Improved macOS support via autoconf; GitHub CI

This patch modifies the autoconf configuration to provide better support
on Mac OS and other BSD-based systems.

Macros are included for the following operations:
* Detect if `sigsetjmp` (BSD) or `__sigsetjmp` (glibc; Linux) is
  available.
* Test the size of jmp_buf and sigjmp_buf

The "sensible" Linux defaults are still present, but autoconf should now
populate these variables when used.

A MacOS CI test for GitHub actions has also been included, but this
probably needs additional work.

.github/actions/macos-setup/action.yml

@@ -0,0 +1,79 @@
+name: 'Build-.testing-prerequisites'
+description: 'Build pre-requisites for .testing including FMS and a symmetric MOM6 executable'
+inputs:
+  build_symmetric:
+    description: 'If true, will build the symmetric MOM6 executable'
+    required: false
+    default: 'true'
+  install_python:
+    description: 'If true, will install the local python env needed for .testing'
+    required: false
+    default: 'true'
+runs:
+  using: 'composite'
+  steps:
+    - name: Git info
+      shell: bash
+      run: |
+        echo "::group::Git commit info"
+        echo "git log:"
+        git log | head -60
+        echo "::endgroup::"
+
+    - name: Env
+      shell: bash
+      run: |
+        echo "::group::Environment"
+        env
+        echo "::endgroup::"
+
+    - name: Install needed packages for compiling
+      shell: bash
+      run: |
+        echo "::group::Install packages"
+        brew update
+        brew install automake
+        brew install gfortran
+        brew install netcdf
+        brew install mpich
+        echo "::endgroup::"
+
+    - name: Compile FMS library
+      shell: bash
+      run: |
+        echo "::group::Compile FMS library"
+        cd .testing
+        make deps/lib/libFMS.a -s -j
+        echo "::endgroup::"
+
+    - name: Store compiler flags used in Makefile
+      shell: bash
+      run: |
+        echo "::group::config.mk"
+        cd .testing
+        echo "FCFLAGS_DEBUG=-g -O0 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
+        echo "FCFLAGS_REPRO=-g -O2 -fbacktrace" >> config.mk
+        echo "FCFLAGS_INIT=-finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
+        cat config.mk
+        echo "::endgroup::"
+
+    - name: Compile MOM6 in symmetric memory mode
+      shell: bash
+      run: |
+        echo "::group::Compile MOM6 in symmetric memory mode"
+        cd .testing
+        test ${{ inputs.build_symmetric }} == true && make build/symmetric/MOM6 -j
+        echo "::endgroup::"
+
+    - name: Install local python venv for generating input data
+      shell: bash
+      run: |
+        echo "::group::Create local python env for input data generation"
+        cd .testing
+        test ${{ inputs.install_python }} == true && make work/local-env
+        echo "::endgroup::"
+
+    - name: Set flags
+      shell: bash
+      run: |
+        echo "TIMEFORMAT=... completed in %lR  (user: %lU, sys: %lS)" >> $GITHUB_ENV

.github/workflows/macos.yml

@@ -0,0 +1,33 @@
+name: MacOS Stencil related verification
+
+on: [push, pull_request]
+
+jobs:
+  test-macos-symmetric-layout-rotation:
+
+    runs-on: macOS-latest
+
+    # TODO: Move these to the macos config file?
+    env:
+      CC: gcc-11
+      FC: gfortran-11
+
+    defaults:
+      run:
+        working-directory: .testing
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        submodules: recursive
+
+    - uses: ./.github/actions/macos-setup
+
+    - name: Compile MOM6 in asymmetric memory mode
+      run: make build/asymmetric/MOM6 -j
+
+    - name: Create validation data
+      run: make run.symmetric -k -s
+
+    - name: Run tests
+      run: make test.grid test.layout test.rotate -k -s

ac/configure.ac

@@ -147,9 +147,9 @@ AX_FC_CHECK_LIB([netcdff], [nf_create], [], [], [
   AC_PATH_PROG([NF_CONFIG], [nf-config])
   AS_IF([test -n "$NF_CONFIG"], [
     AC_SUBST([LDFLAGS],
-      ["$LDFLAGS -L$($NF_CONFIG --prefix)/lib"]
+      ["$LDFLAGS $($NF_CONFIG --flibs | cut -f1 -d" ")"]
     )
-    ], [AC_MSG_ERROR([Could not find nf-config.])]
+    ], [AC_MSG_ERROR([Could not find nf_create.])]
   )
   AX_FC_CHECK_LIB([netcdff], [nf_create], [], [], [
     AC_MSG_ERROR([Could not find libnetcdff.])
@@ -224,6 +224,29 @@ AC_COMPILE_IFELSE(
 )
 
 
+# setjmp verification
+AC_LANG_PUSH([C])
+
+# Verify that either sigsetjmp (POSIX) or __sigsetjmp (glibc) are available.
+AC_CHECK_FUNC([sigsetjmp])
+AS_IF([test "$ac_cv_func_sigsetjmp" == "yes"], [
+  SIGSETJMP_NAME="sigsetjmp"
+], [
+  AC_CHECK_FUNC([__sigsetjmp], [
+    SIGSETJMP_NAME="__sigsetjmp"
+  ], [
+    AC_MSG_ERROR([Could not find a symbol for sigsetjmp.])
+  ])
+])
+AC_DEFINE_UNQUOTED([SIGSETJMP_NAME], ["$SIGSETJMP_NAME"])
+
+# Determine the size of jmp_buf and sigjmp_buf
+AC_CHECK_SIZEOF([jmp_buf], [], [#include <setjmp.h>])
+AC_CHECK_SIZEOF([sigjmp_buf], [], [#include <setjmp.h>])
+
+AC_LANG_POP([C])
+
+
 # Search for mkmf build tools
 AC_PATH_PROG([LIST_PATHS], [list_paths])
 AS_IF([test -z "$LIST_PATHS"], [

src/framework/posix.F90

@@ -19,7 +19,7 @@ module posix
 !! and any information required to restore the process state.
 type, bind(c) :: jmp_buf
   private
-  character(kind=c_char) :: state(JMP_BUF_SIZE)
+  character(kind=c_char) :: state(SIZEOF_JMP_BUF)
     !< Unstructured array of bytes used to store the process state
 end type jmp_buf
 
@@ -28,7 +28,7 @@ module posix
 !! In addition to the content stored by `jmp_buf`, it also stores signal state.
 type, bind(c) :: sigjmp_buf
   private
-  character(kind=c_char) :: state(SIGJMP_BUF_SIZE)
+  character(kind=c_char) :: state(SIZEOF_SIGJMP_BUF)
     !< Unstructured array of bytes used to store the process state
 end type sigjmp_buf
 

src/framework/posix.h

@@ -3,13 +3,13 @@
 
 ! JMP_BUF_SIZE should be set to sizeof(jmp_buf).
 ! If unset, then use a typical glibc value (25 long ints)
-#ifndef JMP_BUF_SIZE
-#define JMP_BUF_SIZE 200
+#ifndef SIZEOF_JMP_BUF
+#define SIZEOF_JMP_BUF 200
 #endif
 
 ! If unset, assume jmp_buf and sigjmp_buf are equivalent (as in glibc).
-#ifndef SIGJMP_BUF_SIZE
-#define SIGJMP_BUF_SIZE JMP_BUF_SIZE
+#ifndef SIZEOF_SIGJMP_BUF
+#define SIZEOF_SIGJMP_BUF SIZEOF_JMP_BUF
 #endif
 
 ! glibc defines sigsetjmp as __sigsetjmp via macro readable from <setjmp.h>.