* Added yaml file for JRA55-DO dataset [#1038](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/1038)
+* Updated `LONG_NAME` attributes to match M21C file specs; conservative regridding of (obs) `PRECIP_FILE` inputs [#1032](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/1032)
+* Updated land-related collections in `HISTORY.rc.tmpl` to match M21C file specs [#663](https://github.com/GEOS-ESM/GEOSgcm_App/pull/663)
+* Convert gcm setup template `>>>`-vars to `@`-vars. This change is consistent with DAS conventions of prefixing setup variables with `@` and runtime variables with `>>><<<` [#666](https://github.com/GEOS-ESM/GEOSgcm_App/pull/666)
+* Satisfy CHEM imports for Lopez LFR scheme [#1021](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/1021)
+* Add dependency to `fms_r4` because of the way FV3 is built as `r4` but links to the `r8` version of FMS [#1037](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/1037)
+* Initial prototype of a CFFI-based fortran/python bridge for MKIAU [#1034](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/1034)
+* Fixes for SCM [#676](https://github.com/GEOS-ESM/GEOSgcm_App/pull/676)
+* Updates to enable jemalloc build [#568](https://github.com/GEOS-ESM/GEOSgcm_App/pull/568)
+
+### Fixture Changes:
+* ESMA_env  [v4.29.1 => v4.29.2](https://github.com/GEOS-ESM/ESMA_env/compare/v4.29.1...v4.29.2)
+* ESMA_cmake  [v3.52.0 => v3.56.0](https://github.com/GEOS-ESM/ESMA_cmake/compare/v3.52.0...v3.56.0)
+* MAPL  [v2.50.1 => v2.51.2](https://github.com/GEOS-ESM/MAPL/compare/v2.50.1...v2.51.2)
+* GEOSgcm_GridComp  [v2.6.2 => v2.6.3](https://github.com/GEOS-ESM/GEOSgcm_GridComp/compare/v2.6.2...v2.6.3)
+* GigaTraj [NEW v1.0.0](https://github.com/GEOS-ESM/gigatraj/releases/tag/geos%2Fv1.0.0)
+* FVdycoreCubed_GridComp  [v2.12.0 => v2.13.0](https://github.com/GEOS-ESM/FVdycoreCubed_GridComp/compare/v2.12.0...v2.13.0)
+* fvdycore  [v2.9.0 => v2.9.1](https://github.com/GEOS-ESM/GFDL_atmos_cubed_sphere/compare/geos/v2.9.0...geos/v2.9.1)
+* GEOSradiation_GridComp  [v1.9.0 => v1.10.0](https://github.com/GEOS-ESM/GEOSradiation_GridComp/compare/v1.9.0...v1.10.0)
+* GEOSgcm_App  [v2.3.5 => v2.3.7](https://github.com/GEOS-ESM/GEOSgcm_App/compare/v2.3.5...v2.3.7)
+
+
 ## [11.6.2] - 2024-10-23
 
 ### Zero-diff to Previous Release: YES

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,10 +1,10 @@
-cmake_minimum_required (VERSION 3.23)
+cmake_minimum_required (VERSION 3.24)
 cmake_policy (SET CMP0053 NEW)
 cmake_policy (SET CMP0054 NEW)
 
 project (
   GEOSgcm
-  VERSION 11.6.2
+  VERSION 11.6.3
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 if ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}")
@@ -80,7 +80,7 @@ if (NOT Baselibs_FOUND)
   # Another issue with historical reasons, old/wrong zlib target used in GEOS
   add_library(ZLIB::zlib ALIAS ZLIB::ZLIB)
 
-  find_package(MAPL 2.50 QUIET)
+  find_package(MAPL 2.51 QUIET)
   if (MAPL_FOUND)
     message(STATUS "Found MAPL: ${MAPL_BASE_DIR} (found version \"${MAPL_VERSION})\"")
   endif ()

diff --git a/README.md b/README.md
@@ -15,24 +15,25 @@
 | [CICE](https://github.com/GEOS-ESM/CICE)                                       | [geos/v0.2.0](https://github.com/GEOS-ESM/CICE/releases/tag/geos%2Fv0.2.0)                          |
 | [CPLFCST_Etc](https://github.com/GEOS-ESM/CPLFCST_Etc)                         | [v1.0.1](https://github.com/GEOS-ESM/CPLFCST_Etc/releases/tag/v1.0.1)                               |
 | [ecbuild](https://github.com/GEOS-ESM/ecbuild)                                 | [geos/v1.4.0](https://github.com/GEOS-ESM/ecbuild/releases/tag/geos%2Fv1.4.0)                       |
-| [ESMA_cmake](https://github.com/GEOS-ESM/ESMA_cmake)                           | [v3.52.0](https://github.com/GEOS-ESM/ESMA_cmake/releases/tag/v3.52.0)                              |
-| [ESMA_env](https://github.com/GEOS-ESM/ESMA_env)                               | [v4.29.1](https://github.com/GEOS-ESM/ESMA_env/releases/tag/v4.29.1)                                |
+| [ESMA_cmake](https://github.com/GEOS-ESM/ESMA_cmake)                           | [v3.56.0](https://github.com/GEOS-ESM/ESMA_cmake/releases/tag/v3.56.0)                              |
+| [ESMA_env](https://github.com/GEOS-ESM/ESMA_env)                               | [v4.29.2](https://github.com/GEOS-ESM/ESMA_env/releases/tag/v4.29.2)                                |
 | [FMS](https://github.com/GEOS-ESM/FMS)                                         | [geos/2019.01.02+noaff.10](https://github.com/GEOS-ESM/FMS/releases/tag/geos%2F2019.01.02%2Bnoaff.10) |
-| [FVdycoreCubed_GridComp](https://github.com/GEOS-ESM/FVdycoreCubed_GridComp)   | [v2.12.0](https://github.com/GEOS-ESM/FVdycoreCubed_GridComp/releases/tag/v2.12.0)                    |
+| [FVdycoreCubed_GridComp](https://github.com/GEOS-ESM/FVdycoreCubed_GridComp)   | [v2.13.0](https://github.com/GEOS-ESM/FVdycoreCubed_GridComp/releases/tag/v2.13.0)                    |
 | [geos-chem](https://github.com/GEOS-ESM/geos-chem)                             | [geos/v13.0.0-rc1](https://github.com/GEOS-ESM/geos-chem/releases/tag/geos%2Fv13.0.0-rc1)           |
 | [GEOS_OceanGridComp](https://github.com/GEOS-ESM/GEOS_OceanGridComp)           | [v2.3.0](https://github.com/GEOS-ESM/GEOS_OceanGridComp/releases/tag/v2.3.0)                        |
 | [GEOS_Util](https://github.com/GEOS-ESM/GEOS_Util)                             | [v2.1.3](https://github.com/GEOS-ESM/GEOS_Util/releases/tag/v2.1.3)                                 |
 | [GEOSchem_GridComp](https://github.com/GEOS-ESM/GEOSchem_GridComp)             | [v1.15.0](https://github.com/GEOS-ESM/GEOSchem_GridComp/releases/tag/v1.15.0)                       |
-| [GEOSgcm_App](https://github.com/GEOS-ESM/GEOSgcm_App)                         | [v2.3.5](https://github.com/GEOS-ESM/GEOSgcm_App/releases/tag/v2.3.5)                               |
-| [GEOSgcm_GridComp](https://github.com/GEOS-ESM/GEOSgcm_GridComp)               | [v2.7.0](https://github.com/GEOS-ESM/GEOSgcm_GridComp/releases/tag/v2.7.0)                          |
+| [GEOSgcm_App](https://github.com/GEOS-ESM/GEOSgcm_App)                         | [v2.3.7](https://github.com/GEOS-ESM/GEOSgcm_App/releases/tag/v2.3.7)                               |
+| [GEOSgcm_GridComp](https://github.com/GEOS-ESM/GEOSgcm_GridComp)               | [v2.6.4](https://github.com/GEOS-ESM/GEOSgcm_GridComp/releases/tag/v2.6.4)                          |
 | [GEOSradiation_GridComp](https://github.com/GEOS-ESM/GEOSradiation_GridComp)   | [v1.10.0](https://github.com/GEOS-ESM/GEOSradiation_GridComp/releases/tag/v1.10.0)                    |
 | [GFDL_atmos_cubed_sphere](https://github.com/GEOS-ESM/GFDL_atmos_cubed_sphere) | [geos/v2.9.1](https://github.com/GEOS-ESM/GFDL_atmos_cubed_sphere/releases/tag/geos%2Fv2.9.1)       |
+| [gigatraj](https://github.com/GEOS-ESM/gigatraj)                               | [geos/v1.0.0](https://github.com/GEOS-ESM/gigatraj/releases/tag/geos%2Fv1.0.0)       |
 | [GMI](https://github.com/GEOS-ESM/GMI)                                         | [v1.3.0](https://github.com/GEOS-ESM/GMI/releases/tag/v1.3.0)                                       |
 | [GMAO_Shared](https://github.com/GEOS-ESM/GMAO_Shared)                         | [v1.9.9](https://github.com/GEOS-ESM/GMAO_Shared/releases/tag/v1.9.9)                               |
 | [GOCART](https://github.com/GEOS-ESM/GOCART)                                   | [sdr_v2.3.0](https://github.com/GEOS-ESM/GOCART/releases/tag/sdr_v2.3.0)                            |
 | [HEMCO](https://github.com/GEOS-ESM/HEMCO)                                     | [geos/v2.2.3](https://github.com/GEOS-ESM/HEMCO/releases/tag/geos%2Fv2.2.3)                         |
 | [Icepack](https://github.com/GEOS-ESM/Icepack)                                 | [geos/v0.3.0](https://github.com/GEOS-ESM/Icepack/releases/tag/geos%2Fv0.3.0)                       |
-| [MAPL](https://github.com/GEOS-ESM/MAPL)                                       | [v2.50.1](https://github.com/GEOS-ESM/MAPL/releases/tag/v2.50.1)                                    |
+| [MAPL](https://github.com/GEOS-ESM/MAPL)                                       | [v2.51.2](https://github.com/GEOS-ESM/MAPL/releases/tag/v2.51.2)                                    |
 | [MITgcm](https://github.com/GEOS-ESM/MITgcm)                                   | [checkpoint68o](https://github.com/GEOS-ESM/MITgcm/releases/tag/checkpoint68o)                      |
 | [MOM5](https://github.com/GEOS-ESM/MOM5)                                       | [geos/5.1.0+1.2.0](https://github.com/GEOS-ESM/MOM5/releases/tag/geos%2F5.1.0%2B1.2.0)              |
 | [MOM6](https://github.com/GEOS-ESM/MOM6)                                       | [geos/v3.3](https://github.com/GEOS-ESM/MOM6/tree/geos/v3.3)                                        |
@@ -155,6 +156,20 @@ Note that when you first use `gh`, it will ask what your preferred git protocol
 is (https or ssh) to use "underneath". The caveats above will apply to whichever
 you choose.
 
+### Setting up `mepo` to use blobless clones
+
+The GEOS GCM uses a Python utility called [mepo](https://github.com/GEOS-ESM/mepo/) to manage **m**ultiple git r**epo**sitories instead of using other technologies like Git
+submodules. `mepo` uses a YAML file that provides a list of components (and their versions) that are required for a particular configuration of GEOS GCM.
+
+We *highly* recommend setting up `mepo` to use [blobless clones](https://github.blog/open-source/git/get-up-to-speed-with-partial-clone-and-shallow-clone/) to speed
+up cloning of the sub-repositories, especially on discover. To do this, there is a one-time command to run:
+
+```
+mepo config set clone.partial blobless
+```
+
+This will set up `mepo` to use blobless clones for all future clones by adding an entry to `~/.mepoconfig`.
+
 ---
 
 ### Single Step Building of the Model

diff --git a/components.yaml b/components.yaml
@@ -5,13 +5,13 @@ GEOSgcm:
 env:
   local: ./@env
   remote: ../ESMA_env.git
-  tag: v4.29.1
+  tag: v4.29.2
   develop: main
 
 cmake:
   local: ./@cmake
   remote: ../ESMA_cmake.git
-  tag: v3.52.0
+  tag: v3.56.0
   develop: develop
 
 ecbuild:
@@ -44,7 +44,7 @@ GEOS_Util:
 MAPL:
   local: ./src/Shared/@MAPL
   remote: ../MAPL.git
-  tag: v2.50.1
+  tag: v2.51.2
   develop: develop
 
 FMS:
@@ -56,14 +56,20 @@ FMS:
 GEOSgcm_GridComp:
   local: ./src/Components/@GEOSgcm_GridComp
   remote: ../GEOSgcm_GridComp.git
-  branch: develop
+  tag: v2.6.4
   sparse: ./config/GEOSgcm_GridComp.sparse
   develop: develop
 
+GigaTraj:
+  local: ./src/Components/@GEOSgcm_GridComp/GEOSgigatraj_GridComp/@GigaTraj
+  remote: ../gigatraj.git
+  tag: geos/v1.0.0
+  develop: develop-GSFC
+
 FVdycoreCubed_GridComp:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSsuperdyn_GridComp/@FVdycoreCubed_GridComp
   remote: ../FVdycoreCubed_GridComp.git
-  tag: v2.12.0
+  tag: v2.13.0
   develop: develop
 
 fvdycore:
@@ -191,7 +197,7 @@ umwm:
 GEOSgcm_App:
   local: ./src/Applications/@GEOSgcm_App
   remote: ../GEOSgcm_App.git
-  tag: v2.3.5
+  tag: v2.3.7
   develop: develop
 
 UMD_Etc: