Merge pull request #1758 from GEOS-ESM/feature/mathomp4/1756-add-farg…

…parse

Fixes #1756. Add fArgParse CLI parser

.circleci/config.yml

@@ -16,7 +16,7 @@ parameters:
 
 # Anchors to prevent forgetting to update a version
 os_version: &os_version ubuntu20
-baselibs_version: &baselibs_version v7.6.1
+baselibs_version: &baselibs_version v7.7.0
 bcs_version: &bcs_version v10.23.0
 tag_build_arg_name: &tag_build_arg_name maplversion
 

.github/workflows/workflow.yml

@@ -17,7 +17,7 @@ jobs:
     name: Build and Test MAPL GNU
     runs-on: ubuntu-latest
     container:
-      image: gmao/ubuntu20-geos-env-mkl:v7.6.1-openmpi_4.1.4-gcc_12.1.0
+      image: gmao/ubuntu20-geos-env-mkl:v7.7.0-openmpi_4.1.4-gcc_12.1.0
       # 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
@@ -77,7 +77,7 @@ jobs:
     name: Build and Test MAPL Intel
     runs-on: ubuntu-latest
     container:
-      image: gmao/ubuntu20-geos-env:v7.6.1-intelmpi_2021.6.0-intel_2022.1.0
+      image: gmao/ubuntu20-geos-env:v7.7.0-intelmpi_2021.6.0-intel_2022.1.0
       # 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

CHANGELOG.md

@@ -9,11 +9,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- Add fArgParse CLI argument parser
 - Added subroutines for reading 4d integers in NetCDF4_FileFormatter
 - Added new option to allow for gaps in datasets ingested by ExtDataNG
 
 ### Changed
 
+- Updated to ESMA_cmake v3.21.0
+  - Adds support for a generic `x86_64` processor for GNU
+- Updated to ESMA_env v4.7.0
+   - Baselibs v7.6.0
+      - fArgParse v1.4.1
+      - pFUnit v4.6.1
 - Move to use GitHub Actions for label enforcement
 
 ### Fixed

CMakeLists.txt

@@ -82,8 +82,16 @@ endif()
 if(NOT TARGET GFTL_SHARED::gftl-shared)
   find_package(GFTL_SHARED REQUIRED)
 endif()
-if(NOT TARGET FARGPARSE::fargparse)
-  find_package(FARGPARSE QUIET)
+
+option(BUILD_WITH_FARGPARSE "Use fArgParse for command line processing" ON)
+if(BUILD_WITH_FARGPARSE)
+  if(NOT TARGET FARGPARSE::fargparse)
+    find_package(FARGPARSE 1.4.1 REQUIRED)
+  else()
+    if (FARGPARSE_VERSION VERSION_LESS 1.4.1)
+      message(FATAL_ERROR "fArgParse must be at least 1.4.1")
+    endif ()
+  endif()
 endif()
 
 option(USE_EXTDATA2G "Use ExtData2G" ON)

Tests/CMakeLists.txt

@@ -18,6 +18,7 @@ if (BUILD_WITH_FLAP)
   endif ()
   set_target_properties(ExtDataDriver.x PROPERTIES Fortran_MODULE_DIRECTORY ${MODULE_DIRECTORY})
   target_compile_definitions (ExtDataDriver.x PRIVATE $<$<BOOL:${USE_EXTDATA2G}>:BUILD_WITH_EXTDATA2G>)
+  add_subdirectory(ExtData_Testing_Framework EXCLUDE_FROM_ALL)
 
   ecbuild_add_executable (TARGET pfio_MAPL_demo.x SOURCES pfio_MAPL_demo.F90)
   target_link_libraries (pfio_MAPL_demo.x PRIVATE MAPL FLAP::FLAP esmf)
@@ -26,6 +27,17 @@ if (BUILD_WITH_FLAP)
     target_link_libraries(pfio_MAPL_demo.x PRIVATE OpenMP::OpenMP_Fortran)
   endif ()
   set_target_properties(pfio_MAPL_demo.x PROPERTIES Fortran_MODULE_DIRECTORY ${MODULE_DIRECTORY})
-  add_subdirectory(ExtData_Testing_Framework EXCLUDE_FROM_ALL)
+
+endif ()
+
+if (BUILD_WITH_FARGPARSE)
+
+  ecbuild_add_executable (TARGET MAPL_demo_fargparse.x SOURCES MAPL_demo_fargparse.F90)
+  target_link_libraries (MAPL_demo_fargparse.x PRIVATE MAPL FARGPARSE::fargparse esmf)
+  # CMake has an OpenMP issue with NAG Fortran: https://gitlab.kitware.com/cmake/cmake/-/issues/21280
+  if (NOT CMAKE_Fortran_COMPILER_ID MATCHES "NAG")
+    target_link_libraries(MAPL_demo_fargparse.x PRIVATE OpenMP::OpenMP_Fortran)
+  endif ()
+  set_target_properties(MAPL_demo_fargparse.x PROPERTIES Fortran_MODULE_DIRECTORY ${MODULE_DIRECTORY})
 
 endif ()

Tests/MAPL_demo_fargparse.F90

@@ -0,0 +1,80 @@
+!------------------------------------------------------------------------------
+!># Standalone Program for Testing fargparse
+!
+!------------------------------------------------------------------------------
+#define I_AM_MAIN
+#include "MAPL_ErrLog.h"
+#include "unused_dummy.H"
+
+program main
+      use MAPL
+      use mpi
+      use fargparse
+
+      implicit none
+
+      type(MAPL_FargparseCLI) :: cli
+      type(MAPL_CapOptions)   :: cap_options
+      integer :: status
+
+!------------------------------------------------------------------------------
+
+      call run(_RC)
+
+   contains
+
+#undef I_AM_MAIN
+#include "MAPL_ErrLog.h"
+      subroutine run(rc)
+
+         integer, intent(out), optional :: rc
+
+         integer :: status
+         character(len=:), allocatable :: input_file
+
+         call MPI_Init(status)
+         _VERIFY(status)
+
+         ! Read and parse the command line, and set parameters
+         ! If you have extra options you make a procedure as seen below and add arguments
+         ! there and pass in here
+         cli = MAPL_FargparseCLI(extra=extra_options)
+
+         ! This does the casting of arguments into cap_options for CAP
+         cap_options = MAPL_CapOptions(cli, _RC)
+
+         write(*,*) "done with MAPL_FargparseCLI"
+         write(*,*) "  cap_options%with_esmf_moab = ", cap_options%with_esmf_moab
+         write(*,*) "  cap_options%npes_input_server = ", cap_options%npes_input_server
+         write(*,*) "  cap_options%nodes_input_server = ", cap_options%nodes_input_server
+         write(*,*) "  cap_options%npes_output_server = ", cap_options%npes_output_server
+         write(*,*) "  cap_options%nodes_output_server = ", cap_options%nodes_output_server
+         write(*,*) "  cap_options%egress_file = ", cap_options%egress_file
+
+         ! For our extra options we have to explicitly cast them
+         call cast(cli%options%at('file'), input_file, _RC)
+
+         write(*,*) ""
+         write(*,*) "Extra arguments"
+         write(*,*) "  input file = ", input_file
+
+         _RETURN(_SUCCESS)
+
+      end subroutine run
+
+      subroutine extra_options(parser, rc)
+         type (ArgParser), intent(inout) :: parser
+         integer, intent(out), optional :: rc
+
+         call parser%add_argument('-f', '--file', &
+              help='A file to read', &
+              type='string', &
+              default='default.config', &
+              action='store')
+
+         !_RETURN(_SUCCESS)
+         if (present(rc)) rc = 0
+
+      end subroutine extra_options
+
+end program main

base/tests/test_sort.pf

@@ -1,34 +1,39 @@
-@test 
-subroutine test_mapl_sort
+module test_sort
    use pfunit
    use mapl_sortMod
    use iso_fortran_env, only: INT32, INT64
-   implicit none
-
-   integer(kind=INT64) :: a(5), c(5)
-   integer(kind=INT32) :: a4(5)
-   integer(kind=INT32) ::  b1(5,3), b2(3,5)
-   integer(kind=INT32) ::  d1(5,3)
-
-   integer :: i, j
-
-   a = [5,3,8,6,-7]
-   do j=1,3
-      b1(:,j) = a
-      b2(j,:) = a
-   enddo
-   a4 = a
-
-
-   C=A
-   d1=b1
-   call MAPL_SORT(C,d1,dim=1)
-
-   do j=1,3
-      do i = 2, size(d1,dim=1)
-         @assertTrue(d1(i-1,j) <= d1(i,j))
+
+contains
+
+   @test
+   subroutine test_mapl_sort
+      implicit none
+
+      integer(kind=INT64) :: a(5), c(5)
+      integer(kind=INT32) :: a4(5)
+      integer(kind=INT32) ::  b1(5,3), b2(3,5)
+      integer(kind=INT32) ::  d1(5,3)
+
+      integer :: i, j
+
+      a = [5,3,8,6,-7]
+      do j=1,3
+         b1(:,j) = a
+         b2(j,:) = a
+      enddo
+      a4 = a
+
+
+      C=A
+      d1=b1
+      call MAPL_SORT(C,d1,dim=1)
+
+      do j=1,3
+         do i = 2, size(d1,dim=1)
+            @assertTrue(d1(i-1,j) <= d1(i,j))
+         end do
       end do
-   end do
 
-end subroutine test_mapl_sort
+   end subroutine test_mapl_sort
 
+end module test_sort

components.yaml

@@ -5,16 +5,16 @@ MAPL:
 ESMA_env:
   local: ./ESMA_env
   remote: ../ESMA_env.git
-  tag: v4.7.0
+  tag: v4.8.0
   develop: main
 
 ESMA_cmake:
   local: ./ESMA_cmake
   remote: ../ESMA_cmake.git
-  tag: v3.20.0
+  tag: v3.21.0
   develop: develop
 
 ecbuild:
   local: ./ESMA_cmake/ecbuild
   remote: ../ecbuild.git
-  tag: geos/v1.2.0
+  tag: geos/v1.3.0

gridcomps/CMakeLists.txt

@@ -3,7 +3,8 @@ esma_add_library (${this}
      SRCS MAPL_GridComps.F90
      DEPENDENCIES MAPL.base MAPL.pfio MAPL_cfio_r4 MAPL.cap
                   $<$<BOOL:${BUILD_WITH_FLAP}>:FLAP::FLAP>
-     TYPE ${MAPL_LIBRARY_TYPE} 
+                  $<$<BOOL:${BUILD_WITH_FARGPARSE}>:FARGPARSE::fargparse>
+     TYPE ${MAPL_LIBRARY_TYPE}
      )
 
 target_include_directories (${this} PUBLIC
@@ -12,6 +13,10 @@ if (BUILD_WITH_FLAP)
   target_link_libraries(${this} PRIVATE FLAP::FLAP)
   target_compile_definitions (${this} PRIVATE USE_FLAP)
 endif()
+if (BUILD_WITH_FARGPARSE)
+  target_link_libraries(${this} PRIVATE FARGPARSE::fargparse)
+  target_compile_definitions (${this} PRIVATE USE_FARGPARSE)
+endif()
 
 add_subdirectory(Cap)
 add_subdirectory(History)

gridcomps/Cap/CMakeLists.txt

@@ -9,12 +9,17 @@ set (srcs
 if (BUILD_WITH_FLAP)
   list (APPEND srcs FlapCLI.F90)
 endif()
+if (BUILD_WITH_FARGPARSE)
+  list (APPEND srcs FargparseCLI.F90)
+endif()
 
 
 esma_add_library (${this} SRCS ${srcs} DEPENDENCIES MAPL.shared MAPL.constants MAPL.base MAPL.profiler MAPL.history
                   MAPL.ExtData ${EXTDATA2G_TARGET} TYPE ${MAPL_LIBRARY_TYPE})
 target_link_libraries (${this} PUBLIC GFTL::gftl GFTL_SHARED::gftl-shared esmf NetCDF::NetCDF_Fortran
-                               PRIVATE MPI::MPI_Fortran $<$<BOOL:${BUILD_WITH_FLAP}>:FLAP::FLAP>)
+                               PRIVATE MPI::MPI_Fortran
+                               $<$<BOOL:${BUILD_WITH_FLAP}>:FLAP::FLAP>
+                               $<$<BOOL:${BUILD_WITH_FARGPARSE}>:FARGPARSE::fargparse>)
 
 target_compile_definitions (${this} PRIVATE $<$<BOOL:${USE_EXTDATA2G}>:BUILD_WITH_EXTDATA2G>)
 
@@ -24,7 +29,6 @@ if (NOT CMAKE_Fortran_COMPILER_ID MATCHES "NAG")
 endif ()
 target_include_directories (${this} PUBLIC $<BUILD_INTERFACE:${MAPL_SOURCE_DIR}/include>)
 if (BUILD_WITH_FLAP)
-  target_link_libraries(${this} PRIVATE FLAP::FLAP)
   target_compile_definitions (${this} PRIVATE USE_FLAP)
 endif()
 

gridcomps/Cap/CapOptions.F90

@@ -28,7 +28,7 @@ module mapl_CapOptionsMod
       ! whether or not the nodes are padding with idle when mod(model total npes , each node npes) /=0
       logical              :: isolate_nodes = .true.
       ! whether or not copy the data before isend to the oserver
-      ! it is faster but demands more memory if it is true 
+      ! it is faster but demands more memory if it is true
       logical              :: fast_oclient  = .false.
       ! whether or not turn on the io profiler
       logical              :: with_io_profiler = .false.
@@ -59,7 +59,7 @@ function new_CapOptions(unusable, cap_rc_file, egress_file, ensemble_subdir_pref
       class (KeywordEnforcer), optional, intent(in) :: unusable
       character(*), optional, intent(in) :: cap_rc_file
       character(*), optional, intent(in) :: egress_file
-      character(*), optional, intent(in) :: ensemble_subdir_prefix 
+      character(*), optional, intent(in) :: ensemble_subdir_prefix
       type(ESMF_LogKind_Flag), optional, intent(in) :: esmf_logging_mode
 
       integer, optional, intent(out) :: rc