Merge branch 'dev/gfdl' into user_module_units

.github/actions/testing-setup/action.yml

@@ -5,10 +5,6 @@ inputs:
     description: 'If true, will build the symmetric MOM6 executable'
     required: false
     default: 'true'
-  install_python:
-    description: 'If true, will install the local python env needed for .testing'
-    required: false
-    default: 'true'
 runs:
   using: 'composite'
   steps:
@@ -54,14 +50,6 @@ runs:
         test ${{ inputs.build_symmetric }} == true && make build/symmetric/MOM6 -j
         echo "::endgroup::"
 
-    - name: Install local python venv for generating input data
-      shell: bash
-      run: |
-        echo "::group::Create local python env for input data generation"
-        cd .testing
-        test ${{ inputs.install_python }} == true && make work/local-env
-        echo "::endgroup::"
-
     - name: Set flags
       shell: bash
       run: |

.github/workflows/coupled-api.yml

@@ -20,7 +20,6 @@ jobs:
     - uses: ./.github/actions/testing-setup
       with:
         build_symmetric: 'false'
-        install_python: 'false'
 
     - name: Compile MOM6 for the GFDL coupled driver
       shell: bash

.gitlab-ci.yml

@@ -26,7 +26,7 @@ p:merge:
 
 # Setup the persistent JOB_DIR for all subsequent stages
 #
-# This basically setups up a complete tree much as a user would in their workflow 
+# This basically setups up a complete tree much as a user would in their workflow
 p:clone:
   stage: setup
   tags:
@@ -181,11 +181,11 @@ actions:gnu:
     - echo -e "\e[0Ksection_start:`date +%s`:compile[collapsed=true]\r\e[0KCompiling executables"
     - cd .testing
     - module unload PrgEnv-pgi PrgEnv-intel PrgEnv-gnu darshan ; module load PrgEnv-gnu ; module unload netcdf gcc ; module load gcc/7.3.0 cray-hdf5 cray-netcdf
-    - make work/local-env
     - make -s -j
     - echo -e "\e[0Ksection_end:`date +%s`:compile\r\e[0K"
-    - (echo '#!/bin/bash';echo '. ./work/local-env/bin/activate';echo 'make MPIRUN="srun -mblock --exclusive" test -s -j') > job.sh
-    - sbatch --clusters=c3,c4 --nodes=5 --time=0:05:00 --account=gfdl_o --qos=debug --job-name=MOM6.gnu.testing --output=log.$CI_JOB_ID --wait job.sh && make test || ( cat log.$CI_JOB_ID ; exit 911 )
+    - (echo '#!/bin/bash';echo 'make MPIRUN="srun -mblock --exclusive" test -s -j') > job.sh
+    - sbatch --clusters=c3,c4 --nodes=5 --time=0:05:00 --account=gfdl_o --qos=debug --job-name=MOM6.gnu.testing --output=log.$CI_JOB_ID --wait job.sh || ( cat log.$CI_JOB_ID ; exit 911 )
+    - make test.summary
 
 actions:intel:
   stage: tests
@@ -200,11 +200,11 @@ actions:intel:
     - echo -e "\e[0Ksection_start:`date +%s`:compile[collapsed=true]\r\e[0KCompiling executables"
     - cd .testing
     - module unload PrgEnv-pgi PrgEnv-intel PrgEnv-gnu darshan; module load PrgEnv-intel; module unload netcdf intel; module load intel/18.0.6.288 cray-hdf5 cray-netcdf
-    - make work/local-env
     - make -s -j
     - echo -e "\e[0Ksection_end:`date +%s`:compile\r\e[0K"
-    - (echo '#!/bin/bash';echo '. ./work/local-env/bin/activate';echo 'make MPIRUN="srun -mblock --exclusive" test -s -j') > job.sh
-    - sbatch --clusters=c3,c4 --nodes=5 --time=0:05:00 --account=gfdl_o --qos=debug --job-name=MOM6.intel.testing --output=log.$CI_JOB_ID --wait job.sh && make test || ( cat log.$CI_JOB_ID ; exit 911 )
+    - (echo '#!/bin/bash';echo 'make MPIRUN="srun -mblock --exclusive" test -s -j') > job.sh
+    - sbatch --clusters=c3,c4 --nodes=5 --time=0:05:00 --account=gfdl_o --qos=debug --job-name=MOM6.intel.testing --output=log.$CI_JOB_ID --wait job.sh || ( cat log.$CI_JOB_ID ; exit 911 )
+    - make test.summary
 
 # Tests
 #

.testing/Makefile

@@ -11,7 +11,7 @@
 #       Delete the MOM6 test executables and dependency builds (FMS)
 #
 #   make clean.build
-#   	Delete only the MOM6 test executables
+#       Delete only the MOM6 test executables
 #
 #
 # Configuration:
@@ -204,34 +204,11 @@ endif
 FMS_SOURCE = $(call SOURCE,deps/fms/src)
 
 
-#---
-# Python preprocessing environment configuration
-
-HAS_NUMPY = $(shell python -c "import numpy" 2> /dev/null && echo "yes")
-HAS_NETCDF4 = $(shell python -c "import netCDF4" 2> /dev/null && echo "yes")
-
-USE_VENV =
-ifneq ($(HAS_NUMPY), yes)
-  USE_VENV = yes
-endif
-ifneq ($(HAS_NETCDF4), yes)
-  USE_VENV = yes
-endif
-
-# When disabled, activation is a null operation (`true`)
-VENV_PATH =
-VENV_ACTIVATE = true
-ifeq ($(USE_VENV), yes)
-  VENV_PATH = work/local-env
-  VENV_ACTIVATE = . $(VENV_PATH)/bin/activate
-endif
-
-
 #---
 # Rules
 
 .PHONY: all build.regressions build.prof
-all: $(foreach b,$(BUILDS),build/$(b)) $(VENV_PATH)
+all: $(foreach b,$(BUILDS),build/$(b))
 build.regressions: $(foreach b,symmetric target,build/$(b)/MOM6)
 build.prof: $(foreach b,opt opt_target,build/$(b)/MOM6)
 
@@ -382,8 +359,8 @@ deps/Makefile: ../ac/deps/Makefile
 # broken the ability to compile.  This is not a means to build a complete
 # coupled executable.
 # TODO:
-# 	- Avoid re-building FMS and MOM6 src by re-using existing object/mod files
-# 	- Use autoconf rather than mkmf templates
+#   - Avoid re-building FMS and MOM6 src by re-using existing object/mod files
+#   - Use autoconf rather than mkmf templates
 MK_TEMPLATE ?= ../../deps/mkmf/templates/ncrc-gnu.mk
 
 # NUOPC driver
@@ -402,21 +379,6 @@ build/mct/mom_ocean_model_mct.o: build/mct/Makefile
 check_mom6_api_mct: build/mct/mom_ocean_model_mct.o
 
 
-#---
-# Python preprocessing
-
-# NOTE: Some less mature environments (e.g. Arm64 Ubuntu) require explicit
-#   installation of numpy before netCDF4, as well as wheel and cython support.
-work/local-env:
-	python3 -m venv $@
-	. $@/bin/activate \
-	  && python3 -m pip install --upgrade pip \
-	  && pip3 install wheel \
-	  && pip3 install cython \
-	  && pip3 install numpy \
-	  && pip3 install netCDF4
-
-
 #---
 # Testing
 
@@ -555,6 +517,20 @@ $(foreach c,$(CONFIGS),$(eval $(call CONFIG_DIM_RULE,$(c))))
 	@echo -e "$(PASS): Diagnostics $*.regression.diag agree."
 
 
+#---
+# Preprocessing
+# NOTE: This only support tc4, but can be generalized over all tests.
+.PHONY: preproc
+preproc: tc4/Makefile
+	cd tc4 && $(MAKE) LAUNCHER="$(MPIRUN)"
+
+tc4/Makefile: tc4/configure tc4/Makefile.in
+	cd $(@D) && ./configure || (cat config.log && false)
+
+tc4/configure: tc4/configure.ac
+	cd $(@D) && autoreconf -if
+
+
 #---
 # Test run output files
 
@@ -567,17 +543,10 @@ $(foreach c,$(CONFIGS),$(eval $(call CONFIG_DIM_RULE,$(c))))
 # $(6): Number of MPI ranks
 
 define STAT_RULE
-work/%/$(1)/ocean.stats work/%/$(1)/chksum_diag: build/$(2)/MOM6 $(VENV_PATH)
+work/%/$(1)/ocean.stats work/%/$(1)/chksum_diag: build/$(2)/MOM6 | preproc
 	@echo "Running test $$*.$(1)..."
 	mkdir -p $$(@D)
 	cp -RL $$*/* $$(@D)
-	if [ -f $$(@D)/Makefile ]; then \
-	  $$(VENV_ACTIVATE) \
-	    && cd $$(@D) \
-	    && $(MAKE); \
-	else \
-	  cd $$(@D); \
-	fi
 	mkdir -p $$(@D)/RESTART
 	echo -e "$(4)" > $$(@D)/MOM_override
 	rm -f results/$$*/std.$(1).{out,err}
@@ -615,7 +584,7 @@ report.cov: run.cov codecov
 	  || { \
 	    cat build/cov/codecov.err ; \
 	    echo -e "${RED}Failed to upload report.${RESET}" ; \
-		if [ "$(REQUIRE_COVERAGE_UPLOAD)" = true ] ; then false ; fi ; \
+	    if [ "$(REQUIRE_COVERAGE_UPLOAD)" = true ] ; then false ; fi ; \
 	  }
 
 # Define $(,) as comma escape character
@@ -643,17 +612,10 @@ $(eval $(call STAT_RULE,cov,cov,true,,,1))
 #  2. Convert DAYMAX from TIMEUNIT to seconds
 #  3. Apply seconds to `ocean_solo_nml` inside input.nml.
 # NOTE: Assumes that runtime set by DAYMAX, will fail if set by input.nml
-work/%/restart/ocean.stats: build/symmetric/MOM6 $(VENV_PATH)
+work/%/restart/ocean.stats: build/symmetric/MOM6 | preproc
 	rm -rf $(@D)
 	mkdir -p $(@D)
 	cp -RL $*/* $(@D)
-	if [ -f $(@D)/Makefile ]; then \
-	  $(VENV_ACTIVATE) \
-	    && cd work/$*/restart \
-	    && $(MAKE); \
-	else \
-	  cd work/$*/restart; \
-	fi
 	mkdir -p $(@D)/RESTART
 	# Set the half-period
 	cd $(@D) \
@@ -754,7 +716,7 @@ report.cov.unit: build/unit/MOM_file_parser_tests.F90.gcov codecov
 	  || { \
 	    cat build/unit/codecov.err ; \
 	    echo -e "${RED}Failed to upload report.${RESET}" ; \
-		if [ "$(REQUIRE_COVERAGE_UPLOAD)" = true ] ; then false ; fi ; \
+	    if [ "$(REQUIRE_COVERAGE_UPLOAD)" = true ] ; then false ; fi ; \
 	  }
 
 
@@ -833,6 +795,13 @@ clean.build:
 
 
 .PHONY: clean.stats
-clean.stats:
+clean.stats: clean.preproc
 	@[ $$(basename $$(pwd)) = .testing ]
 	rm -rf work results
+
+
+.PHONY: clean.preproc
+clean.preproc:
+	@if [ -f tc4/Makefile ] ; then \
+	  cd tc4 && make clean ; \
+	fi

.testing/tc4/.gitignore

@@ -1,4 +1,15 @@
+# Autoconf
+aclocal.m4
+autom4te.cache/
+config.log
+config.status
+configure~
+
+# Output
+gen_grid
 ocean_hgrid.nc
+topog.nc
+
+gen_data
 sponge.nc
 temp_salt_ic.nc
-topog.nc

.testing/tc4/Makefile.in

@@ -0,0 +1,59 @@
+FC = @FC@
+LD = @LD@
+FCFLAGS = @FCFLAGS@
+LDFLAGS = @LDFLAGS@
+LIBS = @LIBS@
+
+LAUNCHER ?=
+
+OUT = ocean_hgrid.nc topog.nc temp_salt_ic.nc sponge.nc
+
+# Since each program generates two outputs, we can only use one to track the
+# creation.  The second rule is used to indirectly re-invoke the first rule.
+#
+# Reference:
+# https://www.gnu.org/software/automake/manual/html_node/Multiple-Outputs.html
+
+# Program output
+all: ocean_hgrid.nc temp_salt_ic.nc
+
+ocean_hgrid.nc: gen_grid
+	$(LAUNCHER) ./gen_grid
+topog.nc: ocean_hgrid.nc
+	@test -f $@ || rm -f $^
+	@test -f $@ || $(MAKE) $^
+
+temp_salt_ic.nc: gen_data ocean_hgrid.nc
+	$(LAUNCHER) ./gen_data
+sponge.nc: temp_salt_ic.nc
+	@test -f $@ || rm -f $^
+	@test -f $@ || $(MAKE) $^
+
+
+# Programs
+
+gen_grid: gen_grid.F90
+	$(FC) $(FCFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS)
+
+gen_data: gen_data.F90
+	$(FC) $(FCFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS)
+
+
+# Support
+
+.PHONY: clean
+clean:
+	rm -rf $(OUT) gen_grid gen_data
+
+.PHONY: distclean
+distclean: clean
+	rm -f config.log
+	rm -f config.status
+	rm -f Makefile
+
+.PHONY: ac-clean
+ac-clean: distclean
+	rm -f aclocal.m4
+	rm -rf autom4te.cache
+	rm -f configure
+	rm -f configure~