From 754531f106adb3b35151f1ccdb9f9ba560729eef Mon Sep 17 00:00:00 2001
From: Alex Richert <alexander.richert@noaa.gov>
Date: Wed, 6 Dec 2023 12:34:34 -0800
Subject: [PATCH 01/13] get 'uppercase' from mpp_mod in
 io/module_wrt_grid_comp.F90

---
 io/module_wrt_grid_comp.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/io/module_wrt_grid_comp.F90 b/io/module_wrt_grid_comp.F90
index b59fe5e45..5ca68f0da 100644
--- a/io/module_wrt_grid_comp.F90
+++ b/io/module_wrt_grid_comp.F90
@@ -29,7 +29,7 @@ module module_wrt_grid_comp
       use mpi
       use esmf
       use fms
-      use mpp_mod, only : mpp_init   ! needed for fms 2023.02
+      use mpp_mod, only : mpp_init, uppercase  ! needed for fms 2023.02
 
       use write_internal_state
       use module_fv3_io_def,   only : num_pes_fcst,                             &

From 8d3927c3c9539c246f08ec79cf018df8fc06e511 Mon Sep 17 00:00:00 2001
From: Alex Richert <alexander.richert@noaa.gov>
Date: Wed, 6 Dec 2023 12:34:13 -0800
Subject: [PATCH 02/13] Add GCC-based CI build

---
 .github/workflows/GCC.yml                     | 90 +++++++++++++++++++
 CMakeLists.txt                                |  8 +-
 ci/CMakeLists.txt                             | 63 +++++++++++++
 ci/spack.yaml                                 | 18 ++++
 .../stochastic_physics_wrapper.F90            |  0
 5 files changed, 178 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/GCC.yml
 create mode 100644 ci/CMakeLists.txt
 create mode 100644 ci/spack.yaml
 rename {stochastic_physics => stochastic_physics_wrapper}/stochastic_physics_wrapper.F90 (100%)

diff --git a/.github/workflows/GCC.yml b/.github/workflows/GCC.yml
new file mode 100644
index 000000000..670c10adc
--- /dev/null
+++ b/.github/workflows/GCC.yml
@@ -0,0 +1,90 @@
+# This is a CI workflow for the fv3atm project.
+#
+# This workflow builds and tests the fv3atm library using GCC, and it tests
+# different CMake build options.
+#
+# Alex Richert, 6 Dec 2023
+
+name: GCC
+on:
+  push:
+    branches:
+    - develop
+  pull_request:
+    branches:
+    - develop
+
+jobs:
+  GCC:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        cmake_opts: ["-D32BIT=ON", "-D32BIT=OFF"]
+        gcc_ver: ["11"]
+        mpi: ["mpich"]
+
+    steps:
+
+    - name: install-mpi
+      run: |
+        sudo apt-get install lib${{ matrix.mpi }}-dev
+
+    - name: checkout-fv3atm
+      uses: actions/checkout@v3
+      with:
+        path: ${{ github.workspace }}/fv3atm
+        submodules: recursive
+
+    - name: cache-spack
+      id: cache-spack
+      uses: actions/cache@v3
+      with:
+        path: ${{ github.workspace }}/spack-develop
+        key: spack-${{ hashFiles('fv3atm/ci/spack.yaml') }}-gcc${{ matrix.gcc_ver }}-1
+
+    - name: spack-install
+      if: steps.cache-spack.outputs.cache-hit != 'true'
+      run: |
+        wget --no-verbose https://github.com/spack/spack/archive/refs/heads/develop.zip
+        unzip develop.zip -d ${GITHUB_WORKSPACE}/ &> unzip.out
+        # temporary fix (https://github.com/spack/spack/pull/41475)
+        wget https://raw.githubusercontent.com/AlexanderRichert-NOAA/spack/e9b6ada157a65a486eb1e039fdbfe66c9eebb842/var/spack/repos/builtin/packages/fms/package.py
+        mv package.py ${GITHUB_WORKSPACE}/spack-develop/var/spack/repos/builtin/packages/fms/package.py
+        #
+        . ${GITHUB_WORKSPACE}/spack-develop/share/spack/setup-env.sh
+        spack env create gcc${{ matrix.gcc_ver }} ${GITHUB_WORKSPACE}/fv3atm/ci/spack.yaml
+        spack env activate gcc${{ matrix.gcc_ver }}
+        spack compiler find | grep gcc@${{ matrix.gcc_ver }}
+        spack external find gmake cmake git git-lfs perl python ${{ matrix.mpi }}
+        spack config add "packages:all:require:['%gcc@${{ matrix.gcc_ver }}']"
+        spack config add "packages:mpi:require:'${{ matrix.mpi }}'"
+        spack concretize |& tee ${SPACK_ENV}/log.concretize
+        spack install -j2 --fail-fast
+
+    - name: cache-save
+      uses: actions/cache/save@v3
+      if: ${{ always() }}
+      with:
+        path: ${{ github.workspace }}/spack-develop
+        key: spack-${{ hashFiles('fv3atm/ci/spack.yaml') }}-gcc${{ matrix.gcc_ver }}-1
+
+    - name: build-fv3atm
+      run: |
+        . ${GITHUB_WORKSPACE}/spack-develop/share/spack/setup-env.sh
+        spack env activate gcc${{ matrix.gcc_ver }}
+        spack load $(spack find --format "{name}")
+        cd ${GITHUB_WORKSPACE}/fv3atm
+        git clone https://github.com/NOAA-EMC/CMakeModules
+        git clone --recurse-submodules https://github.com/NOAA-PSL/stochastic_physics
+        mkdir ${GITHUB_WORKSPACE}/build
+        cd ${GITHUB_WORKSPACE}/build
+        cmake ${GITHUB_WORKSPACE}/fv3atm -DBUILD_TESTING=ON ${{ matrix.cmake_opts }}
+        make -j2
+
+    - name: debug-artifacts
+      uses: actions/upload-artifact@v3
+      if: ${{ failure() }}
+      with:
+        name: ccpp_prebuild_logs
+        path: ${{ github.workspace }}/build/ccpp/ccpp_prebuild.*
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 549738794..f5d86663b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,3 +1,9 @@
+# Enable CI build & unit testing:
+if(BUILD_TESTING)
+  cmake_minimum_required(VERSION 3.19)
+  project(fv3atm VERSION 1.0 LANGUAGES C CXX Fortran)
+  include(ci/CMakeLists.txt)
+endif()
 
 ###############################################################################
 ### CCPP
@@ -81,7 +87,7 @@ add_library(fv3atm
   fv3_cap.F90
   module_fv3_config.F90
   module_fcst_grid_comp.F90
-  stochastic_physics/stochastic_physics_wrapper.F90
+  stochastic_physics_wrapper/stochastic_physics_wrapper.F90
   cpl/module_block_data.F90
   cpl/module_cplfields.F90
   cpl/module_cap_cpl.F90
diff --git a/ci/CMakeLists.txt b/ci/CMakeLists.txt
new file mode 100644
index 000000000..0bfe7680e
--- /dev/null
+++ b/ci/CMakeLists.txt
@@ -0,0 +1,63 @@
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/CMakeModules/Modules)
+
+if(${CMAKE_Fortran_COMPILER_ID} MATCHES "GNU")
+  if(CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 9.0.0)
+    message(FATAL_ERROR "GNU Compiler >= 9 is required")
+  endif()
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -ggdb -fbacktrace -cpp -fcray-pointer -ffree-line-length-none -fno-range-check")
+
+  if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
+    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-argument-mismatch -fallow-invalid-boz")
+  endif()
+
+  if(NOT 32BIT)
+    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fdefault-real-8 -fdefault-double-8")
+  endif()
+elseif(${CMAKE_Fortran_COMPILER_ID} MATCHES "Intel")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback -fpp -fno-alias -auto -safe-cray-ptr -ftz -assume byterecl -nowarn -sox -align array64byte -qno-opt-dynamic-align")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -qno-opt-dynamic-align -sox -fp-model source")
+  set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -debug minimal -qoverride-limits")
+  set(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE} -fp-model consistent")
+  set(CMAKE_C_FLAGS_RELEASE       "-O2 -debug minimal")
+
+  if(NOT 32BIT)
+      set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -real-size 64")
+  endif()
+endif()
+
+set(32BIT           OFF CACHE BOOL "Enable 32BIT (single precision arithmetic in dycore and fast physics)")
+set(CCPP_32BIT      OFF CACHE BOOL "Enable CCPP_32BIT (single precision arithmetic in slow physics)")
+set(INLINE_POST     ON  CACHE BOOL "Enable inline post")
+set(MULTI_GASES     OFF CACHE BOOL "Enable MULTI_GASES")
+set(MOVING_NEST     OFF CACHE BOOL "Enable moving nest code")
+set(OPENMP          ON  CACHE BOOL "Enable OpenMP threading")
+set(PARALLEL_NETCDF OFF CACHE BOOL "Enable parallel NetCDF")
+
+message("32BIT ............ ${32BIT}")
+message("CCPP_32BIT ....... ${CCPP_32BIT}")
+message("INLINE_POST ...... ${INLINE_POST}")
+message("MULTI_GASES ...... ${MULTI_GASES}")
+message("MOVING_NEST ...... ${MOVING_NEST}")
+message("OPENMP ........... ${OPENMP}")
+message("PARALLEL_NETCDF .. ${PARALLEL_NETCDF}")
+
+find_package(MPI REQUIRED)
+if(OPENMP)
+  find_package(OpenMP REQUIRED)
+endif()
+
+find_package(NetCDF 4.7.4 REQUIRED C Fortran)
+find_package(ESMF 8.3.0 MODULE REQUIRED)
+find_package(FMS 2022.04 REQUIRED COMPONENTS R4 R8)
+if(32BIT)
+  add_library(fms ALIAS FMS::fms_r4)
+else()
+  add_library(fms ALIAS FMS::fms_r8)
+endif()
+find_package(bacio 2.4.0 REQUIRED)
+find_package(sp 2.3.3 REQUIRED)
+find_package(w3emc 2.9.2 REQUIRED)
+
+find_package(Python 3.6 REQUIRED COMPONENTS Interpreter)
+
+add_subdirectory(stochastic_physics)
diff --git a/ci/spack.yaml b/ci/spack.yaml
new file mode 100644
index 000000000..4c183f80e
--- /dev/null
+++ b/ci/spack.yaml
@@ -0,0 +1,18 @@
+spack:
+  specs:
+  - w3emc@2.10.0 precision=4,d,8
+  - ip@develop precision=4,d,8
+  - sp@2.4.0 precision=4,d,8
+  - bacio@2.4.1
+  - upp@develop
+  - esmf@8.4.2
+  - fms@2023.04 +gfs_phys +openmp +pic +quad_precision +deprecated_io constants=GFS precision=32,64
+  - netcdf-c ~blosc
+  view: false
+  concretizer:
+    unify: true
+  packages:
+    mpich:
+      require: ['~libxml2 ~hwloc ~pci']
+    yaksa:
+      buildable: false
diff --git a/stochastic_physics/stochastic_physics_wrapper.F90 b/stochastic_physics_wrapper/stochastic_physics_wrapper.F90
similarity index 100%
rename from stochastic_physics/stochastic_physics_wrapper.F90
rename to stochastic_physics_wrapper/stochastic_physics_wrapper.F90

From 8c1fac884c86a487956cff80bde3e51b979f378d Mon Sep 17 00:00:00 2001
From: Alex Richert <alexander.richert@noaa.gov>
Date: Wed, 6 Dec 2023 18:53:02 -0800
Subject: [PATCH 03/13] note dep build time in GCC CI

---
 .github/workflows/GCC.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/GCC.yml b/.github/workflows/GCC.yml
index 670c10adc..2ecb122b7 100644
--- a/.github/workflows/GCC.yml
+++ b/.github/workflows/GCC.yml
@@ -43,6 +43,7 @@ jobs:
         path: ${{ github.workspace }}/spack-develop
         key: spack-${{ hashFiles('fv3atm/ci/spack.yaml') }}-gcc${{ matrix.gcc_ver }}-1
 
+    # Building dependencies takes 40+ min
     - name: spack-install
       if: steps.cache-spack.outputs.cache-hit != 'true'
       run: |

From 435bccde9f65085ac3a1f2146907357cc221790f Mon Sep 17 00:00:00 2001
From: Alex Richert <82525672+AlexanderRichert-NOAA@users.noreply.github.com>
Date: Thu, 7 Dec 2023 14:28:50 -0800
Subject: [PATCH 04/13] Update CMakeLists.txt

---
 ci/CMakeLists.txt | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/ci/CMakeLists.txt b/ci/CMakeLists.txt
index 0bfe7680e..48b356914 100644
--- a/ci/CMakeLists.txt
+++ b/ci/CMakeLists.txt
@@ -1,3 +1,8 @@
+# This file is used by fv3atm's root CMakeLists.txt when BUILD_TESTING=ON. It is
+# used for CI runs and is based on the ufs-weather-model root CMakeLists.txt. It
+# cannot be built directly, and should not be used for compiling for general R&D
+# or operations.
+
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/CMakeModules/Modules)
 
 if(${CMAKE_Fortran_COMPILER_ID} MATCHES "GNU")

From ca53742ce1588ce908f28bd2ccd4bb321ad33e9d Mon Sep 17 00:00:00 2001
From: Alex Richert <82525672+AlexanderRichert-NOAA@users.noreply.github.com>
Date: Thu, 7 Dec 2023 14:41:52 -0800
Subject: [PATCH 05/13] Update spack.yaml

---
 ci/spack.yaml | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/ci/spack.yaml b/ci/spack.yaml
index 4c183f80e..3009df05a 100644
--- a/ci/spack.yaml
+++ b/ci/spack.yaml
@@ -1,3 +1,12 @@
+# This file is used in the CI to define the libraries needed to build fv3atm. It
+# is used by the 'spack env create' command to generate a Spack environment. It
+# is generally preferred to avoid defining settings here that are not shared
+# across CI workflows, such as requiring the use of a specific compiler. Any
+# such modifications should be done in the appropriate CI workflow using the
+# 'spack config add' command, or with search-and-replace.
+# WARNING: Changing this file will automatically cause the cached Spack builds
+# in GitHub Actions to be regenerated, which takes a considerable amount of
+# time.
 spack:
   specs:
   - w3emc@2.10.0 precision=4,d,8
@@ -7,12 +16,12 @@ spack:
   - upp@develop
   - esmf@8.4.2
   - fms@2023.04 +gfs_phys +openmp +pic +quad_precision +deprecated_io constants=GFS precision=32,64
-  - netcdf-c ~blosc
+  - netcdf-c@4.9.2 ~blosc
   view: false
   concretizer:
     unify: true
   packages:
     mpich:
-      require: ['~libxml2 ~hwloc ~pci']
+      require: ['~libxml2 ~hwloc ~pci'] # minimize unneeded dependencies
     yaksa:
-      buildable: false
+      buildable: false # minimize unneeded dependencies

From 08d8e10a1d3c58249c1671ec133b560ba62651ff Mon Sep 17 00:00:00 2001
From: Alex Richert <82525672+AlexanderRichert-NOAA@users.noreply.github.com>
Date: Thu, 7 Dec 2023 17:54:00 -0800
Subject: [PATCH 06/13] Update CMakeLists.txt

---
 ci/CMakeLists.txt | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/ci/CMakeLists.txt b/ci/CMakeLists.txt
index 48b356914..f64bceb8a 100644
--- a/ci/CMakeLists.txt
+++ b/ci/CMakeLists.txt
@@ -2,6 +2,8 @@
 # used for CI runs and is based on the ufs-weather-model root CMakeLists.txt. It
 # cannot be built directly, and should not be used for compiling for general R&D
 # or operations.
+#
+# Alex Richert, 6 Dec 2023
 
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/CMakeModules/Modules)
 

From 06d17f720234adefa05b4ae96bd173d280ff03cd Mon Sep 17 00:00:00 2001
From: Alex Richert <82525672+AlexanderRichert-NOAA@users.noreply.github.com>
Date: Thu, 7 Dec 2023 17:54:20 -0800
Subject: [PATCH 07/13] Update spack.yaml

---
 ci/spack.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/ci/spack.yaml b/ci/spack.yaml
index 3009df05a..400b7e06b 100644
--- a/ci/spack.yaml
+++ b/ci/spack.yaml
@@ -7,6 +7,8 @@
 # WARNING: Changing this file will automatically cause the cached Spack builds
 # in GitHub Actions to be regenerated, which takes a considerable amount of
 # time.
+#
+# Alex Richert, 6 Dec 2023
 spack:
   specs:
   - w3emc@2.10.0 precision=4,d,8

From ca9476729456a854081c78b90586220df8e8ab7f Mon Sep 17 00:00:00 2001
From: Brian Curtis <brian.curtis@noaa.gov>
Date: Mon, 11 Dec 2023 19:11:26 +0000
Subject: [PATCH 08/13] switch to use fms implementation of mpp

---
 io/module_wrt_grid_comp.F90 | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/io/module_wrt_grid_comp.F90 b/io/module_wrt_grid_comp.F90
index b59fe5e45..10df8b51d 100644
--- a/io/module_wrt_grid_comp.F90
+++ b/io/module_wrt_grid_comp.F90
@@ -29,7 +29,6 @@ module module_wrt_grid_comp
       use mpi
       use esmf
       use fms
-      use mpp_mod, only : mpp_init   ! needed for fms 2023.02
 
       use write_internal_state
       use module_fv3_io_def,   only : num_pes_fcst,                             &
@@ -254,7 +253,6 @@ subroutine wrt_initialize_p1(wrt_comp, imp_state_write, exp_state_write, clock,
       lprnt = lead_write_task == wrt_int_state%mype
 
       call fms_init(wrt_mpi_comm)
-      call mpp_init()
 
 !      print *,'in wrt, lead_write_task=', &
 !         lead_write_task,'last_write_task=',last_write_task, &
@@ -1337,7 +1335,7 @@ subroutine wrt_initialize_p1(wrt_comp, imp_state_write, exp_state_write, clock,
 
 ! save calendar_type (as integer) for use in 'coupler.res'
         if (index(trim(attNameList(i)),'time:calendar') > 0) then
-          select case( uppercase(trim(valueS)) )
+          select case( fms_mpp_uppercase(trim(valueS)) )
           case( 'JULIAN' )
               calendar_type = JULIAN
           case( 'GREGORIAN' )
@@ -1349,7 +1347,7 @@ subroutine wrt_initialize_p1(wrt_comp, imp_state_write, exp_state_write, clock,
           case( 'NO_CALENDAR' )
               calendar_type = NO_CALENDAR
           case default
-              call mpp_error ( FATAL, 'fcst_initialize: calendar must be one of '// &
+              call fms_mpp_error ( FATAL, 'fcst_initialize: calendar must be one of '// &
                                       'JULIAN|GREGORIAN|NOLEAP|THIRTY_DAY|NO_CALENDAR.' )
           end select
         endif

From 01bb3e28eca97bd43c66c82d513c10b993803bb3 Mon Sep 17 00:00:00 2001
From: Alex Richert <alexander.richert@noaa.gov>
Date: Thu, 4 Jan 2024 08:36:37 -0800
Subject: [PATCH 09/13] revert stoch phys name change

---
 CMakeLists.txt                                                  | 2 +-
 .../stochastic_physics_wrapper.F90                              | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename {stochastic_physics_wrapper => stochastic_physics}/stochastic_physics_wrapper.F90 (100%)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index f5d86663b..bd40d09df 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -87,7 +87,7 @@ add_library(fv3atm
   fv3_cap.F90
   module_fv3_config.F90
   module_fcst_grid_comp.F90
-  stochastic_physics_wrapper/stochastic_physics_wrapper.F90
+  stochastic_physics/stochastic_physics_wrapper.F90
   cpl/module_block_data.F90
   cpl/module_cplfields.F90
   cpl/module_cap_cpl.F90
diff --git a/stochastic_physics_wrapper/stochastic_physics_wrapper.F90 b/stochastic_physics/stochastic_physics_wrapper.F90
similarity index 100%
rename from stochastic_physics_wrapper/stochastic_physics_wrapper.F90
rename to stochastic_physics/stochastic_physics_wrapper.F90

From d0a7c24ed3d88eaa448712eeaee92230bdce5b88 Mon Sep 17 00:00:00 2001
From: Alex Richert <82525672+AlexanderRichert-NOAA@users.noreply.github.com>
Date: Thu, 4 Jan 2024 11:25:47 -0800
Subject: [PATCH 10/13] Update GCC.yml (remove fms recipe workaround)

---
 .github/workflows/GCC.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/GCC.yml b/.github/workflows/GCC.yml
index 2ecb122b7..c44711a1d 100644
--- a/.github/workflows/GCC.yml
+++ b/.github/workflows/GCC.yml
@@ -49,10 +49,6 @@ jobs:
       run: |
         wget --no-verbose https://github.com/spack/spack/archive/refs/heads/develop.zip
         unzip develop.zip -d ${GITHUB_WORKSPACE}/ &> unzip.out
-        # temporary fix (https://github.com/spack/spack/pull/41475)
-        wget https://raw.githubusercontent.com/AlexanderRichert-NOAA/spack/e9b6ada157a65a486eb1e039fdbfe66c9eebb842/var/spack/repos/builtin/packages/fms/package.py
-        mv package.py ${GITHUB_WORKSPACE}/spack-develop/var/spack/repos/builtin/packages/fms/package.py
-        #
         . ${GITHUB_WORKSPACE}/spack-develop/share/spack/setup-env.sh
         spack env create gcc${{ matrix.gcc_ver }} ${GITHUB_WORKSPACE}/fv3atm/ci/spack.yaml
         spack env activate gcc${{ matrix.gcc_ver }}

From b73d8046bd744f1d897096c27184451ad047f53d Mon Sep 17 00:00:00 2001
From: Alex Richert <alexander.richert@noaa.gov>
Date: Thu, 4 Jan 2024 12:18:46 -0800
Subject: [PATCH 11/13] rename stochastic_physics repo
 dir->stochastic_physics_repo

---
 .github/workflows/GCC.yml | 2 +-
 ci/CMakeLists.txt         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/GCC.yml b/.github/workflows/GCC.yml
index c44711a1d..a5f058340 100644
--- a/.github/workflows/GCC.yml
+++ b/.github/workflows/GCC.yml
@@ -73,7 +73,7 @@ jobs:
         spack load $(spack find --format "{name}")
         cd ${GITHUB_WORKSPACE}/fv3atm
         git clone https://github.com/NOAA-EMC/CMakeModules
-        git clone --recurse-submodules https://github.com/NOAA-PSL/stochastic_physics
+        git clone --recurse-submodules https://github.com/NOAA-PSL/stochastic_physics stochastic_physics_repo
         mkdir ${GITHUB_WORKSPACE}/build
         cd ${GITHUB_WORKSPACE}/build
         cmake ${GITHUB_WORKSPACE}/fv3atm -DBUILD_TESTING=ON ${{ matrix.cmake_opts }}
diff --git a/ci/CMakeLists.txt b/ci/CMakeLists.txt
index f64bceb8a..71412b3af 100644
--- a/ci/CMakeLists.txt
+++ b/ci/CMakeLists.txt
@@ -67,4 +67,4 @@ find_package(w3emc 2.9.2 REQUIRED)
 
 find_package(Python 3.6 REQUIRED COMPONENTS Interpreter)
 
-add_subdirectory(stochastic_physics)
+add_subdirectory(stochastic_physics_repo)

From 435f4d08f2017e4a44251a907b5d5052519487b0 Mon Sep 17 00:00:00 2001
From: Alex Richert <alexander.richert@noaa.gov>
Date: Thu, 4 Jan 2024 12:53:18 -0800
Subject: [PATCH 12/13] remove apt mpi installation

---
 .github/workflows/GCC.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/GCC.yml b/.github/workflows/GCC.yml
index a5f058340..a5f126e49 100644
--- a/.github/workflows/GCC.yml
+++ b/.github/workflows/GCC.yml
@@ -26,10 +26,6 @@ jobs:
 
     steps:
 
-    - name: install-mpi
-      run: |
-        sudo apt-get install lib${{ matrix.mpi }}-dev
-
     - name: checkout-fv3atm
       uses: actions/checkout@v3
       with:

From e993d1596395a37987d2f644d3f2c03a03862fe8 Mon Sep 17 00:00:00 2001
From: Alex Richert <alexander.richert@noaa.gov>
Date: Thu, 4 Jan 2024 13:02:29 -0800
Subject: [PATCH 13/13] increment cache key

---
 .github/workflows/GCC.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/GCC.yml b/.github/workflows/GCC.yml
index a5f126e49..3fb022bae 100644
--- a/.github/workflows/GCC.yml
+++ b/.github/workflows/GCC.yml
@@ -37,7 +37,7 @@ jobs:
       uses: actions/cache@v3
       with:
         path: ${{ github.workspace }}/spack-develop
-        key: spack-${{ hashFiles('fv3atm/ci/spack.yaml') }}-gcc${{ matrix.gcc_ver }}-1
+        key: spack-${{ hashFiles('fv3atm/ci/spack.yaml') }}-gcc${{ matrix.gcc_ver }}-2
 
     # Building dependencies takes 40+ min
     - name: spack-install
@@ -60,7 +60,7 @@ jobs:
       if: ${{ always() }}
       with:
         path: ${{ github.workspace }}/spack-develop
-        key: spack-${{ hashFiles('fv3atm/ci/spack.yaml') }}-gcc${{ matrix.gcc_ver }}-1
+        key: spack-${{ hashFiles('fv3atm/ci/spack.yaml') }}-gcc${{ matrix.gcc_ver }}-2
 
     - name: build-fv3atm
       run: |