Merge pull request #30 from GEOS-ESM/feature/mathomp4/update-ctm-to-p…

…resent

Updates for CTM to Bring in-line with GCM v10.19.0

.circleci/config.yml

@@ -1,28 +1,63 @@
-version: 2
-jobs:
-  build:
+version: 2.1
+
+executors:
+  gcc-build-env:
     docker:
-      - image: gmao/geos-build-env-gcc-source:6.0.4
+      - image: gmao/ubuntu20-geos-env-mkl:v6.1.0-openmpi_4.0.5-gcc_10.2.0
+        auth:
+          username: $DOCKERHUB_USER
+          password: $DOCKERHUB_AUTH_TOKEN
+    environment:
+      OMPI_ALLOW_RUN_AS_ROOT: 1
+      OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
+      OMPI_MCA_btl_vader_single_copy_mechanism: none
+    resource_class: large
+    #MEDIUM# resource_class: medium
+
+workflows:
+  version: 2.1
+  build-test:
+    jobs:
+      - build-GEOSctm:
+          context:
+            - docker-hub-creds
+
+jobs:
+  build-GEOSctm:
+    executor: gcc-build-env
     working_directory: /root/project
     steps:
-      - checkout
+      - checkout:
+          path: GEOSctm
       - run:
           name: "Versions etc"
           command: mpirun --version && gfortran --version && echo $BASEDIR && pwd && ls
       - run:
           name: "Mepo clone external repos"
           command: |
-            mepo init
+            cd ${CIRCLE_WORKING_DIRECTORY}/GEOSctm
             mepo clone
             mepo status
+      - run:
+          name: "Mepo checkout-if-exists"
+          command: |
+            cd ${CIRCLE_WORKING_DIRECTORY}/GEOSctm
+            echo "${CIRCLE_BRANCH}"
+            if [ "${CIRCLE_BRANCH}" != "develop" ] && [ "${CIRCLE_BRANCH}" != "master" ] && [ "${CIRCLE_BRANCH}" != "main" ]
+            then
+               mepo checkout-if-exists ${CIRCLE_BRANCH}
+            fi
+            mepo status
       - run:
           name: "CMake"
           command: |
+            cd ${CIRCLE_WORKING_DIRECTORY}/GEOSctm
             mkdir build
             cd build
-            cmake .. -DBASEDIR=$BASEDIR/Linux -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_BUILD_TYPE=Debug
+            cmake .. -DBASEDIR=$BASEDIR/Linux -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_BUILD_TYPE=Debug -DUSE_F2PY=OFF
       - run:
           name: "Build"
           command: |
-            cd build
-            make -j2 install
+            cd ${CIRCLE_WORKING_DIRECTORY}/GEOSctm/build
+            make -j"$(nproc)" install
+            #MEDIUM# make -j4 install

.github/CODEOWNERS

@@ -3,6 +3,16 @@
 # Order is important; the last matching pattern takes the most
 # precedence.
 
+# Everything in GEOSgcm should be owned by the GCM Gatekeepers
+* @GEOS-ESM/ctm-gatekeepers
+
+# The GCM gatekeepers and CMake should know/approve these
+/.github/    @GEOS-ESM/cmake-team @GEOS-ESM/ctm-gatekeepers
+/.circleci/    @GEOS-ESM/cmake-team @GEOS-ESM/ctm-gatekeepers
+/.codebuild/    @GEOS-ESM/cmake-team @GEOS-ESM/ctm-gatekeepers
+
 # The GEOS CMake Team is the CODEOWNER for the CMakeLists.txt files in this repository
 CMakeLists.txt @GEOS-ESM/cmake-team
 
+# The GEOS CMake Team should be notified about and approve config changes
+/config/       @GEOS-ESM/cmake-team

.github/workflows/workflow.yml

@@ -0,0 +1,61 @@
+name: Build Tests
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+    # Do not run if the only files changed cannot affect the build
+    paths-ignore:
+      - "**.md"
+      - "parallel_build.csh"
+      - ".github/CODEOWNERS"
+      - ".codebuild/**"
+      - ".circleci/**"
+
+jobs:
+  build_ctm:
+    name: Build GEOSctm
+    if: "!contains(github.event.pull_request.labels.*.name, '0 diff trivial')"
+    runs-on: ubuntu-latest
+    container:
+      image: gmao/ubuntu20-geos-env-mkl:v6.1.0-openmpi_4.0.5-gcc_10.2.0
+      credentials:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+    env:
+      OMPI_ALLOW_RUN_AS_ROOT: 1
+      OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
+      OMPI_MCA_btl_vader_single_copy_mechanism: none
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+      - name: Checkout CTM
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 1
+      - name: Versions etc.
+        run: |
+          gfortran --version
+          mpirun --version
+          echo $BASEDIR
+      - name: Mepo clone external repos
+        run: |
+          mepo clone
+          mepo status
+          mepo status
+      - name: Update other branches
+        if:
+          "!contains('refs/heads/main,refs/heads/develop', github.ref)"
+        run: |
+          mepo checkout-if-exists ${GITHUB_HEAD_REF}
+          mepo status
+      - name: CMake
+        run: |
+          mkdir build
+          cd build
+          cmake .. -DBASEDIR=$BASEDIR/Linux -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_BUILD_TYPE=Debug -DMPIEXEC_PREFLAGS='--oversubscribe' -DUSE_F2PY=OFF
+      - name: Build
+        run: |
+          cd build
+          make -j4 install

.gitignore

@@ -1,9 +1,10 @@
 *~
 /@cmake/
-/@modules/
+/cmake/
+/cmake@/
 /@env/
-/BUILD/
-/build*/
-/install*/
-parallel_build.o*
+/env/
+/env@/
 /.mepo/
+parallel_build.o*
+log.*

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_policy (SET CMP0054 NEW)
 
 project (
   GEOSctm
-  VERSION 1.0
+  VERSION 2.0
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 if ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}")
@@ -25,9 +25,7 @@ set (DOING_GEOS5 YES)
 
 # Should find a better place for this - used in Chem component
 set (ACG_FLAGS -v)
-set (F2PYEXT .so)
-set (F2PY_SUFFIX .so)
-set (FV_PRECISION R8)
+set (FV_PRECISION "R8" CACHE STRING "Precision of FV3 core (R4, R4R8, R8)")
 
 list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/@cmake")
 include (esma)
@@ -44,3 +42,16 @@ include_directories(${MPI_Fortran_INCLUDE_PATH})
 add_subdirectory (@env)
 add_subdirectory (src)
 
+# https://www.scivision.dev/cmake-auto-gitignore-build-dir/
+# --- auto-ignore build directory
+if(NOT EXISTS ${PROJECT_BINARY_DIR}/.gitignore)
+  file(WRITE ${PROJECT_BINARY_DIR}/.gitignore "*")
+endif()
+
+# Piggyback that file into install
+install(
+   FILES ${PROJECT_BINARY_DIR}/.gitignore
+   DESTINATION ${CMAKE_INSTALL_PREFIX}
+   )
+
+

README.md

@@ -8,10 +8,9 @@
 
 In your `.bashrc` or `.tcshrc` or other rc file add a line:
 
-##### NCCS (SLES11)
-
+##### NCCS
 ```
-module use -a /discover/swdev/gmao_SIteam/modulefiles-SLES11
+module use -a /discover/swdev/gmao_SIteam/modulefiles-SLES12
 ```
 
 ##### NAS
@@ -33,19 +32,74 @@ Now load the `GEOSenv` module:
 ```
 module load GEOSenv
 ```
-which obtains the latest `git`, `CMake`, and `manage_externals` modules.
+which obtains the latest `git`, `CMake`, and `mepo` modules.
 
 #### Obtain the Model
 
+On GitHub, there are three ways to clone the model: SSH, HTTPS, or GitHub CLI.
+The first two are "git protocols" which determine how `git` communicates with
+GitHub: either through https or ssh. (The latter is a CLI that uses either ssh or
+https protocol underneath.)
+
+For developers of GEOS, the SSH git protocol is recommended as it can avoid some issues if
+[two-factor authentication
+(2FA)](https://docs.github.com/en/github/authenticating-to-github/securing-your-account-with-two-factor-authentication-2fa)
+is enabled on GitHub.
+
+##### SSH
+
+To clone the GEOSctm using the SSH url (starts with `[email protected]`), you run:
 ```
 git clone [email protected]:GEOS-ESM/GEOSctm.git
 ```
 
+###### Permission denied (publickey)
+
+If this is your first time using GitHub with any SSH URL, you might get this
+error:
+```
+Permission denied (publickey).
+fatal: Could not read from remote repository.
+
+Please make sure you have the correct access rights
+and the repository exists.
+```
+
+If you do see this, you need to [upload an ssh
+key](https://docs.github.com/en/github/authenticating-to-github/adding-a-new-ssh-key-to-your-github-account)
+to your GitHub account. This needs to be done on any machine that you want to
+use the SSH URL through.
+
+
+##### HTTPS
+
+To clone the model through HTTPS you run:
+
+```
+git clone https://github.com/GEOS-ESM/GEOSctm.git
+```
+
+Note that if you use the HTTPS URL and have 2FA set up on GitHub, you will need
+to use [personal access
+tokens](https://docs.github.com/en/github/authenticating-to-github/accessing-github-using-two-factor-authentication#authenticating-on-the-command-line-using-https)
+as a password.
+
+##### GitHub CLI
+
+You can also use the [GitHub CLI](https://cli.github.com/) with:
+```
+gh repo clone GEOS-ESM/GEOSctm
+```
+
+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.
+
 ---
 
 ### Single Step Building of the Model
 
-If all you wish is to build the model, you can run `parallel_build.csh` from a head node. Doing so will checkout all the external repositories of the model and build it. When done, the resulting model build will be found in `build/` and the installation will be found in `install/` with setup scripts like `gcm_setup` and `fvsetup` in `install/bin`.
+If all you wish is to build the model, you can run `parallel_build.csh` from a head node. Doing so will checkout all the external repositories of the model and build it. When done, the resulting model build will be found in `build/` and the installation will be found in `install/` with setup scripts like `ctm_setup` in `install/bin`.
 
 #### Debug Version of GEOS
 
@@ -57,12 +111,21 @@ To obtain a debug version, you can run `parallel_build.csh -debug` which will bu
 
 The steps detailed below are essentially those that `parallel_build.csh` performs for you. Either method should yield identical builds.
 
-##### Checkout externals
+#### Mepo
+
+The GEOS CTM is comprised of a set of sub-repositories. These are
+managed by a tool called [mepo](https://github.com/GEOS-ESM/mepo). To
+clone all the sub-repos, you can run `mepo clone` inside the fixture:
+
 ```
 cd GEOSctm
-checkout_externals
+mepo clone
 ```
 
+The first command initializes the multi-repository and the second one
+clones and assembles all the sub-repositories according to
+`components.yaml`
+
 #### Build the Model
 
 ##### Load Compiler, MPI Stack, and Baselibs
@@ -96,6 +159,14 @@ and CMake will install there.
 
 ##### Build and Install with Make
 ```
-make -j6 install
+make -jN install
 ```
+where `N` is the number of parallel processes. On discover head nodes, this should only be as high as 2 due to limits on the head nodes. On a compute node, you can set `N` has high as you like, though 8-12 is about the limit of parallelism in our model's make system.
 
+### Run the CTM
+
+Once the model has built successfully, you will have an `install/` directory in your checkout. To run `ctm_setup` go to the `install/bin/` directory and run it there:
+```
+cd install/bin
+./ctm_setup
+```