Merge branch 'hotfix_3.3'

This merge incorporates twelve fixes to the shared MPAS infrastructure:

    * framework/interval_comparison_fix:
      Add missing comma in generated format string in ESMF time manager.
      Define ESMF_KIND_R4 and ESMF_KIND_R8 to be consistent with CESM
      Wrap long source line in ESMF_TimeMod.F90 to match CESM code.
      Always compute the difference between two time instants in terms of days and seconds.

    * framework/leak_fixes:
      Fixing a memory leak related to setting times

    * framework/io_file_noexist:
      Adding an error for reads of non-existent files

    * framework/stream_filename_write:
      Fixing a problem when using open() on an xml file that doesn't exist

    * framework/registry_var_merge_fix:
      Fix merging of var_struct and var_array elements in Registry.xml files.

    * framework/time_interval_divide_by_zero_fix:
      Resetting s_d regardless of input options

    * framework/r0a_fix:
      Removing an extra if clause to handle r0a field destruction

    * framework/package_allocation_fix:
      Fixing package variables so they don't allocate space

    * framework/building_directory_permission_fix:
      Fixing directory creation when nested in non-writable directories

    * framework/unique_stream_filenames:
      Allow input streams to have the same filename template

    * framework/bootstrapping_fix:
      Updating the bootstrapping process to handle stream attributes properly

    * framework/alarm_reset_fix:
      Fixing an issue with interval division when resetting alarms

README.md

@@ -1,4 +1,4 @@
-MPAS-v3.2
+MPAS-v3.3
 ====
 
 The Model for Prediction Across Scales (MPAS) is a collaborative project for

src/core_atmosphere/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="atmosphere" version="3.2">
+<registry model="mpas" core="atmosphere" version="3.3">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->

src/core_init_atmosphere/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="init_atmosphere" version="3.2">
+<registry model="mpas" core="init_atmosphere" version="3.3">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->

src/core_landice/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="landice" version="3.2">
+<registry model="mpas" core="landice" version="3.3">
 
 
 <!-- ======================================================================= -->

src/core_ocean/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="ocean" version="3.2">
+<registry model="mpas" core="ocean" version="3.3">
 
 	<dims>
 		<dim name="nCells" units="unitless"

src/core_sw/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="sw" version="3.2">
+<registry model="mpas" core="sw" version="3.3">
 	<dims>
 		<dim name="nCells"/>
 		<dim name="nEdges"/>

src/driver/mpas_subdriver.F

@@ -31,7 +31,7 @@ module mpas_subdriver
 
    subroutine mpas_init()
 
-      use mpas_stream_manager, only : MPAS_stream_mgr_init
+      use mpas_stream_manager, only : MPAS_stream_mgr_init, MPAS_build_stream_filename
       use iso_c_binding, only : c_char, c_loc, c_ptr, c_int
       use mpas_c_interfacing, only : mpas_f_to_c_string, mpas_c_to_f_string
       use mpas_timekeeping, only : MPAS_Time_type, mpas_get_clock_time, mpas_get_time
@@ -49,9 +49,15 @@ subroutine mpas_init()
       character(len=StrKIND) :: mesh_stream
       character(len=StrKIND) :: mesh_filename
       character(len=StrKIND) :: mesh_filename_temp
+      character(len=StrKIND) :: ref_time_temp
+      character(len=StrKIND) :: filename_interval_temp
       character(kind=c_char), dimension(StrKIND+1) :: c_mesh_stream
       character(kind=c_char), dimension(StrKIND+1) :: c_mesh_filename_temp
+      character(kind=c_char), dimension(StrKIND+1) :: c_ref_time_temp
+      character(kind=c_char), dimension(StrKIND+1) :: c_filename_interval_temp
       type (MPAS_Time_type) :: start_time
+      type (MPAS_Time_type) :: ref_time
+      type (MPAS_TimeInterval_type) :: filename_interval
       character(len=StrKIND) :: start_timestamp
 
 
@@ -64,14 +70,16 @@ subroutine xml_stream_parser(xmlname, mgr_p, comm, ierr) bind(c)
             integer(kind=c_int), intent(out) :: ierr
          end subroutine xml_stream_parser
 
-         subroutine xml_stream_get_filename(xmlname, streamname, comm, filename, ierr) bind(c)
+         subroutine xml_stream_get_attributes(xmlname, streamname, comm, filename, ref_time, filename_interval, ierr) bind(c)
             use iso_c_binding, only : c_char, c_int
             character(kind=c_char), dimension(*), intent(in) :: xmlname
             character(kind=c_char), dimension(*), intent(in) :: streamname
             integer(kind=c_int), intent(inout) :: comm
             character(kind=c_char), dimension(*), intent(in) :: filename
+            character(kind=c_char), dimension(*), intent(in) :: ref_time
+            character(kind=c_char), dimension(*), intent(in) :: filename_interval
             integer(kind=c_int), intent(out) :: ierr
-         end subroutine xml_stream_get_filename
+         end subroutine xml_stream_get_attributes
       end interface
 
 
@@ -98,16 +106,30 @@ end subroutine xml_stream_get_filename
       call mpas_f_to_c_string(domain % streams_filename, c_filename)
       call mpas_f_to_c_string(mesh_stream, c_mesh_stream)
       c_comm = dminfo % comm
-      call xml_stream_get_filename(c_filename, c_mesh_stream, c_comm, c_mesh_filename_temp, c_ierr)
+      call xml_stream_get_attributes(c_filename, c_mesh_stream, c_comm, &
+                                     c_mesh_filename_temp, c_ref_time_temp, &
+                                     c_filename_interval_temp, c_ierr)
       if (c_ierr /= 0) then
          call mpas_dmpar_abort(dminfo)
       end if
       call mpas_c_to_f_string(c_mesh_filename_temp, mesh_filename_temp)
+      call mpas_c_to_f_string(c_ref_time_temp, ref_time_temp)
+      call mpas_c_to_f_string(c_filename_interval_temp, filename_interval_temp)
+
       start_time = mpas_get_clock_time(domain_ptr % clock, MPAS_START_TIME, ierr)
-      call mpas_get_time(start_time, dateTimeString=start_timestamp, ierr=ierr)
-      call mpas_expand_string(start_timestamp, mesh_filename_temp, mesh_filename)
-      call mpas_bootstrap_framework(domain_ptr, mesh_filename)
+      if ( trim(ref_time_temp) == 'initial_time' ) then
+          call mpas_get_time(start_time, dateTimeString=ref_time_temp, ierr=ierr)
+      end if
 
+      if ( trim(filename_interval_temp) == 'none' ) then
+          call mpas_expand_string(ref_time_temp, mesh_filename_temp, mesh_filename)
+      else
+          call mpas_set_time(ref_time, dateTimeString=ref_time_temp, ierr=ierr)
+          call mpas_set_timeInterval(filename_interval, timeString=filename_interval_temp, ierr=ierr)
+          call mpas_build_stream_filename(ref_time, start_time, filename_interval, mesh_filename_temp, mesh_filename, ierr)
+      end if
+      write(stderrUnit, *) ' ** Attempting to bootstrap MPAS framework using stream: ', trim(mesh_stream)
+      call mpas_bootstrap_framework(domain_ptr, mesh_filename)
 
       !
       ! Set up run-time streams

src/external/esmf_time_f90/ESMF_BaseMod.F90

@@ -102,8 +102,8 @@ module ESMF_BaseMod
                    ESMF_KIND_I2 = selected_int_kind(4), &
                    ESMF_KIND_I4 = selected_int_kind(9), &
                    ESMF_KIND_I8 = selected_int_kind(18), &
-                   ESMF_KIND_R4 = selected_real_kind(3,25), &
-                   ESMF_KIND_R8 = selected_real_kind(6,45), &
+                   ESMF_KIND_R4 = selected_real_kind(6),  & ! 4-byte real
+                   ESMF_KIND_R8 = selected_real_kind(12), & ! 8-byte real
                    ESMF_KIND_C8 = selected_real_kind(3,25), &
                    ESMF_KIND_C16 = selected_real_kind(6,45)
 

src/external/esmf_time_f90/ESMF_TimeMod.F90

@@ -835,7 +835,8 @@ subroutine ESMFold_TimeGetString( year, month, dayofmonth, &
 
 !$$$here...  add negative sign for YR<0
 !$$$here...  add Sn, Sd ??
-      write(TimeFormatString,FMT="(A,I4.4,A,I4.4,A)") "(I", yearWidth, ".", yearWidth, "'-',I2.2,'-',I2.2,'_',I2.2,':',I2.2,':',I2.2)"
+      write(TimeFormatString,FMT="(A,I4.4,A,I4.4,A)") &
+           "(I", yearWidth, ".", yearWidth, ",'-',I2.2,'-',I2.2,'_',I2.2,':',I2.2,':',I2.2)"
       write(TimeString,FMT=TimeFormatString) year,month,dayofmonth,hour,minute,second
 
       end subroutine ESMFold_TimeGetString
@@ -1079,16 +1080,20 @@ function ESMF_TimeDiff(time1, time2)
 
       ! Can either be yr/month based diff if diff is only in year and month
       ! or absolute seconds if diff in day/seconds as well
-
-      if (d1 == d2 .and. s1 == s2) then
-!         write(6,*) 'tcx timedifft ym'
-         ESMF_TimeDiff%YR = y1 - y2
-         ESMF_TimeDiff%MM = m1 - m2
-         cmptime%S  = 0
-         cmptime%Sn = 0
-         cmptime%Sd = 0
-         ESMF_TimeDiff%basetime = cmptime
-      else
+      !
+      ! Update: Actually, the timeintcmp() routine in ESMF_TimeIntervalMod.F90 is not capable 
+      !    of comparing time intervals when one interval has a different year and month than 
+      !    the other. So, it is best here to always compute the interval as day/seconds.
+
+!      if (d1 == d2 .and. s1 == s2) then
+!!         write(6,*) 'tcx timedifft ym'
+!         ESMF_TimeDiff%YR = y1 - y2
+!         ESMF_TimeDiff%MM = m1 - m2
+!         cmptime%S  = 0
+!         cmptime%Sn = 0
+!         cmptime%Sd = 0
+!         ESMF_TimeDiff%basetime = cmptime
+!      else
 !         write(6,*) 'tcx timedifft sec'
          ESMF_TimeDiff%YR = 0
          ESMF_TimeDiff%MM = 0
@@ -1104,7 +1109,7 @@ function ESMF_TimeDiff(time1, time2)
               ESMF_TimeDiff%basetime%S = ESMF_TimeDiff%basetime%S - nsecondsinyear(yr,time2%calendar%type)
             ENDDO
          ENDIF
-      endif
+!      endif
 
 !      write(6,*) 'tcx timediff5 ',ESMF_TimeDiff%YR, ESMF_TimeDiff%MM, ESMF_TimeDiff%basetime%s
 

src/framework/mpas_bootstrapping.F

@@ -145,6 +145,8 @@ subroutine mpas_bootstrap_framework(domain, mesh_filename) !{{{
          write(stderrUnit,*) 'Error: Could not open input file '''//trim(mesh_filename)//''' to read mesh fields'
          write(stderrUnit,*) '************************************************************************************'
          call mpas_dmpar_abort(domain % dminfo)
+      else
+         write(stderrUnit,*) 'Bootstrapping framework with mesh fields from input file '''//trim(mesh_filename)//''''
       end if
 
 

src/framework/mpas_io.F

@@ -70,7 +70,8 @@ module mpas_io
                          MPAS_IO_ERR_WRONG_MODE         = -16, &
                          MPAS_IO_ERR_NO_UNLIMITED_DIM   = -17, &
                          MPAS_IO_ERR_UNIMPLEMENTED      = -18, &
-                         MPAS_IO_ERR_WOULD_CLOBBER      = -19
+                         MPAS_IO_ERR_WOULD_CLOBBER      = -19, &
+                         MPAS_IO_ERR_NOEXIST_READ       = -20
 
 
    type MPAS_IO_Handle_type
@@ -384,6 +385,12 @@ type (MPAS_IO_Handle_type) function MPAS_io_open(filename, mode, ioformat, clobb
             end if
          end if
       else
+         inquire(file=trim(filename), exist=exists)
+
+         if (.not. exists) then
+            if (present(ierr)) ierr = MPAS_IO_ERR_NOEXIST_READ
+            return
+         end if
 !write(stderrUnit,*) 'MGD PIO_openfile'
          pio_ierr = PIO_openfile(pio_iosystem, MPAS_io_open % pio_file, pio_iotype, trim(filename), PIO_nowrite)
       endif
@@ -4394,6 +4401,8 @@ subroutine MPAS_io_err_mesg(ierr, fatal)
             write(stderrUnit,*) 'MPAS IO Error: Unimplemented functionality'
          case (MPAS_IO_ERR_WOULD_CLOBBER)
             write(stderrUnit,*) 'MPAS IO Error: Would clobber existing file'
+         case (MPAS_IO_ERR_NOEXIST_READ)
+            write(stderrUnit,*) 'MPAS IO Error: Attempting to read a file which does not exist.'
          case default
             write(stderrUnit,*) 'MPAS IO Error: Unrecognized error code...'
       end select

src/framework/mpas_io_streams.F

@@ -161,6 +161,10 @@ subroutine MPAS_createStream(stream, fileName, ioFormat, ioDirection, precision,
       !
       ! Catch a few special errors
       !
+      if (io_err == MPAS_IO_ERR_NOEXIST_READ) then
+         if (present(ierr)) ierr = MPAS_IO_ERR_NOEXIST_READ
+         return
+      end if
       if (io_err == MPAS_IO_ERR_WOULD_CLOBBER) then
          if (present(ierr)) ierr = MPAS_STREAM_CLOBBER_FILE
          return

src/framework/mpas_stream_manager.F

@@ -61,7 +61,8 @@ module mpas_stream_manager
               MPAS_stream_mgr_ringing_alarms, &
               MPAS_stream_mgr_add_att, &
               MPAS_stream_mgr_write, &
-              MPAS_stream_mgr_read
+              MPAS_stream_mgr_read, &
+              MPAS_build_stream_filename
 
     private
 
@@ -2431,7 +2432,7 @@ subroutine write_stream(manager, stream, timeLevel, mgLevel, forceWritenow, ierr
             if ( stream % filename_interval /= 'none' ) then
                 now_time = mpas_get_clock_time(manager % streamClock, MPAS_NOW, ierr=local_ierr)
                 call mpas_set_timeInterval(filename_interval, timeString=stream % filename_interval)
-                call build_filename(stream % referenceTime, now_time, filename_interval, stream % filename_template, stream % filename, ierr=local_ierr)
+                call mpas_build_stream_filename(stream % referenceTime, now_time, filename_interval, stream % filename_template, stream % filename, ierr=local_ierr)
             else
                 call mpas_get_time(stream % referenceTime, dateTimeString=time_string)
                 call mpas_expand_string(time_string, stream % filename_template, stream % filename)
@@ -2505,7 +2506,7 @@ subroutine write_stream(manager, stream, timeLevel, mgLevel, forceWritenow, ierr
                 now_time = mpas_get_clock_time(manager % streamClock, MPAS_NOW, ierr=local_ierr)
                 call mpas_set_timeInterval(filename_interval, timeString=stream % filename_interval)
 
-                call build_filename(stream % referenceTime, now_time, filename_interval, stream % filename_template, temp_filename, ierr=local_ierr)
+                call mpas_build_stream_filename(stream % referenceTime, now_time, filename_interval, stream % filename_template, temp_filename, ierr=local_ierr)
             else
                 call mpas_get_time(stream % referenceTime, dateTimeString=time_string)
                 call mpas_expand_string(time_string, stream % filename_template, temp_filename)
@@ -2840,6 +2841,8 @@ subroutine read_stream(manager, stream, timeLevel, mgLevel, forceReadNow, when,
         character (len=*), intent(out), optional :: actualWhen
         integer, intent(out) :: ierr
 
+        character (len=StrKIND) :: err_string
+
         type (MPAS_stream_list_type), pointer :: alarm_cursor
         type (MPAS_Time_type) :: now_time, ref_time, temp_time
         type (MPAS_TimeInterval_type) :: temp_interval
@@ -2907,7 +2910,7 @@ subroutine read_stream(manager, stream, timeLevel, mgLevel, forceReadNow, when,
             call mpas_set_time(now_time, dateTimeString=when, ierr=local_ierr)
             call mpas_set_timeInterval(filename_interval, timeString=stream % filename_interval)
             
-            call build_filename(stream % referenceTime, now_time, filename_interval, stream % filename_template, temp_filename, ierr=local_ierr)
+            call mpas_build_stream_filename(stream % referenceTime, now_time, filename_interval, stream % filename_template, temp_filename, ierr=local_ierr)
         else
             call mpas_expand_string(when, stream % filename_template, temp_filename)
         end if
@@ -2928,7 +2931,13 @@ subroutine read_stream(manager, stream, timeLevel, mgLevel, forceReadNow, when,
             call MPAS_createStream(stream % stream, stream % filename, MPAS_IO_PNETCDF, MPAS_IO_READ, &
                                    precision=stream % precision, ierr=local_ierr)
             if (local_ierr /= MPAS_STREAM_NOERR) then
-                ierr = MPAS_STREAM_MGR_ERROR
+                if (local_ierr == MPAS_IO_ERR_NOEXIST_READ) then
+                    write(err_string,'(a)') 'Stream '''//trim(stream % name)//''' attempted to read non-existent file '''//trim(stream % filename)//''''
+                    STREAM_ERROR_WRITE(trim(err_string))
+                    ierr = MPAS_STREAM_MGR_ERROR
+                else
+                    ierr = MPAS_STREAM_MGR_ERROR
+                end if
                 return
             end if
 
@@ -2959,7 +2968,13 @@ subroutine read_stream(manager, stream, timeLevel, mgLevel, forceReadNow, when,
            !
            call MPAS_createStream(stream % stream, stream % filename, MPAS_IO_PNETCDF, MPAS_IO_READ, precision=stream % precision, ierr=local_ierr)
            if (local_ierr /= MPAS_STREAM_NOERR) then
-               ierr = MPAS_STREAM_MGR_ERROR
+               if (local_ierr == MPAS_IO_ERR_NOEXIST_READ) then
+                   write(err_string,'(a)') 'Stream '''//trim(stream % name)//''' attempted to read non-existent file '''//trim(stream % filename)//''''
+                   STREAM_ERROR_WRITE(trim(err_string))
+                   ierr = MPAS_STREAM_MGR_ERROR
+               else
+                   ierr = MPAS_STREAM_MGR_ERROR
+               end if
                return
            end if
 
@@ -3064,7 +3079,7 @@ subroutine read_stream(manager, stream, timeLevel, mgLevel, forceReadNow, when,
 
            call mpas_set_timeInterval(filename_interval, timeString=stream % filename_interval)
            
-           call build_filename(stream % referenceTime, filenameTime, filename_interval, stream % filename_template, test_filename, ierr=local_ierr)
+           call mpas_build_stream_filename(stream % referenceTime, filenameTime, filename_interval, stream % filename_template, test_filename, ierr=local_ierr)
 
            STREAM_DEBUG_WRITE(' --- Retesting filename is ' COMMA trim(test_filename))
 
@@ -3234,7 +3249,7 @@ end subroutine MPAS_stream_mesg!}}}
 
 
     !-----------------------------------------------------------------------
-    !  routine build_filename
+    !  routine mpas_build_stream_filename
     !
     !> \brief Construct the filename that contains a specific time in a stream
     !> \author Michael Duda, Doug Jacobsen
@@ -3251,7 +3266,7 @@ end subroutine MPAS_stream_mesg!}}}
     !>  Return error codes:
     !>  0 no error
     !-----------------------------------------------------------------------
-    subroutine build_filename(ref_time, when, filename_interval, filename_template, filename, ierr) !{{{
+    subroutine mpas_build_stream_filename(ref_time, when, filename_interval, filename_template, filename, ierr) !{{{
 
         implicit none
 
@@ -3314,7 +3329,7 @@ subroutine build_filename(ref_time, when, filename_interval, filename_template,
 
         call mpas_expand_string(when_string, filename_template, filename)
 
-    end subroutine build_filename !}}}
+    end subroutine mpas_build_stream_filename !}}}
 
 
     !-----------------------------------------------------------------------

src/framework/mpas_timekeeping.F

@@ -822,15 +822,15 @@ subroutine mpas_reset_clock_alarm(clock, alarmID, interval, ierr)
                      end if
 
                      nowInterval = alarmNow - alarmPtr % prevRingTime
-                     call mpas_interval_division(alarmNow, nowInterval, alarmPtr % ringTimeInterval, nDivs, nowRemainder)
+                     call mpas_interval_division(alarmPtr % prevRingTime, nowInterval, alarmPtr % ringTimeInterval, nDivs, nowRemainder)
                      alarmPtr % prevRingTime = alarmNow - nowRemainder
                   else
                      if (present(interval)) then
                         alarmNow = alarmNow - interval
                      end if
 
                      nowInterval = alarmPtr % prevRingTime - alarmNow
-                     call mpas_interval_division(alarmNow, nowInterval, alarmPtr % ringTimeInterval, nDivs, nowRemainder)
+                     call mpas_interval_division(alarmPtr % prevRingTime, nowInterval, alarmPtr % ringTimeInterval, nDivs, nowRemainder)
                      alarmPtr % prevRingTime = alarmNow + nowRemainder
                   end if
                end if
@@ -964,6 +964,8 @@ subroutine mpas_set_time(curr_time, YYYY, MM, DD, DoY, H, M, S, S_n, S_d, dateTi
             if (present(ierr)) ierr = 1
             write(stderrUnit,*) 'ERROR: Invalid DateTime string', dateTimeString
             return
+         else
+            deallocate(subStrings)
          end if
 
          call mpas_split_string(dateTimeString_, "_", subStrings)
@@ -1354,6 +1356,10 @@ subroutine mpas_get_timeInterval(interval, StartTimeIn, DD, H, M, S, S_n, S_d, S
           call ESMF_TimeIntervalGet(interval % ti, D=days, S_i8=seconds, Sn=sn, Sd=sd, rc=ierr)
       endif
 
+      if (sd == 0) then   ! may only occur if (sn == 0)?
+         sd = 1
+      end if
+
       if (present(dt)) then
          dt = (days * 24 * 60 * 60) + seconds + (sn / sd)
       end if
@@ -1390,9 +1396,6 @@ subroutine mpas_get_timeInterval(interval, StartTimeIn, DD, H, M, S, S_n, S_d, S
       end if
 
       if (present(S_d)) then
-         if (sd == 0) then   ! may only occur if (sn == 0)?
-            sd = 1
-         end if
          S_d = sd
       end if