Merge pull request #3 from NOAA-GFDL/dev/gfdl

Updating dev/gfdl to Aug 30th 2019

.gitignore

@@ -3,3 +3,6 @@
 *~
 html
 *.log
+MOM6
+build/
+deps/

.gitlab-ci.yml

@@ -32,6 +32,7 @@ setup:
     - git clone --recursive http://gitlab.gfdl.noaa.gov/ogrp/Gaea-stats-MOM6-examples.git tests && cd tests
     # Install / update testing scripts
     - git clone https://github.com/adcroft/MRS.git MRS
+    - (cd MRS ; git checkout xanadu-fms)
     # Update MOM6-examples and submodules
     - (cd MOM6-examples && git checkout . && git checkout dev/gfdl && git pull && git submodule init && git submodule update)
     - (cd MOM6-examples/src/MOM6 && git submodule update)
@@ -73,7 +74,7 @@ gnu:ice-ocean-nolibs:
     - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
     - make -f MRS/Makefile.build build/gnu/env && cd build/gnu
     # mkdir -p build/gnu/repro/symmetric_dynamic/ocean_only && cd build/gnu/repro/symmetric_dynamic/ocean_only
-    - ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{coupled_driver,dynamic} ../../../src ../../MOM6-examples/src/{FMS,coupler,SIS2,icebergs,ice_ocean_extras,land_null,atmos_null}
+    - ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{coupled_driver,dynamic} ../../../src ../../MOM6-examples/src/{FMS,coupler,SIS2,icebergs,ice_param,land_null,atmos_null}
     - ../../MOM6-examples/src/mkmf/bin/mkmf -t ../../MOM6-examples/src/mkmf/templates/ncrc-gnu.mk -p MOM6 -c"-Duse_libMPI -Duse_netCDF -D_USE_LEGACY_LAND_ -Duse_AM3_physics" path_names
     - time (source ./env ; make NETCDF=3 REPRO=1 MOM6 -s -j)
 
@@ -115,8 +116,8 @@ run:
     - 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=c4,nodes=29,walltime=00:31:00,qos=norm -q debug -S /bin/tcsh -j oe -A gfdl_o -z -o log.$CI_PIPELINE_ID -N mom6_regression -K job.sh
+    - (echo '#!/bin/tcsh';echo 'make -f MRS/Makefile.tests all -B') > job.sh
+    - sbatch --clusters=c3,c4 --nodes=29 --time=0:34:00 --account=gfdl_o --qos=debug --job-name=mom6_regressions --output=log.$CI_PIPELINE_ID --wait job.sh
     - cat log.$CI_PIPELINE_ID
     - test -f restart_results_gnu.tar.gz
     - time tar zvcf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz *.tar.gz

.testing/.gitignore

@@ -0,0 +1,15 @@
+available_diags.*
+CPU_stats
+chksum_diag
+exitcode
+logfile.*.out
+MOM_parameter_doc.*
+ocean_geometry.nc
+ocean.stats*
+RESTART/
+time_stamp.out
+Vertical_coordinate.nc
+GOLD_IC.nc
+debug.out
+chksum_diag.*
+config.mk

.testing/Makefile

@@ -0,0 +1,288 @@
+SHELL = bash
+MPIRUN ?= mpirun
+
+-include config.mk
+
+#---
+# Dependencies
+BASE = $(dir $(abspath $(lastword $(MAKEFILE_LIST))))/..
+DEPS = $(BASE)/deps
+BUILD = $(BASE)/build
+
+# mkmf, list_paths (GFDL build toolchain)
+MKMF_URL ?= https://github.com/NOAA-GFDL/mkmf.git
+MKMF_COMMIT ?= master
+LIST_PATHS := $(abspath $(DEPS)/mkmf/bin/list_paths)
+MKMF := $(abspath $(DEPS)/mkmf/bin/mkmf)
+
+# FMS framework
+FMS_URL ?= https://github.com/NOAA-GFDL/FMS.git
+FMS_COMMIT ?= f2e2c86f6c0eb6d389a20509a8a60fa22924e16b
+FMS := $(DEPS)/fms
+
+#---
+# Build configuration
+
+# Build settings
+MKMF_CPP = "-Duse_libMPI -Duse_netCDF -DSPMD"
+
+# Environment
+# TODO: This info ought to be determined by CMake, automake, etc.
+#MKMF_TEMPLATE ?= .testing/linux-ubuntu-xenial-gnu.mk
+MKMF_TEMPLATE ?= $(DEPS)/mkmf/templates/ncrc-gnu.mk
+#MKMF_TEMPLATE ?= $(DEPS)/mkmf/templates/ncrc-intel.mk
+
+#---
+# Test configuration
+
+# Executables
+BUILDS = symmetric asymmetric repro
+CONFIGS := $(wildcard tc*)
+TESTS = grids layouts restarts repros nans dims
+
+# The following variables are configured by Travis:
+#   DO_REGRESSION_TESTS: true if $(TRAVIS_PULL_REQUEST) is a PR number
+#   MOM_TARGET_SLUG: TRAVIS_REPO_SLUG
+#   MOM_TARGET_LOCAL_BRANCH: TRAVIS_BRANCH
+#
+# These are set to true by Travis if testing a pull request
+DO_REGRESSION_TESTS ?=
+REPORT_COVERAGE ?=
+
+ifeq ($(DO_REGRESSION_TESTS), true)
+	BUILDS += target
+	TEST += regressions
+
+	MOM_TARGET_SLUG ?= NOAA-GFDL/MOM6
+	MOM_TARGET_URL ?= https://github.com/$(MOM_TARGET_SLUG)
+
+	MOM_TARGET_LOCAL_BRANCH ?= dev/gfdl
+	MOM_TARGET_BRANCH := origin/$(MOM_TARGET_LOCAL_BRANCH)
+
+	TARGET_CODEBASE = $(BUILD)/target_codebase
+else
+	MOM_TARGET_URL =
+	MOM_TARGET_BRANCH =
+	TARGET_CODEBASE =
+endif
+
+
+#---
+# Rules
+
+.PHONY: all
+all: $(foreach b,$(BUILDS),$(BUILD)/$(b)/MOM6)
+
+# Executable
+BUILD_TARGETS = MOM6 Makefile path_names
+.PRECIOUS: $(foreach b,$(BUILDS),$(foreach f,$(BUILD_TARGETS),$(BUILD)/$(b)/$(f)))
+
+# Conditionally build symmetric with coverage support
+COVFLAG=$(if $(REPORT_COVERAGE),COVERAGE=1,)
+
+$(BUILD)/target/MOM6: MOMFLAGS=NETCDF=3 DEBUG=1
+$(BUILD)/symmetric/MOM6: MOMFLAGS=NETCDF=3 DEBUG=1 $(COVFLAG)
+$(BUILD)/asymmetric/MOM6: MOMFLAGS=NETCDF=3 DEBUG=1
+$(BUILD)/repro/MOM6: MOMFLAGS=NETCDF=3 REPRO=1
+
+$(BUILD)/asymmetric/path_names: GRID_SRC=config_src/dynamic
+$(BUILD)/%/path_names: GRID_SRC=config_src/dynamic_symmetric
+
+$(BUILD)/%/MOM6: $(BUILD)/%/Makefile $(FMS)/lib/libfms.a
+	make -C $(@D) $(MOMFLAGS) $(@F)
+
+$(BUILD)/%/Makefile: $(BUILD)/%/path_names
+	cp $(MKMF_TEMPLATE) $(@D)
+	cd $(@D) && $(MKMF) \
+		-t $(notdir $(MKMF_TEMPLATE)) \
+		-o '-I $(FMS)/build' \
+		-p MOM6 \
+		-l '$(FMS)/lib/libfms.a' \
+		-c $(MKMF_CPP) \
+		path_names
+
+# NOTE: These path_names rules could be merged
+
+$(BUILD)/target/path_names: $(LIST_PATHS) $(TARGET_CODEBASE)
+	mkdir -p $(@D)
+	cd $(@D) && $(LIST_PATHS) -l \
+		$(TARGET_CODEBASE)/src \
+		$(TARGET_CODEBASE)/config_src/solo_driver \
+		$(TARGET_CODEBASE)/$(GRID_SRC)
+
+$(BUILD)/%/path_names: $(LIST_PATHS)
+	mkdir -p $(@D)
+	cd $(@D) && $(LIST_PATHS) -l \
+		$(BASE)/src \
+		$(BASE)/config_src/solo_driver \
+		$(BASE)/$(GRID_SRC)
+
+# Target repository for regression tests
+$(TARGET_CODEBASE):
+	git clone --recursive $(MOM_TARGET_URL) $@
+	cd $@ && git checkout $(MOM_TARGET_BRANCH)
+
+
+#----
+# FMS build
+
+$(FMS)/lib/libfms.a: $(FMS)/build/Makefile
+	mkdir -p $(FMS)/lib
+	cd $(FMS)/build && make NETCDF=3 DEBUG=1 ../lib/libfms.a
+
+$(FMS)/build/Makefile: $(FMS)/build/path_names
+	cp $(MKMF_TEMPLATE) $(@D)
+	cd $(@D) && $(MKMF) \
+		-t $(notdir $(MKMF_TEMPLATE)) \
+		-p ../lib/libfms.a \
+		-c $(MKMF_CPP) \
+		path_names
+
+$(FMS)/build/path_names: $(FMS)/src $(FMS_FILES) $(LIST_PATHS)
+	mkdir -p $(@D)
+	cd $(@D) && $(LIST_PATHS) -l ../src
+
+$(FMS)/src:
+	git clone $(FMS_URL) $@
+	cd $@; git checkout $(FMS_COMMIT)
+
+
+#---
+# Build Toolchain
+
+$(LIST_PATHS) $(MKMF):
+	git clone $(MKMF_URL) $(DEPS)/mkmf
+	cd $(DEPS)/mkmf; git checkout $(MKMF_COMMIT)
+
+
+#----
+# Testing
+
+.PHONY: test
+test: $(foreach t,$(TESTS),test.$(t))
+
+# NOTE: We remove tc3 (OBC) from grid test since it cannot run asymmetric grids
+
+.PHONY: $(foreach t,$(TESTS),test.$(t))
+test.regressions: $(foreach c,$(CONFIGS),$(c).regression $(c).regression.diag)
+test.grids: $(foreach c,$(filter-out tc3,$(CONFIGS)),$(c).grid $(c).grid.diag)
+test.layouts: $(foreach c,$(CONFIGS),$(c).layout $(c).layout.diag)
+test.restarts: $(foreach c,$(CONFIGS),$(c).restart)
+test.repros: $(foreach c,$(CONFIGS),$(c).repro $(c).repro.diag)
+test.nans: $(foreach c,$(CONFIGS),$(c).nan $(c).nan.diag)
+test.dims: $(foreach c,$(CONFIGS),$(foreach d,t l h z,$(c).dim.$(d) $(c).dim.$(d).diag))
+
+# NOTE: chksum_diag return code of cmp is currently ignored since many fail!
+define CMP_RULE
+.PRECIOUS: $(foreach b,$(2),$(BASE)/.testing/%/ocean.stats.$(b))
+%.$(1): $(foreach b,$(2),$(BASE)/.testing/%/ocean.stats.$(b))
+	cmp $$^
+
+.PRECIOUS: $(foreach b,$(2),$(BASE)/.testing/%/chksum_diag.$(b))
+%.$(1).diag: $(foreach b,$(2),$(BASE)/.testing/%/chksum_diag.$(b))
+	cmp $$^ || true
+endef
+
+$(eval $(call CMP_RULE,regression,symmetric target))
+$(eval $(call CMP_RULE,grid,symmetric asymmetric))
+$(eval $(call CMP_RULE,layout,symmetric layout))
+$(eval $(call CMP_RULE,repro,symmetric repro))
+$(eval $(call CMP_RULE,nan,symmetric nan))
+$(foreach d,t l h z,$(eval $(call CMP_RULE,dim.$(d),symmetric dim.$(d))))
+
+# Restart tests only compare the final stat record
+.PRECIOUS: $(foreach b,symmetric restart,$(BASE)/.testing/%/ocean.stats.$(b))
+%.restart: $(foreach b,symmetric restart,$(BASE)/.testing/%/ocean.stats.$(b))
+	cmp $(foreach f,$^,<(tr -s ' ' < $(f) | cut -d ' ' -f3- | tail -n 1))
+
+# TODO: chksum_diag parsing of restart files
+
+
+#---
+# Test run output files
+
+#(1): Configuration name
+#(2): Executable type
+#(3): Enable coverage flag
+#(4): MOM_override configuration
+#(5): Environment variables
+#(6): Number of MPI ranks
+
+# Simple function for generalised Slurm (srun) and OpenMPI (mpirun) support
+# (1): Environment variables
+
+ifeq ($(MPIRUN), srun)
+MPIRUN_CMD=$(1) $(MPIRUN)
+else
+MPIRUN_CMD=$(MPIRUN) $(if $(1),-x $(1),)
+endif
+
+define STAT_RULE
+$$(BASE)/.testing/%/ocean.stats.$(1): $$(BUILD)/$(2)/MOM6
+	if [ $(3) ]; then find $$(BUILD) -name *.gcda -exec rm -f '{}' \; ; fi
+	mkdir -p $$(@D)/RESTART
+	echo $(4) > $$(@D)/MOM_override
+	cd $$(@D) && $$(call MPIRUN_CMD,$(5)) -n $(6) $$< 2> debug.out
+	cp $$(@D)/ocean.stats $$@
+	> $$(@D)/MOM_override
+	if [ $(3) ]; then cd $$(BASE) && bash <(curl -s https://codecov.io/bash) -n $$@; fi
+
+$$(BASE)/.testing/%/chksum_diag.$(1): $$(BASE)/.testing/%/ocean.stats.$(1)
+	cp $$(@D)/chksum_diag $$@
+endef
+
+# Define $(,) as comma escape character
+, := ,
+
+$(eval $(call STAT_RULE,symmetric,symmetric,$(REPORT_COVERAGE),,,1))
+$(eval $(call STAT_RULE,asymmetric,asymmetric,,,,1))
+$(eval $(call STAT_RULE,target,target,,,,1))
+$(eval $(call STAT_RULE,repro,repro,,,,1))
+$(eval $(call STAT_RULE,layout,symmetric,,LAYOUT=2$(,)1,,2))
+$(eval $(call STAT_RULE,nan,symmetric,,,MALLOC_PERTURB_=256,1))
+$(eval $(call STAT_RULE,dim.t,symmetric,,T_RESCALE_POWER=11,,1))
+$(eval $(call STAT_RULE,dim.l,symmetric,,L_RESCALE_POWER=11,,1))
+$(eval $(call STAT_RULE,dim.h,symmetric,,H_RESCALE_POWER=11,,1))
+$(eval $(call STAT_RULE,dim.z,symmetric,,Z_RESCALE_POWER=11,,1))
+
+# Restart tests require signicant preprocessing, and are handled separately.
+$(BASE)/.testing/%/ocean.stats.restart: $(BUILD)/symmetric/MOM6
+	# Cleanup
+	mkdir -p $(@D)/RESTART
+	git checkout $(@D)/input.nml
+	> $(@D)/MOM_override
+	# Generate the half-period input namelist
+	# TODO: Assumes runtime set by DAYMAX, will fail if set by input.nml
+	cd $(@D) \
+		&& daymax=$$(grep DAYMAX MOM_input | cut -d '!' -f 1 | cut -d '=' -f 2 | xargs) \
+		&& timeunit=$$(grep TIMEUNIT MOM_input | cut -d '!' -f 1 | cut -d '=' -f 2 | xargs) \
+		&& if [ -z "$${timeunit}" ]; then timeunit="8.64e4"; fi \
+		&& printf -v timeunit_int "%.f" "$${timeunit}" \
+		&& halfperiod=$$(printf "%.f" $$(bc <<< "scale=10; 0.5 * $${daymax} * $${timeunit_int}")) \
+		&& printf "\n&ocean_solo_nml\n    seconds = $${halfperiod}\n/\n" >> input.nml \
+		&& echo $${daymax} $${timeunit}
+	# Run the first half-period
+	cd $(@D) && $(MPIRUN) -n 1 $< 2> debug.out
+	# Setup the next inputs
+	rm -rf $(@D)/INPUT && mv $(@D)/RESTART $(@D)/INPUT
+	mkdir $(@D)/RESTART
+	cd $(@D) && sed -i -e "s/input_filename *= *'n'/input_filename = 'r'/g" input.nml
+	# Run the second half-period
+	cd $(@D) && $(MPIRUN) -n 1 $< 2> debug.out
+	# Archive the results and cleanup
+	cp $(@D)/ocean.stats $@
+	rm -rf $(@D)/INPUT
+	git checkout $(@D)/input.nml
+
+# TODO: Restart checksum diagnostics
+
+
+#----
+.PHONY: clean
+clean: clean.stats
+	rm -rf $(BUILD)
+
+.PHONY: clean.stats
+clean.stats:
+	find $(BASE)/.testing -name ocean.stats* -exec rm {} \;
+	find $(BASE)/.testing -name chksum_diag* -exec rm {} \;