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Ticket Resolution Summary Owner Reporter
#1472 fixed Temporary development branch for testing use of file attributes to control starting j-row from input netcdf files. acc acc
Description

The extended grids for use with the under-shelf ice cavities will result in redundant rows around Antarctica if the ice cavities are not active. To avoid the need to maintain different sets of input fields, it is proposed to subset the full datasets on input. The existing zoom options are overly complex for this task and marked for deletion anyway. This branch introduces code to optionally look for and use a global file attribute (provisionally named: open_ocean_jstart) to determine the starting j-row for input. It remains the user's responsibility to adjust the jpjdta and jpjglo values in the namelist_cfg file according to their needs. Further details will appear on an associated Wiki page (see later comment).

#1510 fixed Bug in hpg_prj (dynhpg.F90) reported by hliu acc acc
Description

As reported: Revision: 5212 Author: hliu Date: 2015-04-15 13:14:00 +0200 (Wed, 15 Apr 2015) Log Message:

A serious mistake in dynhpg: hpg_prj, which should also be corrected in v3.6 main trunk 

Modified Paths:
--------------
    branches/2015/dev_r4826_NOC_WAD/NEMOGCM/NEMO/OPA_SRC/DYN/dynhpg.F90

Modified: branches/2015/dev_r4826_NOC_WAD/NEMOGCM/NEMO/OPA_SRC/DYN/dynhpg.F90
===================================================================
--- branches/2015/dev_r4826_NOC_WAD/NEMOGCM/NEMO/OPA_SRC/DYN/dynhpg.F90	2015-04-15 10:10:56 UTC (rev 5211)
+++ branches/2015/dev_r4826_NOC_WAD/NEMOGCM/NEMO/OPA_SRC/DYN/dynhpg.F90	2015-04-15 11:14:00 UTC (rev 5212)
@@ -793,6 +793,7 @@
       REAL(wp) :: zdpdx1, zdpdx2, zdpdy1, zdpdy2
       REAL(wp), POINTER, DIMENSION(:,:,:) ::   zdept, zrhh
       REAL(wp), POINTER, DIMENSION(:,:,:) ::   zhpi, zu, zv, fsp, xsp, asp, bsp, csp, dsp
+      REAL(wp), POINTER, DIMENSION(:,:)   ::   sshu_n, sshv_n
       REAL(wp), POINTER, DIMENSION(:,:)   ::  zcpx, zcpy    !W/D pressure filter
       !!----------------------------------------------------------------------
       !
@@ -799,6 +800,7 @@
       !
       CALL wrk_alloc( jpi,jpj,jpk, zhpi, zu, zv, fsp, xsp, asp, bsp, csp, dsp )
       CALL wrk_alloc( jpi,jpj,jpk, zdept, zrhh )
+      CALL wrk_alloc( jpi,jpj, sshu_n, sshv_n )
       IF(ln_wd) CALL wrk_alloc( jpi,jpj, zcpx, zcpy )
       !
       IF( kt == nit000 ) THEN
@@ -909,10 +911,31 @@
       END DO
       ! Z coordinate of U(ji,jj,1:jpkm1) and V(ji,jj,1:jpkm1)
+
+      ! The following modification "sshu_n -> sshn" is a big mistake, this
+      ! should never happen here, remember to correct this in NEMO v3.6
+      ! trunk.  H.L.
+
+      !prepare sshu_n and sshv_n
+      DO jj = 1, jpjm1
+        DO ji = 1, jpim1
+          sshu_n(ji,jj) = (e12u(ji,jj) * sshn(ji,jj) + e12u(ji+1, jj) * sshn(ji+1,jj)) * &
+                        & r1_e12u(ji,jj) * umask(ji,jj,1) * 0.5_wp
+          sshv_n(ji,jj) = (e12v(ji,jj) * sshn(ji,jj) + e12v(ji+1, jj) * sshn(ji,jj+1)) * &
+                        & r1_e12v(ji,jj) * vmask(ji,jj,1) * 0.5_wp
+        END DO
+      END DO
+
+      CALL lbc_lnk (sshu_n, 'U', 1)
+      CALL lbc_lnk (sshv_n, 'V', 1)
+
       DO jj = 2, jpjm1
         DO ji = 2, jpim1
-          zu(ji,jj,1) = - ( fse3u(ji,jj,1) - sshn(ji,jj) * znad)    ! probable bug: changed from sshu_n for ztilde compilation
-          zv(ji,jj,1) = - ( fse3v(ji,jj,1) - sshn(ji,jj) * znad)    ! probable bug: changed from sshv_n for ztilde compilation
+          !zu(ji,jj,1) = - ( fse3u(ji,jj,1) - sshn(ji,jj) * znad)    ! probable bug: changed from sshu_n for ztilde compilation
+          !zv(ji,jj,1) = - ( fse3v(ji,jj,1) - sshn(ji,jj) * znad)    ! probable bug: changed from sshv_n for ztilde compilation
+
+          zu(ji,jj,1) = - ( fse3u(ji,jj,1) - sshu_n(ji,jj) * znad)
+          zv(ji,jj,1) = - ( fse3v(ji,jj,1) - sshv_n(ji,jj) * znad)
         END DO
       END DO
@@ -1081,6 +1104,7 @@
       !
       CALL wrk_dealloc( jpi,jpj,jpk, zhpi, zu, zv, fsp, xsp, asp, bsp, csp, dsp )
       CALL wrk_dealloc( jpi,jpj,jpk, zdept, zrhh )
+      CALL wrk_dealloc( jpi,jpj, sshu_n, sshv_n )
       IF(ln_wd) CALL wrk_dealloc( jpi,jpj, zcpx, zcpy )
       !
    END SUBROUTINE hpg_prj

Corrected in trunk at rev 5224 as follows: 

Index: NEMOGCM/NEMO/OPA_SRC/DYN/dynhpg.F90
===================================================================
--- NEMOGCM/NEMO/OPA_SRC/DYN/dynhpg.F90 (revision 5223)
+++ NEMOGCM/NEMO/OPA_SRC/DYN/dynhpg.F90 (working copy)
@@ -955,10 +955,12 @@
       REAL(wp) :: zdpdx1, zdpdx2, zdpdy1, zdpdy2
       REAL(wp), POINTER, DIMENSION(:,:,:) ::   zdept, zrhh
       REAL(wp), POINTER, DIMENSION(:,:,:) ::   zhpi, zu, zv, fsp, xsp, asp, bsp, csp, dsp
+      REAL(wp), POINTER, DIMENSION(:,:)   ::   zsshu_n, zsshv_n
       !!----------------------------------------------------------------------
       !
       CALL wrk_alloc( jpi,jpj,jpk, zhpi, zu, zv, fsp, xsp, asp, bsp, csp, dsp )
       CALL wrk_alloc( jpi,jpj,jpk, zdept, zrhh )
+      CALL wrk_alloc( jpi,jpj, zsshu_n, zsshv_n )
       !
       IF( kt == nit000 ) THEN
          IF(lwp) WRITE(numout,*)
@@ -1039,13 +1041,24 @@
       END DO
 
       ! Z coordinate of U(ji,jj,1:jpkm1) and V(ji,jj,1:jpkm1)
+
+      ! Prepare zsshu_n and zsshv_n
       DO jj = 2, jpjm1
         DO ji = 2, jpim1
-          zu(ji,jj,1) = - ( fse3u(ji,jj,1) - sshn(ji,jj) * znad)    ! probable bug: changed from sshu_n for ztilde compilation
-          zv(ji,jj,1) = - ( fse3v(ji,jj,1) - sshn(ji,jj) * znad)    ! probable bug: changed from sshv_n for ztilde compilation
+          zsshu_n(ji,jj) = (e12u(ji,jj) * sshn(ji,jj) + e12u(ji+1, jj) * sshn(ji+1,jj)) * &
+                         & r1_e12u(ji,jj) * umask(ji,jj,1) * 0.5_wp 
+          zsshv_n(ji,jj) = (e12v(ji,jj) * sshn(ji,jj) + e12v(ji+1, jj) * sshn(ji,jj+1)) * &
+                         & r1_e12v(ji,jj) * vmask(ji,jj,1) * 0.5_wp 
         END DO
       END DO
 
+      DO jj = 2, jpjm1
+        DO ji = 2, jpim1
+          zu(ji,jj,1) = - ( fse3u(ji,jj,1) - zsshu_n(ji,jj) * znad) 
+          zv(ji,jj,1) = - ( fse3v(ji,jj,1) - zsshv_n(ji,jj) * znad)
+        END DO
+      END DO
+
       DO jk = 2, jpkm1
         DO jj = 2, jpjm1
           DO ji = 2, jpim1
@@ -1204,6 +1217,7 @@
       !
       CALL wrk_dealloc( jpi,jpj,jpk, zhpi, zu, zv, fsp, xsp, asp, bsp, csp, dsp )
       CALL wrk_dealloc( jpi,jpj,jpk, zdept, zrhh )
+      CALL wrk_dealloc( jpi,jpj, zsshu_n, zsshv_n )
       !
    END SUBROUTINE hpg_prj

The differences being the removal of redundant comments and lbc_lnk calls and the correct naming convention for local variables.

#1660 fixed sette_xios.sh now tests the XIOS2.0 interface but changes are required to the supporting scripts to allow automation. acc acc
Description

The nemo_v3_6_stable SETTE/sette_xios.sh script is now intended to test two GYRE configurations using the new XIOS 2.0 library. This involves some syntax changes in the parent XML files (held in CONFIG/GYRE_XIOS) which break some of the SETTE support scripts. The changes ticketed here should allow the sette_xios.sh tests to exist alongside the full sette.sh tests.

The structural and syntax changes that cause issues are:

  1. The splitting of the file descriptions from iodef.xml to an included file: file_def.xml. This causes three problems: a. sette_xios.sh fails to set the output file_type (one_file or multiple_file) because this is no longer in iodef.xml; b. prepare_exe_dir.sh (run by sette_xios.sh) will overwrite iodef.xml with SETTE/iodef_sette.xml but this is now incompatible because it doesn't include file_def.xml. c. file_def.xml is not copied from the reference directory to any new configuration.
  2. Allowing XIOS2 tests to coexist alongside XIOS1 tests means an alternative arch file is needed to link in the correct library. The prepare_job.sh script needs generalisation for the NOC cluster
  3. The syntax changes include reduction of the type of 'using_server' from "boolean" to "bool" (iodef.xml). The set_xio_using_server function needs adapting to try the alternative if the first string is not found.
  4. Finally, an updated sette_rpt.sh script is added which reports on both sette.sh and sette_xios.sh tests.

The solutions fully tested include:

  1. adding a line to TOOLS/COMPILE/Fmake_config.sh so that file_def.xml is copied if it is found in any reference configuration.
  2. Changing prepare_exe_dir.sh so that it doesn't overwrite iodef.xml with iodef_sette.xml if file_def.xml exists in the target directory.
  3. Adapting set_xio_using_server function (all_functions.sh) to look for "bool" if attempts to locate "boolean" fail when searching for the using_server setting in iodef.xml.
  4. Adapting set_xio_file_type function (all_functions.sh) to check for and alter settings in file_def.xml if it is not successful at finding the file_type in iodef.xml

The last point is the least satisfactory since the name file_def.xml is hardwired into the function but this should only be a temporary measure pending the establishment of XIOS2.0.

Changes committed to revision 6224. sette_rpt.sh now reports as follows: 

./sette_rpt.sh
WGYRE_LONG            solver.stat restartability  passed :  20160106
WISOMIP_LONG          solver.stat restartability  passed :  20160106
WORCA2LIMPIS_LONG     solver.stat restartability  passed :  20160106
WORCA2LIMPIS_LONG     tracer.stat restartability  passed :  20160106
WORCA2OFFPIS_LONG     tracer.stat restartability  passed :  20160106
WAMM12_LONG           solver.stat restartability  passed :  20160106
WORCA2LIM3_LONG       solver.stat restartability  passed :  20160106
WSAS_LONG             incomplete test
WGYRE_XIOS_LR         checking against  ATTACHED_MULTIPLE
WGYRE_XIOS_LR         solver.stat restartability  passed :  20160107 ATTACHED_ONE
WGYRE_XIOS_LR         solver.stat restartability  passed :  20160107 DETACHED_MULTIPLE
WGYRE_XIOS_LR         solver.stat restartability  passed :  20160107 DETACHED_ONE
WGYRE_XIOS_HR         checking against  ATTACHED_MULTIPLE
WGYRE_XIOS_HR         solver.stat restartability  passed :  20160107 ATTACHED_ONE
WGYRE_XIOS_HR         solver.stat restartability  passed :  20160107 DETACHED_MULTIPLE
WGYRE_XIOS_HR         solver.stat restartability  passed :  20160107 DETACHED_ONE
WGYRE_4               solver.stat reproducibility passed :  20160106
WISOMIP_4             solver.stat reproducibility passed :  20160106
WORCA2LIMPIS_16       solver.stat reproducibility passed :  20160106
WORCA2LIMPIS_16       tracer.stat reproducibility passed :  20160106
WORCA2OFFPIS_16       tracer.stat reproducibility passed :  20160106
WAMM12_32             solver.stat reproducibility passed :  20160106
WORCA2LIM3_16         solver.stat reproducibility passed :  20160106
WSAS_32               incomplete test
WORCA2AGUL_1_2        solver.stat reproducibility passed :  20160106
---------------2nd pass------------------
WSAS_LONG             incomplete test
WSAS_32               incomplete test
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