Merge pull request #579 from NOAA-GFDL/candidate-dev-master-2017-08-17

mom-ocean · Aug 22, 2017 · da77242 · da77242
2 parents ae22a0f + da8f186
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diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -1,138 +1,202 @@
 stages:
-  - merge
-  - setup
+  - merge+setup
   - builds
   - run
   - tests
+  - cleanup
 
-# Moves to re-used workspace
+# Merges MOM6 with dev/gfdl. Changes directory to test directory, if it exists.
 before_script:
   - MOM6_SRC=$CI_PROJECT_DIR
-  - WORKSPACE=`pwd | sed 's:/[0-9]/:/:'`
-  - git pull --no-edit https://github.com/NOAA-GFDL/MOM6.git dev/gfdl
-  - test -d $WORKSPACE/tests && cd $WORKSPACE/tests
+  - CACHE_DIR=/lustre/f1/oar.gfdl.ogrp-account/runner/cache/
+  - git pull --no-edit https://github.com/NOAA-GFDL/MOM6.git dev/gfdl && git submodule init && git submodule update
+  - pwd ; ls
 
-# Merge
+# Tests that merge with dev/gfdl works.
 merge:
-  stage: merge
+  stage: merge+setup
   tags:
     - ncrc3
   script:
-    - cd $CI_PROJECT_DIR
+    - pwd ; ls
     - git pull --no-edit https://github.com/NOAA-GFDL/MOM6.git dev/gfdl
 
 # Clones regression repo, if necessary, pulls latest of everything, and sets up working space
 setup:
-  stage: setup
+  stage: merge+setup
   tags:
     - ncrc3
   script:
-    - mkdir -p $WORKSPACE && cd $WORKSPACE
-    - ln -sf $MOM6_SRC/{config_src,src,pkg} .
-    - test -d tests || (git clone --recursive http://gitlab.gfdl.noaa.gov/ogrp/Gaea_c3-stats-MOM6-examples.git tests)
-    - cd tests
-    - git checkout . && git checkout dev/gfdl
-    - git pull
-    - git status
-    - bash Gitlab/before_script.sh
-    - (cd MOM6-examples/src/mkmf && git pull https://github.com/adcroft/mkmf.git add_coverage_mode)
+    - pwd ; ls
+    # Clone regressions directory
+    - git clone --recursive http://gitlab.gfdl.noaa.gov/ogrp/Gaea_c3-stats-MOM6-examples.git tests && cd tests
+    # Install / update testing scripts
+    - git clone https://github.com/adcroft/MRS.git MRS
+    # Update MOM6-examples and submodules
+    - (cd MOM6-examples && git checkout . && git checkout dev/gfdl && git pull && git submodule init && git submodule update)
+    - test -d MOM6-examples/src/LM3 || make -f MRS/Makefile.clone clone_gfdl -s
+    - make -f MRS/Makefile.clone MOM6-examples/.datasets -s
+    #- (cd MOM6-examples/src/mkmf && git pull https://github.com/adcroft/mkmf.git add_coverage_mode)
+    - env > gitlab_session.log
+    - cd ../ ; time tar zcf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz tests
 
 # Compiles
 gnu:repro:
   stage: builds
   tags:
     - ncrc3
   script:
-    - make -f Gitlab/Makefile.build MOM6_SRC=../ build_gnu -s -j
-    - make -f Gitlab/Makefile.build MOM6_SRC=../ static_gnu -s -j #coverage_gnu
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - time make -f MRS/Makefile.build MOM6_SRC=../ build_gnu -s -j
+    - time make -f MRS/Makefile.build MOM6_SRC=../ static_gnu -s -j
+    - time tar zvcf $CACHE_DIR/build-gnu-repro-$CI_PIPELINE_ID.tgz `find build/gnu -name MOM6`
 
 intel:repro:
   stage: builds
   tags:
     - ncrc3
   script:
-    - make -f Gitlab/Makefile.build MOM6_SRC=../ build_intel -s -j
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - make -f MRS/Makefile.build MOM6_SRC=../ build_intel -s -j
+    - time tar zvcf $CACHE_DIR/build-intel-repro-$CI_PIPELINE_ID.tgz `find build/intel -name MOM6`
 
 pgi:repro:
   stage: builds
   tags:
     - ncrc3
   script:
-    - make -f Gitlab/Makefile.build MOM6_SRC=../ build_pgi -s -j
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - make -f MRS/Makefile.build MOM6_SRC=../ build_pgi -s -j
+    - time tar zvcf $CACHE_DIR/build-pgi-repro-$CI_PIPELINE_ID.tgz `find build/pgi -name MOM6`
 
 gnu:debug:
   stage: builds
   tags:
     - ncrc3
   script:
-    - make -f Gitlab/Makefile.build MOM6_SRC=../ debug_gnu -s -j
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - make -f MRS/Makefile.build MOM6_SRC=../ debug_gnu -s -j
+    - time tar zvcf $CACHE_DIR/build-gnu-debug-$CI_PIPELINE_ID.tgz `find build/gnu -name MOM6`
 
 # Runs
 run:
   stage: run
   tags:
     - ncrc3
   script:
-    - rm -f MOM6-examples/*.tar
-    - bash Gitlab/run_stage.sh
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - time tar zxf $CACHE_DIR/build-gnu-repro-$CI_PIPELINE_ID.tgz
+    - time tar zxf $CACHE_DIR/build-intel-repro-$CI_PIPELINE_ID.tgz
+    - time tar zxf $CACHE_DIR/build-pgi-repro-$CI_PIPELINE_ID.tgz
+    # time tar zxf $CACHE_DIR/build-gnu-debug-$CI_PIPELINE_ID.tgz
+    - echo "make -f MRS/Makefile.tests all -B" > job.sh
+    - msub -l partition=c3,nodes=29,walltime=00:24:00,qos=norm -q debug -S /bin/tcsh -j oe -A gfdl_o -z -o log.$CI_PIPELINE_ID -N mom6_regression -K job.sh
+    - cat log.$CI_PIPELINE_ID
+    - time tar zvcf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz *.tar.gz
 
 # Tests
-gnu:regressions:
+gnu:non-symmetric:
   stage: tests
   tags:
     - ncrc3
   script:
-    - cd regressions && git checkout .
-    - md5sum `find . -name ocean.stats.gnu` > all_gnu.md5 && find . -name ocean.stats.gnu -exec rm {} \;
-    - echo "Regression results for non-symmetric gnu executables"
-    - tar xf ../MOM6-examples/non_symmetric_gnu.tar && md5sum -c all_gnu.md5 && rm all_gnu.md5
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - time tar zxf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz
+    - make -f MRS/Makefile.tests gnu_non_symmetric
 
-intel:regressions:
+intel:non-symmetric:
   stage: tests
   tags:
     - ncrc3
   script:
-    - cd regressions && git checkout .
-    - md5sum `find . -name ocean.stats.intel` > all_intel.md5 && find . -name ocean.stats.intel -exec rm {} \;
-    - echo "Regression results for non-symmetric intel executables"
-    - tar xf ../MOM6-examples/non_symmetric_intel.tar && md5sum -c all_intel.md5 && rm all_intel.md5
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - time tar zxf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz
+    - make -f MRS/Makefile.tests intel_non_symmetric
 
-pgi:regressions:
+pgi:non-symmetric:
   stage: tests
   tags:
     - ncrc3
   script:
-    - cd regressions && git checkout .
-    - md5sum `find . -name ocean.stats.pgi` > all_pgi.md5 && find . -name ocean.stats.pgi -exec rm {} \;
-    - echo "Regression results for non-symmetric pgi executables"
-    - tar xf ../MOM6-examples/non_symmetric_pgi.tar && md5sum -c all_pgi.md5 && rm all_pgi.md5
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - time tar zxf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz
+    - make -f MRS/Makefile.tests pgi_non_symmetric
 
 gnu:symmetric:
   stage: tests
   tags:
     - ncrc3
   script:
-    - mkdir -p _gnu && cd _gnu
-    - tar xf ../MOM6-examples/non_symmetric_gnu.tar && md5sum `find . -name ocean.stats.gnu` > all_gnu.md5 && find . -name ocean.stats.gnu -exec rm {} \;
-    - echo "Regression results for symmetric executables"
-    - tar xf ../MOM6-examples/symmetric_gnu.tar && md5sum -c all_gnu.md5 && rm all_gnu.md5
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - time tar zxf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz
+    - make -f MRS/Makefile.tests gnu_symmetric
 
 intel:symmetric:
   stage: tests
   tags:
     - ncrc3
   script:
-    - mkdir -p _intel && cd _intel
-    - tar xf ../MOM6-examples/non_symmetric_intel.tar && md5sum `find . -name ocean.stats.intel` > all_intel.md5 && find . -name ocean.stats.intel -exec rm {} \;
-    - echo "Regression results for symmetric executables"
-    - tar xf ../MOM6-examples/symmetric_intel.tar && md5sum -c all_intel.md5 && rm all_intel.md5
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - time tar zxf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz
+    - make -f MRS/Makefile.tests intel_symmetric
 
 pgi:symmetric:
   stage: tests
   tags:
     - ncrc3
   script:
-    - mkdir -p _pgi && cd _pgi
-    - tar xf ../MOM6-examples/non_symmetric_pgi.tar && md5sum `find . -name ocean.stats.pgi` > all_pgi.md5 && find . -name ocean.stats.pgi -exec rm {} \;
-    - echo "Regression results for symmetric executables"
-    - tar xf ../MOM6-examples/symmetric_pgi.tar && md5sum -c all_pgi.md5 && rm all_pgi.md5
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - time tar zxf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz
+    - make -f MRS/Makefile.tests pgi_symmetric
+
+gnu:layout:
+  stage: tests
+  tags:
+    - ncrc3
+  script:
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - time tar zxf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz
+    - make -f MRS/Makefile.tests gnu_layout
+
+intel:layout:
+  stage: tests
+  tags:
+    - ncrc3
+  script:
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - time tar zxf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz
+    - make -f MRS/Makefile.tests intel_layout
+
+pgi:layout:
+  stage: tests
+  tags:
+    - ncrc3
+  script:
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - time tar zxf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz
+    - make -f MRS/Makefile.tests pgi_layout
+
+gnu:static:
+  stage: tests
+  tags:
+    - ncrc3
+  script:
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - time tar zxf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz
+    - make -f MRS/Makefile.tests gnu_static
+
+gnu:restart:
+  stage: tests
+  tags:
+    - ncrc3
+  script:
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - time tar zxf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz
+    - make -f MRS/Makefile.tests gnu_check_restarts
+
+cleanup:
+  stage: cleanup
+  tags:
+    - ncrc3
+  script:
+    - rm $CACHE_DIR/*$CI_PIPELINE_ID.tgz
diff --git a/.travis.yml b/.travis.yml
@@ -17,7 +17,7 @@ addons:
 cache:
   directories:
     - MOM6-examples
-    - build
+#   - build # Uncomment this line to save time building. Less robust when FMS changes version!
 
 # Install tools and clone the configurations repository
 before_install:

diff --git a/config_src/coupled_driver/MOM_surface_forcing.F90 b/config_src/coupled_driver/MOM_surface_forcing.F90
@@ -67,12 +67,15 @@ module MOM_surface_forcing
 use MOM_string_functions, only : uppercase
 use MOM_spatial_means,    only : adjust_area_mean_to_zero
 use MOM_variables,        only : surface
-use user_revise_forcing,  only : user_alter_forcing, user_revise_forcing_init, user_revise_forcing_CS
-
-use coupler_types_mod,        only : coupler_2d_bc_type
-use data_override_mod,        only : data_override_init, data_override
-use fms_mod,                  only : read_data, stdout
-use mpp_mod,                  only : mpp_chksum
+use user_revise_forcing,  only : user_alter_forcing, user_revise_forcing_init
+use user_revise_forcing,  only : user_revise_forcing_CS
+
+use coupler_types_mod,    only : coupler_2d_bc_type, coupler_type_write_chksums
+use coupler_types_mod,    only : coupler_type_initialized, coupler_type_spawn
+use coupler_types_mod,    only : coupler_type_copy_data
+use data_override_mod,    only : data_override_init, data_override
+use fms_mod,              only : read_data, stdout
+use mpp_mod,              only : mpp_chksum
 use time_interp_external_mod, only : init_external_field, time_interp_external
 use time_interp_external_mod, only : time_interp_external_init
 
@@ -356,6 +359,15 @@ subroutine convert_IOB_to_fluxes(IOB, fluxes, index_bounds, Time, G, CS, state,
     fluxes%dt_buoy_accum = 0.0
   endif   ! endif for allocation and initialization
 
+  if ((.not.coupler_type_initialized(fluxes%tr_fluxes)) .and. &
+      coupler_type_initialized(IOB%fluxes)) &
+    call coupler_type_spawn(IOB%fluxes, fluxes%tr_fluxes, &
+                            (/is,is,ie,ie/), (/js,js,je,je/))
+  !   It might prove valuable to use the same array extents as the rest of the
+  ! ocean model, rather than using haloless arrays, in which case the last line
+  ! would be: (             (/isd,is,ie,ied/), (/jsd,js,je,jed/))
+
+
   if (CS%allow_flux_adjustments) then
    fluxes%heat_added(:,:)=0.0
    fluxes%salt_flux_added(:,:)=0.0
@@ -729,10 +741,9 @@ subroutine convert_IOB_to_fluxes(IOB, fluxes, index_bounds, Time, G, CS, state,
     enddo ; enddo
   endif
 
-  !   At a later time, it might prove valuable to translate this array into the
-  ! index space of the ocean model, rather than leaving it in the (haloless)
-  ! arrays that come in from the surface forcing.
-  fluxes%tr_fluxes => IOB%fluxes
+  if (coupler_type_initialized(fluxes%tr_fluxes) .and. &
+      coupler_type_initialized(IOB%fluxes)) &
+    call coupler_type_copy_data(IOB%fluxes, fluxes%tr_fluxes)
 
   if (CS%allow_flux_adjustments) then
     ! Apply adjustments to fluxes
@@ -1227,16 +1238,9 @@ subroutine ice_ocn_bnd_type_chksum(id, timestep, iobt)
       write(outunit,100) 'iobt%area_berg      ', mpp_chksum( iobt%area_berg      )
     if (ASSOCIATED(iobt%mass_berg)) &
       write(outunit,100) 'iobt%mass_berg      ', mpp_chksum( iobt%mass_berg      )
-
 100 FORMAT("   CHECKSUM::",A20," = ",Z20)
-    do n = 1, iobt%fluxes%num_bcs  !{
-       do m = 1, iobt%fluxes%bc(n)%num_fields  !{
-          write(outunit,101) 'iobt%',trim(iobt%fluxes%bc(n)%name), &
-               trim(iobt%fluxes%bc(n)%field(m)%name), &
-               mpp_chksum(iobt%fluxes%bc(n)%field(m)%values)
-       enddo  !} m
-    enddo  !} n
-101 FORMAT("   CHECKSUM::",A6,a,'%',a," = ",Z20)
+
+    call coupler_type_write_chksums(iobt%fluxes, outunit, 'iobt%')
 
 end subroutine ice_ocn_bnd_type_chksum