Gwd latr merge

.github/workflows/atlantis_basic_checks.yml

@@ -0,0 +1,32 @@
+name: Basic checks for CCPP physics schemes
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - release/*
+      - neptune
+    types: [opened, synchronize, reopened]
+
+jobs:
+  basic-checks:
+    #if: github.repository == 'NCAR/ccpp-physics' || github.repository == 'ufs-community/ccpp-physics'
+
+    #runs-on: macos-latest
+    runs-on: ['self-hosted','neptune-org-atlantis']
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+    - name: Init submodules
+      run: git submodule update --init --recursive
+    #- name: Update packages
+    #  run: |
+    #    /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
+    #    #brew install autoconf automake coreutils gcc@9 libtool mpich gnu-sed wget
+    #    brew install automake coreutils mpich gnu-sed
+    - name: Check for ASCII encoding
+      run: |
+        module use ${PWD}/modulefiles
+        module load atlantis/llvm-21.1.0
+        ./tools/check_encoding.py

.gitignore

@@ -1,2 +1,7 @@
 # Auto-generated include files in Fortran code
 *.inc
+
+# VIM swap files
+*.swp
+*.swo
+*.swn

.gitmodules

@@ -1,8 +1,8 @@
 [submodule "physics/Radiation/RRTMGP/rte-rrtmgp"]
   path = physics/Radiation/RRTMGP/rte-rrtmgp
-  url = https://github.com/NCAR/rte-rrtmgp
+  url = https://github.nrlmry.navy.mil/NEPTUNE/rte-rrtmgp
   branch = main
 [submodule "physics/MP/TEMPO/TEMPO"]
   path = physics/MP/TEMPO/TEMPO
-  url = https://github.com/NCAR/TEMPO
+  url = https://github.nrlmry.navy.mil/NEPTUNE/TEMPO
   branch = main

CMakeLists.txt

@@ -173,21 +173,33 @@ if(CMAKE_BUILD_TYPE STREQUAL "Release" AND (${CMAKE_Fortran_COMPILER_ID} STREQUA
     # Need to determine the name of the scheme with its path
     list(FILTER SCHEMES_TMP INCLUDE REGEX ".*${SCHEME_NAME}$")
     SET_SOURCE_FILES_PROPERTIES(${SCHEMES_TMP}
-                                APPEND_STRING PROPERTY COMPILE_FLAGS
-                                " ${CMAKE_Fortran_FLAGS_PHYSICS} ${OpenMP_Fortran_FLAGS} -O1")
+                                APPEND_STRING PROPERTY COMPILE_FLAGS " -O1")
   endforeach()
 endif()
 
 # No optimization for certain schemes when compiling with Intel in Release mode
 if(CMAKE_BUILD_TYPE STREQUAL "Release" AND (${CMAKE_Fortran_COMPILER_ID} STREQUAL "Intel" OR ${CMAKE_Fortran_COMPILER_ID} STREQUAL "IntelLLVM"))
   # Define a list of schemes that can't be optimized with Intel in Release mode
-  set(SCHEME_NAMES_NO_OPTIMIZATION GFS_typedefs.F90)
+  set(SCHEME_NAMES_NO_OPTIMIZATION aerinterp.F90
+                                   GFS_typedefs.F90)
   foreach(SCHEME_NAME IN LISTS SCHEME_NAMES_NO_OPTIMIZATION)
     set(SCHEMES_TMP ${SCHEMES})
     # Need to determine the name of the scheme with its path
     list(FILTER SCHEMES_TMP INCLUDE REGEX ".*${SCHEME_NAME}$")
     SET_SOURCE_FILES_PROPERTIES(${SCHEMES_TMP}
-                                APPEND_STRING PROPERTY COMPILE_FLAGS " ${CMAKE_Fortran_FLAGS_PHYSICS} ${OpenMP_Fortran_FLAGS} -O0")
+                                APPEND_STRING PROPERTY COMPILE_FLAGS " -O0")
+  endforeach()
+endif()
+
+if(${CMAKE_Fortran_COMPILER_ID} STREQUAL "GNU")
+  # Define a list of schemes that can't be compiled with GNU's range check
+  set(SCHEME_NAMES_NO_RANGE_CHECK mersenne_twister.f)
+  foreach(SCHEME_NAME IN LISTS SCHEME_NAMES_NO_RANGE_CHECK)
+    set(SCHEMES_TMP ${SCHEMES})
+    # Need to determine the name of the scheme with its path
+    list(FILTER SCHEMES_TMP INCLUDE REGEX ".*${SCHEME_NAME}$")
+    SET_SOURCE_FILES_PROPERTIES(${SCHEMES_TMP}
+                                APPEND_STRING PROPERTY COMPILE_FLAGS " -fno-range-check")
   endforeach()
 endif()
 
@@ -207,12 +219,12 @@ target_include_directories(ccpp_physics PUBLIC
 
 target_link_libraries(ccpp_physics PRIVATE MPI::MPI_Fortran)
 target_link_libraries(ccpp_physics PUBLIC w3emc::w3emc_d
-                                          sp::sp_d
-                                          NetCDF::NetCDF_Fortran
-				             )
-#add FMS for FV3 only
-if(FV3 OR MPAS)
-  target_link_libraries(ccpp_physics PUBLIC fms)
+                                          NetCDF::NetCDF_Fortran)
+target_link_libraries(ccpp_physics PRIVATE ESMF::ESMF)
+
+if(HA_PHYSICS)
+  target_link_libraries(ccpp_physics PRIVATE msis)
+  target_link_libraries(ccpp_physics PRIVATE iri)
 endif()
 
 # Define where to install the library

modulefiles/atlantis/llvm-21.1.0

@@ -0,0 +1,26 @@
+#%Module
+#
+# neptune-atmos wrapper module
+#
+
+proc ModulesHelp {} {
+    puts -nonewline stderr "Load neptune-atmos environment on Atlantis for spack-stack with clang-21.1.0"
+}
+
+module-whatis "neptune-atmos environment"
+
+# Conflicts
+conflict atlantis
+
+# Prerequisite modules
+module purge
+prepend-path MODULEPATH /gpfs/neptune/spack-stack/llvm-21.1.0/modulefiles
+prepend-path MODULEPATH /gpfs/neptune/spack-stack/openmpi-4.1.8/llvm-21.1.0/modulefiles
+module load slurm
+
+# spack-stack modules
+prepend-path MODULEPATH /gpfs/neptune/spack-stack/spack-stack-2.0.0/envs/ne-clang-21.1.0/modules/Core
+module load stack-llvm/21.1.0
+module load stack-openmpi/4.1.8
+module load python/3.11.11
+module load cmake/3.31.8

physics/CONV/Grell_Freitas/cu_gf_deep.F90

@@ -1375,8 +1375,9 @@ subroutine cu_gf_deep_run(        &
       tau_ecmwf    (:) = 0.
 !$acc end kernels
       !- way to calculate the fraction of cape consumed by shallow convection
-      !iversion=1 ! ecmwf
-      iversion=0 ! orig
+!NRL?
+      iversion=1 ! ecmwf
+      !iversion=0 ! orig
       !
       ! betchold et al 2008 time-scale of cape removal
 !
@@ -2534,7 +2535,7 @@ subroutine fct1d3 (ktop,n,dt,z,tracr,massflx,trflx_in,dellac,g)
 !       'final', tracr(k)-(trflx_out(k+1)-trflx_out(k))*dtovdz(k)
 ! 99    format ('(trc1d)   k =',i4/(3(a13,'=',es13.6)))
 !     end do
-     if (error) stop '(fct1d error)'
+     if (error) call ccpp_external_abort('(fct1d error)')
    end if
 #endif
 

physics/GWD/cires_tauamf_data.F90

@@ -4,6 +4,7 @@
 module cires_tauamf_data
 
   use machine, only: kind_phys
+  use mpi_f08
 !...........................................................................................
 ! tabulated GW-sources: GRACILE/Ern et al., 2018 and/or Resolved GWs from C384-Annual run
 !...........................................................................................
@@ -20,27 +21,28 @@ module cires_tauamf_data
 contains
 
 !>
-   subroutine read_tau_amf(me, master, errmsg, errflg)
+   subroutine read_tau_amf(mpicomm, mpirank, mpiroot, errmsg, errflg)
 
-    use  netcdf
-    integer, intent(in) ::  me, master   
+    use netcdf
+    use mpiutil, only: ccpp_bcast
+    type(MPI_Comm), intent(in) :: mpicomm
+    integer, intent(in) :: mpirank, mpiroot
     integer :: ncid,  iernc, vid, dimid, status         
     integer :: k
 
     character(len=*), intent(out) :: errmsg
     integer,          intent(out) :: errflg    
 !
-      
-      iernc=NF90_OPEN(trim(ugwp_taufile), nf90_nowrite, ncid)
+    read_and_broadcast_1: if (mpirank==mpiroot) then
+       iernc=NF90_OPEN(trim(ugwp_taufile), nf90_nowrite, ncid)
 
        if(iernc.ne.0) then         
           write(errmsg,'(*(a))') "read_tau_amf: cannot open file_limb_tab data-file ",  &
                                     trim(ugwp_taufile)
           print *, 'cannot open ugwp-v1 tau-file=',trim(ugwp_taufile)
           errflg = 1
           return
-        else
-
+       endif
 
        status = nf90_inq_dimid(ncid, "lat", DimID)
 !      if (status /= nf90_noerr) call handle_err(status)
@@ -50,28 +52,36 @@ subroutine read_tau_amf(me, master, errmsg, errflg)
        status = nf90_inq_dimid(ncid, "days", DimID)
        status = nf90_inquire_dimension(ncid, DimID,  len =ntau_d2t )
 
-           if (me == master)  print *, ntau_d1y, ntau_d2t, ' dimd of tau_ngw ugwp-v1 '
-           if (ntau_d2t .le. 0 .or. ntau_d1y .le. 0) then 
-               print *, 'ugwp-v1 tau-file=',    trim(ugwp_taufile)
-               print *, '  ugwp-v1: ', 'ntau_d2t=',ntau_d2t, 'ntau_d2t=',ntau_d1y
-               stop
-           endif
-
-        if (.not.allocated(ugwp_taulat))  allocate (ugwp_taulat(ntau_d1y ))
-        if (.not.allocated(days_limb))    allocate (days_limb(ntau_d2t))
-        if (.not.allocated(tau_limb))     allocate (tau_limb(ntau_d1y, ntau_d2t ))
-
-        iernc=nf90_inq_varid( ncid, 'DAYS', vid )
-        iernc= nf90_get_var( ncid, vid, days_limb)
-        iernc=nf90_inq_varid( ncid, 'LATS', vid )
-        iernc= nf90_get_var( ncid, vid, ugwp_taulat)
-        iernc=nf90_inq_varid( ncid, 'ABSMF', vid )
-        iernc= nf90_get_var( ncid, vid, tau_limb)
-
-        iernc=nf90_close(ncid)
-
-        endif
-
+       print *, ntau_d1y, ntau_d2t, ' dimd of tau_ngw ugwp-v1 '
+       if (ntau_d2t .le. 0 .or. ntau_d1y .le. 0) then 
+          print *, 'ugwp-v1 tau-file=',    trim(ugwp_taufile)	   
+          print *, '  ugwp-v1: ', 'ntau_d2t=',ntau_d2t, 'ntau_d2t=',ntau_d1y
+          errflg = 1
+          return
+       endif
+    endif read_and_broadcast_1
+
+    call ccpp_bcast(ntau_d1y, mpiroot, mpicomm, errflg)
+    call ccpp_bcast(ntau_d2t, mpiroot, mpicomm, errflg)
+
+    if (.not.allocated(ugwp_taulat))  allocate (ugwp_taulat(ntau_d1y ))
+    if (.not.allocated(days_limb))    allocate (days_limb(ntau_d2t))
+    if (.not.allocated(tau_limb))     allocate (tau_limb(ntau_d1y, ntau_d2t ))   	   
+
+    read_and_broadcast_2: if (mpirank==mpiroot) then
+      iernc=nf90_inq_varid( ncid, 'DAYS', vid )
+      iernc= nf90_get_var( ncid, vid, days_limb)
+      iernc=nf90_inq_varid( ncid, 'LATS', vid )
+      iernc= nf90_get_var( ncid, vid, ugwp_taulat)
+      iernc=nf90_inq_varid( ncid, 'ABSMF', vid )
+      iernc= nf90_get_var( ncid, vid, tau_limb)
+      iernc=nf90_close(ncid)
+    endif read_and_broadcast_2
+
+    call ccpp_bcast(days_limb,   mpiroot, mpicomm, errflg)
+    call ccpp_bcast(tau_limb,    mpiroot, mpicomm, errflg)
+    call ccpp_bcast(ugwp_taulat, mpiroot, mpicomm, errflg)
+
   end  subroutine read_tau_amf  
 
 !>
@@ -153,7 +163,7 @@ subroutine tau_amf_interp(me, master, im, idate, fhour, j1_tau,j2_tau, ddy_j1, d
           print *, ' Error in time-interpolation for tau_amf_interp '
           print *, ' it1, it2, ntau_d2t ', it1, it2, ntau_d2t
           print *, ' Error in time-interpolation see cires_tauamf_data.F90 '
-          stop
+          call ccpp_external_abort('')
          endif
 
          w2 = (fddd-days_limb(it1))/(days_limb(it2)-days_limb(it1))

physics/GWD/cires_ugwp.F90

@@ -82,8 +82,15 @@ subroutine cires_ugwp_init (me, master, nlunit, input_nml_file, logunit, &
 
     if (do_ugwp .or. cdmbgwd(3) > 0.0) then
       call cires_ugwpv0_mod_init (me, master, nlunit, input_nml_file, logunit, &
+<<<<<<< HEAD
                                 fn_nml2, lonr, levs, ak, bk, con_p0, dtp, &
                                 cdmbgwd(1:2), cgwf, pa_rf_in, tau_rf_in)
+=======
+                                fn_nml2, lonr, latr, levs, ak, bk, con_p0, dtp, &
+                                cdmbgwd(1:2), cgwf, pa_rf_in, tau_rf_in, &
+                                errmsg, errflg)
+      if (errflg/=0) return
+>>>>>>> neptune
     else
       write(errmsg,'(*(a))') "Logic error: cires_ugwp_init called but do_ugwp is false and cdmbgwd(3) <= 0"
       errflg = 1