alarms based on nsteps

cime_config/buildnml

@@ -50,7 +50,10 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
     config["continue_run"] = ".true." if case.get_value("CONTINUE_RUN") else ".false."
     config["flux_epbal"] = "ocn" if case.get_value("CPL_EPBAL") == "ocn" else "off"
     config["mask_grid"] = case.get_value("MASK_GRID")
-    config["rest_option"] = case.get_value("REST_OPTION")
+    for val in ("HIST", "REST", "STOP"):
+        config[val.lower()+"_option"] = case.get_value(val+"_OPTION")
+
+
     config["comp_ocn"] = case.get_value("COMP_OCN")
 
     atm_grid = case.get_value("ATM_GRID")
@@ -199,6 +202,19 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
             coupling_times[comp.lower() + "_cpl_dt"] = cpl_dt
             mindt = min(mindt, cpl_dt)
 
+    # Here we convert "nsteps" to "nseconds", this simplifies the fortran
+
+    for val in ("REST", "HIST", "STOP"):
+        if case.get_value(val+"_OPTION") == "nsteps":
+            nsteps = case.get_value(val+"_N")
+            if val == "REST":
+                nmlgen.set_value("restart_n", value=mindt*nsteps)
+            elif val == "HIST":
+                nmlgen.set_value("history_n", value=mindt*nsteps)
+            else:
+                nmlgen.set_value("stop_n", value=mindt*nsteps)
+
+
     # sanity check
     comp_atm = case.get_value("COMP_ATM")
     if comp_atm is not None and comp_atm not in ("datm", "xatm", "satm"):
@@ -305,7 +321,7 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
 
     for item in case.get_values("COMP_CLASSES"):
         comp = case.get_value("COMP_" + item)
-        if case.get_value(f"PIO_ASYNC_INTERFACE", {"compclass":item}):
+        if case.get_value("PIO_ASYNC_INTERFACE", {"compclass":item}):
             asyncio = True
 
         valid = True
@@ -608,8 +624,6 @@ def buildnml(case, caseroot, component):
     if component != "drv":
         raise AttributeError
 
-    #   Do a check here of ESMF VERSION, requires 8.1.0 or newer (8.2.0 or newer for esmf_aware_threading)
-    esmf_aware_threading = case.get_value("ESMF_AWARE_THREADING")
     esmfmkfile = os.getenv("ESMFMKFILE")
     expect(
         esmfmkfile and os.path.isfile(esmfmkfile),
@@ -623,7 +637,7 @@ def buildnml(case, caseroot, component):
                 major = line[-2] if "MAJOR" in line else major
                 minor = line[-2] if "MINOR" in line else minor
         logger.debug("ESMF version major {} minor {}".format(major, minor))
-        expect(int(major) >= 8 and int(minor) >=4, "ESMF version should be 8.4.1 or newer")
+        expect(int(major) >= 8 and int(minor) >=6, "ESMF version should be 8.6.1 or newer")
 
     confdir = os.path.join(case.get_value("CASEBUILD"), "cplconf")
     if not os.path.isdir(confdir):

cime_config/config_component.xml

@@ -334,7 +334,7 @@
     <group>run_begin_stop_restart</group>
     <file>env_run.xml</file>
     <desc>
-      Run start time-of-day
+      Run start time-of-day, units are seconds with values from 0 to 86400.
     </desc>
   </entry>
 

cime_config/namelist_definition_drv.xml

@@ -233,17 +233,15 @@
     </values>
   </entry>
 
-  <!-- =========================================== -->
-  <!-- All components orbital attributes           -->
-  <!-- =========================================== -->
-
+  <!-- not yet fully implemented, set to false -->
   <entry id="write_restart_at_endofrun">
     <type>logical</type>
     <category>nuopc</category>
     <group>ALLCOMP_attributes</group>
     <values>
       <value>.false.</value>
-      <value rest_option="end">.true.</value>
+      <value rest_option='none'>.false.</value>
+      <value rest_option='never'>.false.</value>
     </values>
   </entry>
 
@@ -256,6 +254,10 @@
     </values>
   </entry>
 
+  <!-- =========================================== -->
+  <!-- All components orbital attributes           -->
+  <!-- =========================================== -->
+
   <entry id="orb_mode">
     <type>char</type>
     <category>orbital</category>
@@ -1117,13 +1119,12 @@
     <type>char</type>
     <category>time</category>
     <group>ALLCOMP_attributes</group>
-    <valid_values>none,never,nsteps,nseconds,nminutes,nhours,ndays,nmonths,nyears,monthly,yearly,date,end</valid_values>
+    <valid_values>none,never,nseconds,nminutes,nhours,ndays,nmonths,nyears,monthly,yearly,date,end</valid_values>
     <desc>
       mediator history snapshot option (used with history_n and history_ymd)
       set by HIST_OPTION in env_run.xml.
       history_option alarms are:
       [none/never], turns option off
-      [nsteps]   , history snapshot every history_n nsteps  , relative to current run start time
       [nseconds] , history snapshot every history_n nseconds, relative to current run start time
       [nminutes] , history snapshot every history_n nminutes, relative to current run start time
       [nhours]   , history snapshot every history_n nhours  , relative to current run start time
@@ -1136,6 +1137,7 @@
     </desc>
     <values>
       <value>$HIST_OPTION</value>
+      <value hist_option="nsteps">nseconds</value>
     </values>
   </entry>
 
@@ -2720,12 +2722,11 @@
     <type>char</type>
     <category>time</category>
     <group>CLOCK_attributes</group>
-    <valid_values>none,never,nsteps,nseconds,nminutes,nhours,ndays,monthly,nmonths,nyears,date,end</valid_values>
+    <valid_values>none,never,nseconds,nminutes,nhours,ndays,monthly,nmonths,nyears,date,end</valid_values>
     <desc>
       sets the run length with stop_n and stop_ymd
       stop_option alarms are:
       [none/never] , turns option off
-      [nsteps]     , stops every stop_n nsteps  , relative to current run start time
       [nseconds]   , stops every stop_n nseconds, relative to current run start time
       [nminutes]   , stops every stop_n nminutes, relative to current run start time
       [nhours]     , stops every stop_n nhours  , relative to current run start time
@@ -2739,6 +2740,7 @@
     </desc>
     <values>
       <value>$STOP_OPTION</value>
+      <value stop_option='nsteps'>nseconds</value>
     </values>
   </entry>
 
@@ -2784,12 +2786,11 @@
     <type>char</type>
     <category>time</category>
     <group>CLOCK_attributes</group>
-    <valid_values>none,never,nsteps,nseconds,nminutes,nhours,ndays,nmonths,nyears,monthly,yearly,date,end</valid_values>
+    <valid_values>none,never,nseconds,nminutes,nhours,ndays,nmonths,nyears,monthly,yearly,date,end</valid_values>
     <desc>
       sets the restart frequency with restart_n and restart_ymd
       restart_option alarms are:
       [none/never], turns option off
-      [nsteps]   , restarts every restart_n nsteps  , relative to current run start time
       [nseconds] , restarts every restart_n nseconds, relative to current run start time
       [nminutes] , restarts every restart_n nminutes, relative to current run start time
       [nhours]   , restarts every restart_n nhours  , relative to current run start time
@@ -2803,6 +2804,7 @@
     </desc>
     <values>
       <value>$REST_OPTION</value>
+      <value rest_option="nsteps">nseconds</value>
     </values>
   </entry>
 

cime_config/runseq/driver_config.py

@@ -64,7 +64,7 @@ def __compute_glc(self, case, coupling_times):
         # However will still need to call the exchange at the end if the stop_option
         # is nsteps or days - or otherwise just every ndays
         # Note that nsteps is the minimum component coupling time
-        if (comp_glc == 'cism'):
+        if comp_glc == 'cism':
             glc_coupling_time = coupling_times["glc_cpl_dt"]
             if not case.get_value("CISM_EVOLVE"):
                 stop_option = case.get_value('STOP_OPTION')
@@ -77,15 +77,7 @@ def __compute_glc(self, case, coupling_times):
                     glc_coupling_time = stop_n * 86400
                 else:
                     glc_coupling_time = 86400
-        elif (comp_glc == 'dglc'):
-            glc_coupling_time = coupling_times["glc_cpl_dt"]
-            is_test = case.get_value("TEST")
-            if not is_test:
-                stop_option = case.get_value('STOP_OPTION')
-                if stop_option == 'nsteps':
-                    stop_n = case.get_value('STOP_N')
-                    glc_coupling_time = stop_n*coupling_times["atm_cpl_dt"]
-        elif (comp_glc == 'xglc'):
+        elif comp_glc == 'dglc' or comp_glc == 'xglc':
             glc_coupling_time = coupling_times["glc_cpl_dt"]
         else:
             glc_coupling_time = 0

mediator/CMakeLists.txt

@@ -4,7 +4,7 @@ set(SRCFILES esmFldsExchange_cesm_mod.F90 med_fraction_mod.F90
               med_methods_mod.F90 med_phases_prep_ice_mod.F90
               med_phases_restart_mod.F90 esmFldsExchange_hafs_mod.F90
               med_internalstate_mod.F90 med_phases_aofluxes_mod.F90
-              med_phases_prep_lnd_mod.F90 med_time_mod.F90
+              med_phases_prep_lnd_mod.F90
               esmFldsExchange_ufs_mod.F90 med_io_mod.F90
               med_phases_history_mod.F90 med_phases_prep_ocn_mod.F90
               med_utils_mod.F90 esmFlds.F90 med_kind_mod.F90

mediator/Makefile

@@ -39,7 +39,7 @@ esmFldsExchange_hafs_mod.o : med_kind_mod.o med_methods_mod.o esmFlds.o med_inte
 med.o : med_kind_mod.o med_phases_profile_mod.o med_utils_mod.o med_phases_prep_rof_mod.o med_phases_aofluxes_mod.o \
    med_phases_prep_ice_mod.o med_fraction_mod.o med_map_mod.o med_constants_mod.o med_phases_prep_wav_mod.o \
    med_phases_prep_lnd_mod.o med_phases_history_mod.o med_phases_ocnalb_mod.o med_phases_restart_mod.o \
-   med_time_mod.o med_internalstate_mod.o med_phases_prep_atm_mod.o esmFldsExchange_cesm_mod.o esmFldsExchange_ufs_mod.o \
+   med_internalstate_mod.o med_phases_prep_atm_mod.o esmFldsExchange_cesm_mod.o esmFldsExchange_ufs_mod.o \
    esmFldsExchange_hafs_mod.o med_phases_prep_glc_mod.o esmFlds.o med_io_mod.o med_methods_mod.o med_phases_prep_ocn_mod.o \
    med_phases_post_atm_mod.o med_phases_post_ice_mod.o med_phases_post_lnd_mod.o med_phases_post_glc_mod.o med_phases_post_rof_mod.o \
    med_phases_post_wav_mod.o
@@ -50,7 +50,7 @@ med_map_mod.o : med_kind_mod.o med_internalstate_mod.o med_constants_mod.o med_m
 med_merge_mod.o : med_kind_mod.o med_constants_mod.o med_internalstate_mod.o esmFlds.o med_methods_mod.o med_utils_mod.o
 med_methods_mod.o : med_kind_mod.o med_utils_mod.o med_constants_mod.o
 med_phases_aofluxes_mod.o : med_kind_mod.o med_utils_mod.o med_map_mod.o med_constants_mod.o med_internalstate_mod.o esmFlds.o med_methods_mod.o
-med_phases_history_mod.o : med_kind_mod.o med_utils_mod.o med_time_mod.o med_internalstate_mod.o med_constants_mod.o med_map_mod.o med_methods_mod.o med_io_mod.o esmFlds.o
+med_phases_history_mod.o : med_kind_mod.o med_utils_mod.o med_internalstate_mod.o med_constants_mod.o med_map_mod.o med_methods_mod.o med_io_mod.o esmFlds.o
 med_phases_ocnalb_mod.o : med_kind_mod.o med_utils_mod.o med_map_mod.o med_constants_mod.o med_internalstate_mod.o esmFlds.o med_methods_mod.o
 med_phases_prep_atm_mod.o : med_kind_mod.o esmFlds.o med_methods_mod.o med_merge_mod.o med_map_mod.o med_constants_mod.o med_phases_ocnalb_mod.o med_internalstate_mod.o med_utils_mod.o
 med_phases_prep_glc_mod.o : med_kind_mod.o med_utils_mod.o med_internalstate_mod.o med_map_mod.o med_constants_mod.o med_methods_mod.o esmFlds.o
@@ -68,6 +68,5 @@ med_phases_post_rof_mod.o : med_kind_mod.o esmFlds.o med_methods_mod.o med_map_m
 med_phases_post_wav_mod.o : med_kind_mod.o esmFlds.o med_methods_mod.o med_map_mod.o med_constants_mod.o med_internalstate_mod.o med_utils_mod.o
 med_phases_profile_mod.o : med_kind_mod.o med_utils_mod.o med_constants_mod.o med_internalstate_mod.o med_time_mod.o
 med_phases_restart_mod.o : med_kind_mod.o med_utils_mod.o med_constants_mod.o med_internalstate_mod.o esmFlds.o med_io_mod.o
-med_time_mod.o : med_kind_mod.o med_utils_mod.o med_constants_mod.o
 med_utils_mod.o : med_kind_mod.o
-med_diag_mod.o : med_kind_mod.o med_time_mod.o med_utils_mod.o med_methods_mod.o med_internalstate_mod.o
+med_diag_mod.o : med_kind_mod.o med_utils_mod.o med_methods_mod.o med_internalstate_mod.o

mediator/med.F90

@@ -38,7 +38,6 @@ module MED
   use med_methods_mod          , only : FB_getFieldN       => med_methods_FB_getFieldN
   use med_methods_mod          , only : clock_timeprint    => med_methods_clock_timeprint
   use med_utils_mod            , only : memcheck           => med_memcheck
-  use med_time_mod             , only : med_time_alarmInit
   use med_internalstate_mod    , only : InternalState, med_internalstate_init, med_internalstate_coupling
   use med_internalstate_mod    , only : med_internalstate_defaultmasks, logunit, maintask
   use med_internalstate_mod    , only : ncomps, compname
@@ -2261,7 +2260,9 @@ subroutine SetRunClock(gcomp, rc)
     use ESMF                  , only : ESMF_ClockGetAlarmList
     use NUOPC                 , only : NUOPC_CompCheckSetClock, NUOPC_CompAttributeGet
     use NUOPC_Mediator        , only : NUOPC_MediatorGet
-
+    ! NUOPC_shr_methods is now in cesm_share and cdeps 
+    use nuopc_shr_methods, only : AlarmInit
+
     ! input/output variables
     type(ESMF_GridComp)  :: gcomp
     integer, intent(out) :: rc
@@ -2318,7 +2319,7 @@ subroutine SetRunClock(gcomp, rc)
        call NUOPC_CompAttributeGet(gcomp, name="stop_ymd", value=cvalue, rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
        read(cvalue,*) stop_ymd
-       call med_time_alarmInit(mclock, stop_alarm, stop_option, opt_n=stop_n, opt_ymd=stop_ymd, &
+       call AlarmInit(mclock, stop_alarm, stop_option, opt_n=stop_n, opt_ymd=stop_ymd, &
             alarmname='alarm_stop', rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
        stopalarmcreated = .true.

mediator/med_diag_mod.F90

@@ -31,7 +31,6 @@ module med_diag_mod
   use med_methods_mod       , only : fldbun_getdata2d => med_methods_FB_getdata2d
   use med_methods_mod       , only : fldbun_getdata1d => med_methods_FB_getdata1d
   use med_methods_mod       , only : fldbun_fldChk    => med_methods_FB_FldChk
-  use med_time_mod          , only : alarmInit        => med_time_alarmInit
   use med_utils_mod         , only : chkerr           => med_utils_ChkErr
   use perf_mod              , only : t_startf, t_stopf
 

mediator/med_phases_aofluxes_mod.F90

@@ -1720,9 +1720,6 @@ subroutine set_aoflux_out_pointers(fldbun, lsize, aoflux_out, xgrid, rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return
     call fldbun_getfldptr(fldbun, 'So_duu10n', aoflux_out%duu10n, xgrid=xgrid, rc=rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return
-
-    call fldbun_getfldptr(fldbun, 'So_u10withGust', aoflux_out%u10_withGust, xgrid=xgrid, rc=rc)
-    if (chkerr(rc,__LINE__,u_FILE_u)) return
     call fldbun_getfldptr(fldbun, 'So_u10res', aoflux_out%u10res, xgrid=xgrid, rc=rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return
     call fldbun_getfldptr(fldbun, 'Faox_taux', aoflux_out%taux, xgrid=xgrid, rc=rc)
@@ -1753,8 +1750,11 @@ subroutine set_aoflux_out_pointers(fldbun, lsize, aoflux_out, xgrid, rc)
     if (add_gusts) then
        call fldbun_getfldptr(fldbun, 'So_ugustOut', aoflux_out%ugust_out, xgrid=xgrid, rc=rc)
        if (chkerr(rc,__LINE__,u_FILE_u)) return
+       call fldbun_getfldptr(fldbun, 'So_u10withGust', aoflux_out%u10_withGust, xgrid=xgrid, rc=rc)
+       if (chkerr(rc,__LINE__,u_FILE_u)) return
     else
        allocate(aoflux_out%ugust_out(lsize)); aoflux_out%ugust_out(:) = 0._R8
+       allocate(aoflux_out%u10_withGust(lsize)); aoflux_out%u10_withGust(:) = 0._R8
     end if
 
   end subroutine set_aoflux_out_pointers

mediator/med_phases_history_mod.F90

@@ -21,7 +21,6 @@ module med_phases_history_mod
   use med_utils_mod         , only : chkerr => med_utils_ChkErr
   use med_internalstate_mod , only : ncomps, compname
   use med_internalstate_mod , only : InternalState, maintask, logunit
-  use med_time_mod          , only : med_time_alarmInit
   use med_io_mod            , only : med_io_write, med_io_wopen, med_io_enddef, med_io_close
   use perf_mod              , only : t_startf, t_stopf
   use pio                   , only : file_desc_t
@@ -153,6 +152,7 @@ subroutine med_phases_history_write(gcomp, rc)
     use ESMF      , only : ESMF_Alarm, ESMF_AlarmSet
     use ESMF      , only : ESMF_FieldBundleIsCreated
     use med_internalstate_mod, only : compocn, compatm
+    use nuopc_shr_methods    , only : alarmInit
 
     ! input/output variables
     type(ESMF_GridComp)  :: gcomp
@@ -184,6 +184,7 @@ subroutine med_phases_history_write(gcomp, rc)
     type(ESMF_TimeInterval) :: ringInterval
     integer                 :: ringInterval_length
     logical                 :: first_time = .true.
+
     character(len=*), parameter :: subname='(med_phases_history_write)'
     !---------------------------------------
 
@@ -221,7 +222,7 @@ subroutine med_phases_history_write(gcomp, rc)
           if (ChkErr(rc,__LINE__,u_FILE_u)) return
           call ESMF_ClockGet(mclock, startTime=starttime,  rc=rc)
           if (ChkErr(rc,__LINE__,u_FILE_u)) return
-          call med_time_alarmInit(mclock, alarm, option=hist_option_all_inst, opt_n=hist_n_all_inst, &
+          call alarmInit(mclock, alarm, option=hist_option_all_inst, opt_n=hist_n_all_inst, &
                reftime=starttime, alarmname=alarmname, rc=rc)
           call ESMF_AlarmSet(alarm, clock=mclock, rc=rc)
           if (ChkErr(rc,__LINE__,u_FILE_u)) return
@@ -1550,7 +1551,7 @@ subroutine med_phases_history_init_histclock(gcomp, hclock, alarm, alarmname, hi
 
     use NUOPC_Mediator, only : NUOPC_MediatorGet
     use ESMF          , only : ESMF_ClockCreate, ESMF_ClockGet, ESMF_ClockSet
-    use med_time_mod  , only : med_time_alarmInit
+    use nuopc_shr_methods, only: AlarmInit
 
     ! input/output variables
     type(ESMF_GridComp) , intent(in)    :: gcomp
@@ -1566,6 +1567,7 @@ subroutine med_phases_history_init_histclock(gcomp, hclock, alarm, alarmname, hi
     type(ESMF_Time)         :: StartTime
     type(ESMF_TimeInterval) :: mtimestep, dtimestep
     integer                 :: msec, dsec
+    integer                 :: min_timestep
     character(len=*), parameter :: subname='(med_phases_history_init_histclock) '
     !---------------------------------------
 
@@ -1593,9 +1595,7 @@ subroutine med_phases_history_init_histclock(gcomp, hclock, alarm, alarmname, hi
     hclock = ESMF_ClockCreate(mclock, rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
-    ! Initialize history alarm and advance history clock to trigger
-    ! alarms then reset history clock back to mcurrtime
-    call med_time_alarmInit(hclock, alarm, option=hist_option, opt_n=hist_n, &
+    call alarmInit(hclock, alarm, option=hist_option, opt_n=hist_n, &
          reftime=StartTime, alarmname=trim(alarmname), advance_clock=.true., rc=rc)
 
     ! Write diagnostic info

mediator/med_phases_prep_glc_mod.F90

@@ -39,7 +39,7 @@ module med_phases_prep_glc_mod
   use med_methods_mod       , only : field_getdata1d  => med_methods_Field_getdata1d
   use med_methods_mod       , only : fldchk           => med_methods_FB_FldChk
   use med_utils_mod         , only : chkerr           => med_utils_ChkErr
-  use med_time_mod          , only : med_time_alarmInit
+  use nuopc_shr_methods     , only : alarmInit
   use glc_elevclass_mod     , only : glc_get_num_elevation_classes
   use glc_elevclass_mod     , only : glc_get_elevation_classes
   use glc_elevclass_mod     , only : glc_get_fractional_icecov
@@ -532,7 +532,7 @@ subroutine med_phases_prep_glc_avg(gcomp, rc)
        call NUOPC_CompAttributeGet(gcomp, name="glc_avg_period", value=glc_avg_period, rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
        if (trim(glc_avg_period) == 'yearly') then
-          call med_time_alarmInit(prepglc_clock, glc_avg_alarm, 'yearly', alarmname='alarm_glc_avg', rc=rc)
+          call alarmInit(prepglc_clock, glc_avg_alarm, 'yearly', alarmname='alarm_glc_avg', rc=rc)
           if (ChkErr(rc,__LINE__,u_FILE_u)) return
           if (maintask) then
              write(logunit,'(a,i10)') trim(subname)//&
@@ -542,7 +542,7 @@ subroutine med_phases_prep_glc_avg(gcomp, rc)
           call NUOPC_CompAttributeGet(gcomp, name="glc_cpl_dt", value=cvalue, rc=rc)
           if (ChkErr(rc,__LINE__,u_FILE_u)) return
           read(cvalue,*) glc_cpl_dt
-          call med_time_alarmInit(prepglc_clock, glc_avg_alarm, 'nseconds', opt_n=glc_cpl_dt, alarmname='alarm_glc_avg', rc=rc)
+          call alarmInit(prepglc_clock, glc_avg_alarm, 'nseconds', opt_n=glc_cpl_dt, alarmname='alarm_glc_avg', rc=rc)
           if (ChkErr(rc,__LINE__,u_FILE_u)) return
           if (maintask) then
              write(logunit,'(a,i10)') trim(subname)//&