Merge pull request #2255 from GEOS-ESM/feature/mathomp4/update-to-bas…

…elibs-7.14.0

Update to Baselibs 7.14.0 (ESMF 8.5.0, GFE 1.11.0)

.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 v7.13.0
+baselibs_version: &baselibs_version v7.14.0
 bcs_version: &bcs_version v11.1.0
 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:v7.13.0-openmpi_4.1.4-gcc_12.1.0
+      image: gmao/ubuntu20-geos-env-mkl:v7.14.0-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:v7.13.0-intelmpi_2021.6.0-intel_2022.1.0
+      image: gmao/ubuntu20-geos-env:v7.14.0-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

@@ -19,7 +19,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - sampling IODA file with trajectory sampler (step-1): make it run
 - Convert ExtData to use ESMF HConfig for YAML parsing rather than YaFYAML
   - Set required ESMF version to 8.5.0
-  - Add check in CMake to make sure ESMF version is at least 8.5.0b22 if using a beta snapshot
 - Add StationSamplerMod for station sampler
 - Added ReplaceMetadata message and method to replace oserver's metadata
 - Added field utilities to perform basic numeric operations on fields
@@ -29,23 +28,32 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- Updates to GFE library dependency
+  - Require gFTL v1.10.0
+  - Require gFTL-shared v1.6.1
+  - Require fArgParse v1.5.0
+  - Require pFlogger v1.9.5
+  - Removed yaFyaml as dependency
 - Updated programs using FLAP for command line parsing to use fArgParse instead
-- Updated `components.yaml` to match GEOSgcm v11.1.0
-  - ESMA_env v4.9.1 → v4.17.0
-    - Baselibs 7.13.0
-      - esmf v8.5.0b22
-      - GFE v1.10.0
-      - curl 8.1.1
+- Updated `components.yaml` to use Baselibs 7.14.0
+  - ESMA_env v4.9.1 → v4.19.0
+    - Baselibs 7.14.0
+      - esmf v8.5.0
+      - GFE v1.11.0
+      - curl 8.2.1
       - HDF5 1.10.10
       - netCDF-C 4.9.2
       - netCDF-Fortran 4.6.1
-      - CDO 2.2.0
-      - NCO 5.1.5
+      - CDO 2.2.1
+      - NCO 5.1.7
     - Move to MPT 2.28 at NAS, and other various changes for TOSS4 at NAS
-  - ESMA_cmake v3.28.0 → v3.29.0
+    - Remove Haswell from `build.csh`
+  - ESMA_cmake v3.28.0 → v3.31.0
     - Clean up for TOSS4 changes at NAS
+    - Add `QUIET_DEBUG` flag
+    - Suppress some common warnings with Intel Debug
 - Make the GEOSadas CI build separate as it often fails due to race conditions in GSI
-- Update CI to use BCs v11.1.0
+- Update CI to use BCs v11.1.0 and Baselibs 7.14.0
 - Updates to support building MAPL with spack instead of Baselibs
   - Add `FindESMF.cmake` file to `cmake` directory (as it can't easily be found via spack)
   - Move `CMAKE_MODULE_PATH` append statement up to find `FindESMF.cmake` before we `find_package(ESMF)`

CMakeLists.txt

@@ -73,38 +73,40 @@ message (STATUS "Building MAPL as ${MAPL_LIBRARY_TYPE} libraries")
 # This would then populate the target already leading to find_package()
 # errors.
 if(NOT TARGET GFTL::gftl)
-  # MAPL currently requires at least GFTL 1.5.1
-  find_package(GFTL 1.5.1 REQUIRED)
+  find_package(GFTL 1.10.0 REQUIRED)
 else()
-  if (GFTL_VERSION VERSION_LESS 1.5.1)
-    message(FATAL_ERROR "GFTL must be at least 1.5.1")
+  if (GFTL_VERSION VERSION_LESS 1.10.0)
+    message(FATAL_ERROR "gFTL must be at least 1.10.0")
   endif ()
 endif()
+message (STATUS "Found gFTL: ${GFTL_DIR} (found version ${GFTL_VERSION})")
+
 if(NOT TARGET GFTL_SHARED::gftl-shared)
-  find_package(GFTL_SHARED REQUIRED)
+  # MAPL currently requires at least gFTL-shared 1.6.1
+  find_package(GFTL_SHARED 1.6.1 REQUIRED)
+else ()
+  if (GFTL_SHARED_VERSION VERSION_LESS 1.6.1)
+    message(FATAL_ERROR "gFTL-shared must be at least 1.6.1")
+  endif ()
 endif()
+message (STATUS "Found gFTL-shared: ${GFTL_DIR} (found version ${GFTL_SHARED_VERSION})")
 
 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)
+    find_package(FARGPARSE 1.5.0 REQUIRED)
   else()
-    if (FARGPARSE_VERSION VERSION_LESS 1.4.1)
-      message(FATAL_ERROR "fArgParse must be at least 1.4.1")
+    if (FARGPARSE_VERSION VERSION_LESS 1.5.0)
+      message(FATAL_ERROR "fArgParse must be at least 1.5.0")
     endif ()
   endif()
+  message (STATUS "Building with fArgParse")
+  message (STATUS "Found fArgParse: ${FARGPARSE_DIR} (found version ${FARGPARSE_VERSION})")
 endif()
 
 option(USE_EXTDATA2G "Use ExtData2G" ON)
 if(USE_EXTDATA2G)
   set (EXTDATA2G_TARGET "MAPL.ExtData2G" CACHE STRING "ExtData2G Target")
-  if(NOT TARGET YAFYAML::yafyaml)
-    find_package(YAFYAML 1.0.4 REQUIRED)
-  else()
-    if (YAFYAML_VERSION VERSION_LESS 1.0.4)
-      message(FATAL_ERROR "yaFyaml must be at least 1.0.4")
-    endif ()
-  endif()
   message (STATUS "Building with ExtData2G")
 else()
   set (EXTDATA2G_TARGET "" CACHE STRING "ExtData2G Target")
@@ -113,12 +115,14 @@ endif()
 option(BUILD_WITH_PFLOGGER "Build MAPL with pFlogger library support" ON)
 if (BUILD_WITH_PFLOGGER)
   if(NOT TARGET PFLOGGER::pflogger)
-    find_package(PFLOGGER 1.9.1 REQUIRED)
+    find_package(PFLOGGER 1.9.5 REQUIRED)
   else()
-    if (PFLOGGER_VERSION VERSION_LESS 1.9.1)
-      message(FATAL_ERROR "pFlogger must be at least 1.9.1")
+    if (PFLOGGER_VERSION VERSION_LESS 1.9.5)
+      message(FATAL_ERROR "pFlogger must be at least 1.9.5")
     endif ()
   endif()
+  message (STATUS "Building with pFlogger")
+  message (STATUS "Found pFlogger: ${PFLOGGER_DIR} (found version ${PFLOGGER_VERSION})")
 endif()
 
 option(BUILD_WITH_FLAP "Use FLAP for command line processing" OFF)
@@ -168,30 +172,6 @@ else ()
   endif ()
 endif ()
 
-# Due to use of a feature of ESMF that came in with ESMF v8.5.0b22,
-# a beta version of ESMF, we need to make sure that if we are using
-# ESMF 8.5.0, that we are using at least ESMF 8.5.0b22. This is
-# a temporary fix until ESMF 8.5.0 final is released. Our criterion are:
-#  1. ESMF version is 8.5.0 (from ESMF_VERSION)
-#  2. We are using a beta snapshot of ESMF (from ESMF_BETA_RELEASE)
-#  3. The ESMF version is at least v8.5.0b22 (from ESMF_BETA_SNAPSHOT)
-
-if (ESMF_VERSION VERSION_EQUAL 8.5.0 AND ESMF_BETA_RELEASE)
-  # So now we are using a beta version of ESMF 8.5.0. We need to make sure
-  # that the version is at least 8.5.0b22. That version information
-  # is stored in ESMF_BETA_SNAPSHOT and is of the form "v8.5.0b22"
-  set (ESMF_BETA_SNAPSHOT_TARGET 22)
-  string(REGEX REPLACE "v8.5.0b([0-9]+)" "\\1" ESMF_BETA_SNAPSHOT_NUMBER ${ESMF_BETA_SNAPSHOT})
-  if (ESMF_BETA_SNAPSHOT_NUMBER LESS ESMF_BETA_SNAPSHOT_TARGET)
-    message(FATAL_ERROR
-      "ERROR! ESMF version must be at least v8.5.0b22, but you are using ${ESMF_BETA_SNAPSHOT}\n"
-      ""
-      "This is due to the use of a feature of ESMF that came in with ESMF v8.5.0b22, a beta version of ESMF.\n"
-      "This is a temporary fix until stable ESMF 8.5.0 is released.\n"
-      )
-  endif ()
-endif ()
-
 # We wish to add extra flags when compiling as Debug. We should only
 # do this if we are using esma_cmake since the flags are defined
 # there. Note that some flags like STANDARD_F18 might be available on

Ford/docs-with-remote-esmf.md

@@ -21,7 +21,6 @@ exclude_dir: ../Ford
              ../build
              ../gFTL
              ../esmf
-             ../yaFyaml
              ../pFUnit
              ../fArgParse
              ../pFlogger

Ford/docs-with-remote-esmf.public_private_protected.md

@@ -22,7 +22,6 @@ exclude_dir: ../Ford
              ../build
              ../gFTL
              ../esmf
-             ../yaFyaml
              ../pFUnit
              ../fArgParse
              ../pFlogger

components.yaml

@@ -5,13 +5,13 @@ MAPL:
 ESMA_env:
   local: ./ESMA_env
   remote: ../ESMA_env.git
-  tag: v4.17.0
+  tag: v4.19.0
   develop: main
 
 ESMA_cmake:
   local: ./ESMA_cmake
   remote: ../ESMA_cmake.git
-  tag: v3.29.0
+  tag: v3.31.0
   develop: develop
 
 ecbuild:

geom/CMakeLists.txt

@@ -30,7 +30,6 @@ endif ()
 
 esma_add_library(${this}
   SRCS ${srcs}
-#  DEPENDENCIES MAPL.oomph MAPL.shared MAPL.profiler MAPL.base YAFYAML::yafyaml PFLOGGER::pflogger GFTL_SHARED::gftl-shared-v2 GFTL::gftl-v2
   DEPENDENCIES MAPL.shared PFLOGGER::pflogger
   TYPE ${MAPL_LIBRARY_TYPE}
   )

gridcomps/ExtData2G/CMakeLists.txt

@@ -24,7 +24,7 @@ set (srcs
 
 
 esma_add_library (${this} SRCS ${srcs} DEPENDENCIES MAPL.shared MAPL.base MAPL.generic MAPL.griddedio TYPE SHARED)
-target_link_libraries (${this} PUBLIC GFTL::gftl GFTL_SHARED::gftl-shared YAFYAML::yafyaml esmf NetCDF::NetCDF_Fortran
+target_link_libraries (${this} PUBLIC GFTL::gftl GFTL_SHARED::gftl-shared esmf NetCDF::NetCDF_Fortran
                                PRIVATE MPI::MPI_Fortran)
 target_include_directories (${this} PUBLIC $<BUILD_INTERFACE:${MAPL_SOURCE_DIR}/include>)
 

gridcomps/ExtData2G/ExtDataAbstractFileHandler.F90

@@ -3,7 +3,6 @@
 #include "unused_dummy.H"
 module MAPL_ExtdataAbstractFileHandler
    use ESMF
-   use yafYaml
    use MAPL_KeywordEnforcerMod
    use MAPL_ExceptionHandling
    use MAPL_ExtDataBracket
@@ -28,7 +27,7 @@ module MAPL_ExtdataAbstractFileHandler
       type(ESMF_Time), allocatable :: valid_range(:)
       logical :: persist_closest
       contains
-         procedure :: initialize 
+         procedure :: initialize
          procedure :: make_metadata
          procedure :: get_time_on_file
          procedure(get_file_bracket), deferred :: get_file_bracket
@@ -48,7 +47,7 @@ subroutine get_file_bracket(this, input_time, source_time, bracket, fail_on_miss
       end subroutine get_file_bracket
 
    end interface
-   
+
 contains
 
    subroutine initialize(this,file_series,persist_closest,unusable,rc)
@@ -93,7 +92,7 @@ subroutine get_time_on_file(this,filename,target_time,bracketside,time_index,out
       type(ESMF_Time), allocatable :: time_series(:)
       logical :: in_bounds, found_time, wrap_
       integer :: i,num_times
-    
+
       _UNUSED_DUMMY(unusable)
       if (present(wrap)) then
          wrap_= .true.
@@ -105,7 +104,7 @@ subroutine get_time_on_file(this,filename,target_time,bracketside,time_index,out
          _RETURN(_SUCCESS)
       end if
 
-      call this%make_metadata(filename,file_metadata,_RC) 
+      call this%make_metadata(filename,file_metadata,_RC)
       call file_metadata%get_time_info(timeVector=time_series,_RC)
       num_times = size(time_series)
       found_time = .false.
@@ -120,14 +119,14 @@ subroutine get_time_on_file(this,filename,target_time,bracketside,time_index,out
                   exit
                end if
             enddo
-         else 
+         else
             if (wrap_) then
                output_time=time_series(num_times)
                time_index = num_times
                found_time = .true.
-               wrap = -1   
+               wrap = -1
             end if
-         end if         
+         end if
       else if (bracketside == 'R') then
          in_bounds = .not.(target_time >= time_series(num_times))
          if (in_bounds) then
@@ -139,12 +138,12 @@ subroutine get_time_on_file(this,filename,target_time,bracketside,time_index,out
                   exit
                end if
             enddo
-         else 
+         else
             if (wrap_) then
                output_time=time_series(1)
                time_index = 1
                found_time = .true.
-               wrap = 1   
+               wrap = 1
             end if
          end if
       else
@@ -161,11 +160,11 @@ subroutine make_metadata(this,file,metadata,rc)
       type(FileMetadataUtils), pointer, intent(inout)   :: metadata
       integer, optional,          intent(out  ) :: rc
       type(MAPLDataCollection), pointer :: collection => null()
- 
+
       Collection => DataCollections%at(this%collection_id)
       metadata => collection%find(file)
      _RETURN(_SUCCESS)
 
   end subroutine make_metadata
- 
+
 end module MAPL_ExtdataAbstractFileHandler

gridcomps/ExtData2G/ExtDataConfig.F90

@@ -1,7 +1,6 @@
 #include "MAPL_ErrLog.h"
 module MAPL_ExtDataConfig
    use ESMF
-   use yaFyaml
    use PFIO
    use gFTL_StringVector
    use MAPL_KeywordEnforcerMod
@@ -93,7 +92,7 @@ recursive subroutine new_ExtDataConfig_from_yaml(ext_config,config_file,current_
          hconfigIterEnd = ESMF_HConfigIterEnd(temp_configs)
          do while (ESMF_HConfigIterLoop(hconfigIter,hconfigIterBegin,hconfigIterEnd))
             hconfig_key = ESMF_HConfigAsStringMapKey(hconfigIter,_RC)
-            single_sample = ESMF_HConfigCreateAtMapVal(hconfigIter,_RC) 
+            single_sample = ESMF_HConfigCreateAtMapVal(hconfigIter,_RC)
             ts = ExtDataTimeSample(single_sample,_RC)
             call ext_config%sample_map%insert(trim(hconfig_key),ts)
          enddo
@@ -108,7 +107,7 @@ recursive subroutine new_ExtDataConfig_from_yaml(ext_config,config_file,current_
             hconfig_key = ESMF_HConfigAsStringMapKey(hconfigIter,_RC)
             temp_ds => ext_config%file_stream_map%at(hconfig_key)
             _ASSERT(.not.associated(temp_ds),"defined duplicate named collection")
-            single_collection = ESMF_HConfigCreateAtMapVal(hconfigIter,_RC) 
+            single_collection = ESMF_HConfigCreateAtMapVal(hconfigIter,_RC)
             ds = ExtDataFileStream(single_collection,current_time,_RC)
             call ext_config%file_stream_map%insert(trim(hconfig_key),ds)
          enddo
@@ -133,7 +132,7 @@ recursive subroutine new_ExtDataConfig_from_yaml(ext_config,config_file,current_
                   new_key = hconfig_key//rule_sep//i_char
                   call ext_config%add_new_rule(new_key,rule_map,multi_rule=.true.,_RC)
                enddo
-            else 
+            else
                _FAIL("Unsupported type")
             end if
          enddo
@@ -419,7 +418,7 @@ function has_rule_for(this,base_name,rc) result(found_rule)
             found_rule = (key(:rule_sep_loc-1) == base_name)
          else
             found_rule = (key == base_name)
-         end if 
+         end if
          if (found_rule) exit
          call iter%next()
       enddo