Merge branch 'dev/gfdl' into add_set_initialized

.gitlab/mom6-ci-run-gnu-restarts-script.sh

@@ -0,0 +1,47 @@
+#!/bin/bash
+
+sect=none
+clean_stats () { # fn to clean up stats files
+  find [oicl]* -name "*.stats.*[a-z][a-z][a-z]" -delete
+}
+section_start () { # fn to print fold-able banner in CI
+  echo -e "\e[0Ksection_start:`date +%s`:$1[collapsed=true]\r\e[0K$2"
+  sect=$1
+}
+section_end () { # fn to close fold-able banner in CI and clean up stats
+  echo -e "\e[0Ksection_end:`date +%s`:$sect\r\e[0K"
+  clean_stats
+}
+check_for_core_files () {
+  EXIT_CODE=0
+  find [oilc]* -name core | grep . && EXIT_CODE=1
+  if [[ $EXIT_CODE -gt 0 ]]
+  then
+    echo "Error: core files found!"
+    exit 911
+  fi
+}
+
+# Make sure we have a clean start
+clean_stats
+find [oilc]* -name core -delete
+rm -f .CI-GNU-RESTARTS-BATCH-SUCCESS
+
+set -e
+set -v
+
+# Run symmetric gnu restart tests
+section_start gnu_restarts "Running symmetric gnu restart tests"
+time make -f tools/MRS/Makefile.restart gnu_ocean_only -s -j RESTART_STAGE=01
+time make -f tools/MRS/Makefile.restart gnu_ice_ocean_SIS2 -s -j RESTART_STAGE=01
+time make -f tools/MRS/Makefile.restart gnu_ocean_only -s -j RESTART_STAGE=02
+time make -f tools/MRS/Makefile.restart gnu_ice_ocean_SIS2 -s -j RESTART_STAGE=02
+time make -f tools/MRS/Makefile.restart gnu_ocean_only -s -j RESTART_STAGE=12
+time make -f tools/MRS/Makefile.restart gnu_ice_ocean_SIS2 -s -j RESTART_STAGE=12
+tar cf - `find [oilc]*/ -path "*/??.ignore/*" -name "ocean.stats.*[a-z][a-z][a-z]"` | tar --one-top-level=results/gnu_restarts -xf -
+check_for_core_files
+find [oilc]* -name "*.ignore" -type d -prune -exec rm -rf {} \;
+section_end
+
+# Indicate all went well
+touch .CI-GNU-RESTARTS-BATCH-SUCCESS

.gitlab/mom6-ci-run-gnu-script.sh

@@ -0,0 +1,71 @@
+#!/bin/bash
+
+sect=none
+clean_stats () { # fn to clean up stats files
+  find [oicl]* -name "*.stats.*[a-z][a-z][a-z]" -delete
+}
+section_start () { # fn to print fold-able banner in CI
+  echo -e "\e[0Ksection_start:`date +%s`:$1[collapsed=true]\r\e[0K$2"
+  sect=$1
+}
+section_end () { # fn to close fold-able banner in CI and clean up stats
+  echo -e "\e[0Ksection_end:`date +%s`:$sect\r\e[0K"
+  clean_stats
+}
+check_for_core_files () {
+  EXIT_CODE=0
+  find [oilc]* -name core | grep . && EXIT_CODE=1
+  if [[ $EXIT_CODE -gt 0 ]]
+  then
+    echo "Error: core files found!"
+    exit 911
+  fi
+}
+
+# Make sure we have a clean start
+clean_stats
+find [oilc]* -name core -delete
+rm -f .CI-GNU-BATCH-SUCCESS
+
+set -e
+set -v
+
+# Run symmetric gnu regressions
+section_start gnu_all_sym "Running symmetric gnu"
+time make -f tools/MRS/Makefile.run gnu_all -s -j
+tar cf - `find [oicl]* -name "*.stats.*[a-z][a-z][a-z]"` | tar --one-top-level=results/gnu_all_sym -xf -
+tar cf - `find [oicl]* -name "*_parameter_doc.*"` | tar --one-top-level=results/gnu_params -xf -
+check_for_core_files
+section_end
+
+# Run non-symmetric gnu regressions
+section_start gnu_all_nonsym "Running nonsymmetric gnu"
+time make -f tools/MRS/Makefile.run ocean_only/circle_obcs/ocean.stats.gnu
+time make -f tools/MRS/Makefile.run gnu_all -s -j MEMORY=dynamic_nonsymmetric
+tar cf - `find [oicl]* -name "*.stats.*[a-z][a-z][a-z]"` | tar --one-top-level=results/gnu_all_nonsym -xf -
+check_for_core_files
+section_end
+
+# Run symmetric gnu regressions with alternate layout
+section_start gnu_all_layout "Running symmetric gnu with alternate layouts"
+time make -f tools/MRS/Makefile.run gnu_all -s -j LAYOUT=alt
+tar cf - `find [oicl]* -name "*.stats.*[a-z][a-z][a-z]"` | tar --one-top-level=results/gnu_all_layout -xf -
+check_for_core_files
+section_end
+
+# Run symmetric gnu regressions with debug executable
+section_start gnu_ocean_only_debug "Running symmetric gnu_ocean_only with debug executable"
+time make -f tools/MRS/Makefile.run gnu_ocean_only -s -j MODE=debug
+tar cf - `find [oicl]* -name "*.stats.*[a-z][a-z][a-z]"` | tar --one-top-level=results/gnu_ocean_only_debug -xf -
+check_for_core_files
+section_end
+
+# Run symmetric static gnu regressions
+section_start gnu_all_static "Running symmetric gnu with static executable"
+time make -f tools/MRS/Makefile.run gnu_static_ocean_only MEMORY=static -s -j
+tar cf - `find [oicl]* -name "*.stats.*[a-z][a-z][a-z]"` | tar --one-top-level=results/gnu_all_static -xf -
+check_for_core_files
+section_end
+
+# Indicate all went well
+touch .CI-GNU-BATCH-SUCCESS

.gitlab/mom6-ci-run-intel-script.sh

@@ -0,0 +1,57 @@
+#!/bin/bash
+
+sect=none
+clean_stats () { # fn to clean up stats files
+  find [oicl]* -name "*.stats.*[a-z][a-z][a-z]" -delete
+}
+section_start () { # fn to print fold-able banner in CI
+  echo -e "\e[0Ksection_start:`date +%s`:$1[collapsed=true]\r\e[0K$2"
+  sect=$1
+}
+section_end () { # fn to close fold-able banner in CI and clean up stats
+  echo -e "\e[0Ksection_end:`date +%s`:$sect\r\e[0K"
+  clean_stats
+}
+check_for_core_files () {
+  EXIT_CODE=0
+  find [oilc]* -name core | grep . && EXIT_CODE=1
+  if [[ $EXIT_CODE -gt 0 ]]
+  then
+    echo "Error: core files found!"
+    exit 911
+  fi
+}
+
+# Make sure we have a clean start
+clean_stats
+find [oilc]* -name core -delete
+rm -f .CI-INTEL-BATCH-SUCCESS
+
+set -e
+set -v
+
+# Run symmetric intel regressions
+section_start intel_all_sym "Running symmetric intel"
+time make -f tools/MRS/Makefile.run intel_all -s -j
+tar cf - `find [oicl]* -name "*.stats.*[a-z][a-z][a-z]"` | tar --one-top-level=results/intel_all_sym -xf -
+tar cf - `find [oicl]* -name "*_parameter_doc.*"` | tar --one-top-level=results/intel_params -xf -
+check_for_core_files
+section_end
+
+# Run non-symmetric intel regressions
+section_start intel_all_nonsym "Running nonsymmetric intel"
+time make -f tools/MRS/Makefile.run ocean_only/circle_obcs/ocean.stats.intel -s
+time make -f tools/MRS/Makefile.run intel_all -s -j MEMORY=dynamic_nonsymmetric
+tar cf - `find [oicl]* -name "*.stats.*[a-z][a-z][a-z]"` | tar --one-top-level=results/intel_all_nonsym -xf -
+check_for_core_files
+section_end
+
+# Run symmetric intel regressions with alternate layout
+section_start intel_all_layout "Running symmetric intel with alternate layouts"
+time make -f tools/MRS/Makefile.run intel_all -s -j LAYOUT=alt
+tar cf - `find [oicl]* -name "*.stats.*[a-z][a-z][a-z]"` | tar --one-top-level=results/intel_all_layout -xf -
+check_for_core_files
+section_end
+
+# Indicate all went well
+touch .CI-INTEL-BATCH-SUCCESS

.gitlab/mom6-ci-run-pgi-script.sh

@@ -0,0 +1,57 @@
+#!/bin/bash
+
+sect=none
+clean_stats () { # fn to clean up stats files
+  find [oicl]* -name "*.stats.*[a-z][a-z][a-z]" -delete
+}
+section_start () { # fn to print fold-able banner in CI
+  echo -e "\e[0Ksection_start:`date +%s`:$1[collapsed=true]\r\e[0K$2"
+  sect=$1
+}
+section_end () { # fn to close fold-able banner in CI and clean up stats
+  echo -e "\e[0Ksection_end:`date +%s`:$sect\r\e[0K"
+  clean_stats
+}
+check_for_core_files () {
+  EXIT_CODE=0
+  find [oilc]* -name core | grep . && EXIT_CODE=1
+  if [[ $EXIT_CODE -gt 0 ]]
+  then
+    echo "Error: core files found!"
+    exit 911
+  fi
+}
+
+# Make sure we have a clean start
+clean_stats
+find [oilc]* -name core -delete
+rm -f .CI-PGI-BATCH-SUCCESS
+
+set -e
+set -v
+
+# Run symmetric pgi regressions
+section_start pgi_all_sym "Running symmetric pgi"
+time make -f tools/MRS/Makefile.run pgi_all -s -j
+tar cf - `find [oicl]* -name "*.stats.*[a-z][a-z][a-z]"` | tar --one-top-level=results/pgi_all_sym -xf -
+tar cf - `find [oicl]* -name "*_parameter_doc.*"` | tar --one-top-level=results/pgi_params -xf -
+check_for_core_files
+section_end
+
+# Run non-symmetric pgi regressions
+section_start pgi_all_nonsym "Running nonsymmetric pgi"
+time make -f tools/MRS/Makefile.run ocean_only/circle_obcs/ocean.stats.pgi -s
+time make -f tools/MRS/Makefile.run pgi_all -s -j MEMORY=dynamic_nonsymmetric
+tar cf - `find [oicl]* -name "*.stats.*[a-z][a-z][a-z]"` | tar --one-top-level=results/pgi_all_nonsym -xf -
+check_for_core_files
+section_end
+
+# Run symmetric pgi regressions with alternate layout
+section_start pgi_all_layout "Running symmetric pgi with alternate layouts"
+time make -f tools/MRS/Makefile.run gnu_all -s -j LAYOUT=alt
+tar cf - `find [oicl]* -name "*.stats.*[a-z][a-z][a-z]"` | tar --one-top-level=results/pgi_all_layout -xf -
+check_for_core_files
+section_end
+
+# Indicate all went well
+touch .CI-PGI-BATCH-SUCCESS

.testing/tc2/MOM_input

@@ -297,7 +297,7 @@ BOUND_CORIOLIS = True           !   [Boolean] default = False
                                 ! v-points, and similarly at v-points.  This option would
                                 ! have no effect on the SADOURNY Coriolis scheme if it
                                 ! were possible to use centered difference thickness fluxes.
-PGF_STANLEY_T2_DET_COEFF = 0.5  !   [nondim] default = -1.0
+PGF_STANLEY_T2_DET_COEFF = -1.0 !   [nondim] default = -1.0
                                 ! The coefficient correlating SGS temperature variance with the mean temperature
                                 ! gradient in the deterministic part of the Stanley form of the Brankart
                                 ! correction. Negative values disable the scheme.
@@ -430,7 +430,7 @@ KHTH = 1.0                      !   [m2 s-1] default = 0.0
                                 ! The background horizontal thickness diffusivity.
 KHTH_MAX = 900.0                !   [m2 s-1] default = 0.0
                                 ! The maximum horizontal thickness diffusivity.
-STANLEY_PRM_DET_COEFF = 0.5     !   [nondim] default = -1.0
+STANLEY_PRM_DET_COEFF = -1.0    !   [nondim] default = -1.0
                                 ! The coefficient correlating SGS temperature variance with the mean temperature
                                 ! gradient in the deterministic part of the Stanley parameterization. Negative
                                 ! values disable the scheme.

config_src/drivers/FMS_cap/ocean_model_MOM.F90

@@ -276,7 +276,7 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, wind_stagger, gas
   OS%Time = Time_in ; OS%Time_dyn = Time_in
   call initialize_MOM(OS%Time, Time_init, param_file, OS%dirs, OS%MOM_CSp, &
                       OS%restart_CSp, Time_in, offline_tracer_mode=OS%offline_tracer_mode, &
-                      diag_ptr=OS%diag, count_calls=.true.)
+                      diag_ptr=OS%diag, count_calls=.true., waves_CSp=OS%Waves)
   call get_MOM_state_elements(OS%MOM_CSp, G=OS%grid, GV=OS%GV, US=OS%US, C_p=OS%C_p, &
                               C_p_scaled=OS%fluxes%C_p, use_temp=use_temperature)