Merge branch 'dev/ncar' into fix_debug_mode

.testing/Makefile

@@ -0,0 +1,77 @@
+# Makefile steps to run on Travis-CI
+# e.g. make MEMORY_SHAPE=dynamic_symmetric REPRO=1 OPENMP=1
+
+# Versions to use
+FMS_COMMIT ?= xanadu
+MKMF_COMMIT ?= master
+
+# Where to clone from
+FMS_URL ?= https://github.com/NOAA-GFDL/FMS.git
+MKMF_URL ?= https://github.com/NOAA-GFDL/mkmf.git
+CONFIGS_URL ?= https://github.com/NOAA-GFDL/MOM6-examples.git
+REGRESSIONS_URL ?= https://github.com/adcroft/Gaea-stats-MOM6-examples
+
+# Experiments to run
+ifeq ($(MEMORY_SHAPE),"dynamic_symmetric")
+EXPERIMENTS ?= unit_tests double_gyre flow_downslope/z CVmix_SCM_tests/cooling_only/EPBL circle_obcs
+else
+EXPERIMENTS ?= unit_tests double_gyre flow_downslope/z CVmix_SCM_tests/cooling_only/EPBL
+endif
+
+FMS_PACKAGES ?= platform,include,memutils,constants,mpp,fms,time_manager,diag_manager,data_override,coupler/ensemble_manager.F90,axis_utils,horiz_interp,time_interp,astronomy,mosaic,random_numbers
+TEMPLATE ?= .testing/linux-ubuntu-xenial-gnu.mk
+MPIRUN ?= mpirun
+
+# MEMORY_SHAPE must be defined for this Makefile to work
+MEMORY_SHAPE ?= dynamic_symmetric
+
+# Everything above is above is "configurable" with environment variables
+SHELL = bash
+
+# Path where executable will be built
+BUILD_PATH = build
+###/$(MEMORY_SHAPE)-$(EXEC_MODE)
+# Root of configurations (MOM6-examples)
+EXPERIMENTS_ROOT = experiments
+# Regression results
+REGRESSIONS_ROOT = answers
+
+.PRECIOUS: %/ocean.stats
+
+run: $(foreach e,$(EXPERIMENTS),$(EXPERIMENTS_ROOT)/ocean_only/$(e)/ocean.stats)
+
+test: $(foreach e,$(EXPERIMENTS),$(REGRESSIONS_ROOT)/regressions/ocean_only/$(e)/ocean.stats.gnu)
+
+compile: $(BUILD_PATH)/MOM6
+
+$(BUILD_PATH)/MOM6: FMS mkmf
+	mkdir -p $(@D)
+	cd $(@D); \
+	../mkmf/bin/list_paths -l ../FMS/{$(FMS_PACKAGES)} ../config_src/{$(MEMORY_SHAPE),solo_driver} ../src \
+	&& ../mkmf/bin/mkmf -t ../$(TEMPLATE) -c '-Duse_libMPI -Duse_netCDF -DSPMD -DUSE_LOG_DIAG_FIELD_INFO -DMAXFIELDMETHODS_=500' -p $(@F) path_names \
+	&& make -j NETCDF=3 $(@F)
+
+$(EXPERIMENTS_ROOT)/%/ocean.stats: $(EXPERIMENTS_ROOT)
+	mkdir -p $(@D)/RESTART
+	cd $(@D) ; $(MPIRUN) -n 1 $(PWD)/$(BUILD_PATH)/MOM6
+
+$(REGRESSIONS_ROOT)/regressions/%/ocean.stats.gnu: $(EXPERIMENTS_ROOT)/%/ocean.stats $(REGRESSIONS_ROOT)
+	cp $< $@
+	cd $(@D) ; git status --porcelain $(@F)
+
+# Targets to clone repositories needed to build
+FMS:
+	git clone -q $(FMS_URL)
+	cd $@ ; git checkout -q $(FMS_COMMIT)
+
+mkmf:
+	git clone -q $(MKMF_URL)
+	cd $@ ; git checkout -q $(MKMF_COMMIT)
+
+$(EXPERIMENTS_ROOT):
+	mkdir -p $(@D)
+	cd $(@D) ; git clone --depth 1 $(CONFIGS_URL) experiments
+
+$(REGRESSIONS_ROOT):
+	mkdir -p $(@D)
+	cd $(@D) ; git clone --depth 1 $(REGRESSIONS_URL) answers

.testing/README.md

@@ -0,0 +1,3 @@
+# .testing
+
+This directory contains scripts used when evaluating commits on Travis-CI

.testing/configure

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+echo "Configured!" $MAKEARGS
+touch build/test_${MAKEARGS//\ /_}

.testing/linux-ubuntu-xenial-gnu.mk

@@ -0,0 +1,273 @@
+# Template for the GNU Compiler Collection on Xenial version of Ubuntu Linux systems (used by Travis-CI)
+#
+# Typical use with mkmf
+# mkmf -t linux-ubuntu-xenial-gnu.mk -c"-Duse_libMPI -Duse_netCDF" path_names /usr/local/include
+
+############
+# Commands Macors
+FC = mpif90
+CC = mpicc
+LD = mpif90 $(MAIN_PROGRAM)
+
+#######################
+# Build target macros
+#
+# Macros that modify compiler flags used in the build.  Target
+# macrose are usually set on the call to make:
+#
+#    make REPRO=on NETCDF=3
+#
+# Most target macros are activated when their value is non-blank.
+# Some have a single value that is checked.  Others will use the
+# value of the macro in the compile command.
+
+DEBUG =              # If non-blank, perform a debug build (Cannot be
+                     # mixed with REPRO or TEST)
+
+REPRO =              # If non-blank, erform a build that guarentees
+                     # reprodicuibilty from run to run.  Cannot be used
+                     # with DEBUG or TEST
+
+TEST  =              # If non-blank, use the compiler options defined in
+                     # the FFLAGS_TEST and CFLAGS_TEST macros.  Cannot be
+                     # use with REPRO or DEBUG
+
+VERBOSE =            # If non-blank, add additional verbosity compiler
+                     # options
+
+OPENMP =             # If non-blank, compile with openmp enabled
+
+NO_OVERRIDE_LIMITS = # If non-blank, do not use the -qoverride-limits
+                     # compiler option.  Default behavior is to compile
+                     # with -qoverride-limits.
+
+NETCDF =             # If value is '3' and CPPDEFS contains
+                     # '-Duse_netCDF', then the additional cpp macro
+                     # '-Duse_LARGEFILE' is added to the CPPDEFS macro.
+
+INCLUDES =           # A list of -I Include directories to be added to the
+                     # the compile command.
+
+SSE =                # The SSE options to be used to compile.  If blank,
+                     # than use the default SSE settings for the host.
+                     # Current default is to use SSE2.
+
+COVERAGE =           # Add the code coverage compile options.
+
+# Need to use at least GNU Make version 3.81
+need := 3.81
+ok := $(filter $(need),$(firstword $(sort $(MAKE_VERSION) $(need))))
+ifneq ($(need),$(ok))
+$(error Need at least make version $(need).  Load module gmake/3.81)
+endif
+
+# REPRO, DEBUG and TEST need to be mutually exclusive of each other.
+# Make sure the user hasn't supplied two at the same time
+ifdef REPRO
+ifneq ($(DEBUG),)
+$(error Options REPRO and DEBUG cannot be used together)
+else ifneq ($(TEST),)
+$(error Options REPRO and TEST cannot be used together)
+endif
+else ifdef DEBUG
+ifneq ($(TEST),)
+$(error Options DEBUG and TEST cannot be used together)
+endif
+endif
+
+MAKEFLAGS += --jobs=$(shell grep '^processor' /proc/cpuinfo | wc -l)
+
+# Macro for Fortran preprocessor
+FPPFLAGS := $(INCLUDES)
+# Fortran Compiler flags for the NetCDF library
+FPPFLAGS += $(shell nf-config --fflags)
+
+# Base set of Fortran compiler flags
+FFLAGS := -fcray-pointer -fdefault-double-8 -fdefault-real-8 -Waliasing -ffree-line-length-none -fno-range-check
+
+# Flags based on perforance target (production (OPT), reproduction (REPRO), or debug (DEBUG)
+FFLAGS_OPT = -O3
+FFLAGS_REPRO = -O2 -fbounds-check
+FFLAGS_DEBUG = -O0 -g -W -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow
+
+# Flags to add additional build options
+FFLAGS_OPENMP = -fopenmp
+FFLAGS_VERBOSE =
+FFLAGS_COVERAGE =
+
+# Macro for C preprocessor
+CPPFLAGS = $(INCLUDES)
+# C Compiler flags for the NetCDF library
+CPPFLAGS += $(shell nf-config --cflags)
+
+# Base set of C compiler flags
+CFLAGS := -D__IFC
+
+# Flags based on perforance target (production (OPT), reproduction (REPRO), or debug (DEBUG)
+CFLAGS_OPT = -O2
+CFLAGS_REPRO = -O2
+CFLAGS_DEBUG = -O0 -g
+
+# Flags to add additional build options
+CFLAGS_OPENMP = -fopenmp
+CFLAGS_VERBOSE =
+CFLAGS_COVERAGE =
+
+# Optional Testing compile flags.  Mutually exclusive from DEBUG, REPRO, and OPT
+# *_TEST will match the production if no new option(s) is(are) to be tested.
+FFLAGS_TEST = $(FFLAGS_OPT)
+CFLAGS_TEST = $(CFLAGS_OPT)
+
+# Linking flags
+LDFLAGS :=
+LDFLAGS_OPENMP := -fopenmp
+LDFLAGS_VERBOSE :=
+LDFLAGS_COVERAGE :=
+
+# Start with a blank LIBS
+LIBS =
+# NetCDF library flags
+LIBS += $(shell nf-config --flibs)
+
+# Get compile flags based on target macros.
+ifdef REPRO
+CFLAGS += $(CFLAGS_REPRO)
+FFLAGS += $(FFLAGS_REPRO)
+else ifdef DEBUG
+CFLAGS += $(CFLAGS_DEBUG)
+FFLAGS += $(FFLAGS_DEBUG)
+else ifdef TEST
+CFLAGS += $(CFLAGS_TEST)
+FFLAGS += $(FFLAGS_TEST)
+else
+CFLAGS += $(CFLAGS_OPT)
+FFLAGS += $(FFLAGS_OPT)
+endif
+
+ifdef OPENMP
+CFLAGS += $(CFLAGS_OPENMP)
+FFLAGS += $(FFLAGS_OPENMP)
+LDFLAGS += $(LDFLAGS_OPENMP)
+endif
+
+ifdef SSE
+CFLAGS += $(SSE)
+FFLAGS += $(SSE)
+endif
+
+ifdef NO_OVERRIDE_LIMITS
+FFLAGS += $(FFLAGS_OVERRIDE_LIMITS)
+endif
+
+ifdef VERBOSE
+CFLAGS += $(CFLAGS_VERBOSE)
+FFLAGS += $(FFLAGS_VERBOSE)
+LDFLAGS += $(LDFLAGS_VERBOSE)
+endif
+
+ifeq ($(NETCDF),3)
+  # add the use_LARGEFILE cppdef
+  ifneq ($(findstring -Duse_netCDF,$(CPPDEFS)),)
+    CPPDEFS += -Duse_LARGEFILE
+  endif
+endif
+
+ifdef COVERAGE
+ifdef BUILDROOT
+PROF_DIR=-prof-dir=$(BUILDROOT)
+endif
+CFLAGS += $(CFLAGS_COVERAGE) $(PROF_DIR)
+FFLAGS += $(FFLAGS_COVERAGE) $(PROF_DIR)
+LDFLAGS += $(LDFLAGS_COVERAGE) $(PROF_DIR)
+endif
+
+LDFLAGS += $(LIBS)
+
+#---------------------------------------------------------------------------
+# you should never need to change any lines below.
+
+# see the MIPSPro F90 manual for more details on some of the file extensions
+# discussed here.
+# this makefile template recognizes fortran sourcefiles with extensions
+# .f, .f90, .F, .F90. Given a sourcefile <file>.<ext>, where <ext> is one of
+# the above, this provides a number of default actions:
+
+# make <file>.opt	create an optimization report
+# make <file>.o		create an object file
+# make <file>.s		create an assembly listing
+# make <file>.x		create an executable file, assuming standalone
+#			source
+# make <file>.i		create a preprocessed file (for .F)
+# make <file>.i90	create a preprocessed file (for .F90)
+
+# The macro TMPFILES is provided to slate files like the above for removal.
+
+RM = rm -f
+TMPFILES = .*.m *.B *.L *.i *.i90 *.l *.s *.mod *.opt
+
+.SUFFIXES: .F .F90 .H .L .T .f .f90 .h .i .i90 .l .o .s .opt .x
+
+.f.L:
+	$(FC) $(FFLAGS) -c -listing $*.f
+.f.opt:
+	$(FC) $(FFLAGS) -c -opt_report_level max -opt_report_phase all -opt_report_file $*.opt $*.f
+.f.l:
+	$(FC) $(FFLAGS) -c $(LIST) $*.f
+.f.T:
+	$(FC) $(FFLAGS) -c -cif $*.f
+.f.o:
+	$(FC) $(FFLAGS) -c $*.f
+.f.s:
+	$(FC) $(FFLAGS) -S $*.f
+.f.x:
+	$(FC) $(FFLAGS) -o $*.x $*.f *.o $(LDFLAGS)
+.f90.L:
+	$(FC) $(FFLAGS) -c -listing $*.f90
+.f90.opt:
+	$(FC) $(FFLAGS) -c -opt_report_level max -opt_report_phase all -opt_report_file $*.opt $*.f90
+.f90.l:
+	$(FC) $(FFLAGS) -c $(LIST) $*.f90
+.f90.T:
+	$(FC) $(FFLAGS) -c -cif $*.f90
+.f90.o:
+	$(FC) $(FFLAGS) -c $*.f90
+.f90.s:
+	$(FC) $(FFLAGS) -c -S $*.f90
+.f90.x:
+	$(FC) $(FFLAGS) -o $*.x $*.f90 *.o $(LDFLAGS)
+.F.L:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -listing $*.F
+.F.opt:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -opt_report_level max -opt_report_phase all -opt_report_file $*.opt $*.F
+.F.l:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c $(LIST) $*.F
+.F.T:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -cif $*.F
+.F.f:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) -EP $*.F > $*.f
+.F.i:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) -P $*.F
+.F.o:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c $*.F
+.F.s:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -S $*.F
+.F.x:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -o $*.x $*.F *.o $(LDFLAGS)
+.F90.L:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -listing $*.F90
+.F90.opt:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -opt_report_level max -opt_report_phase all -opt_report_file $*.opt $*.F90
+.F90.l:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c $(LIST) $*.F90
+.F90.T:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -cif $*.F90
+.F90.f90:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) -EP $*.F90 > $*.f90
+.F90.i90:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) -P $*.F90
+.F90.o:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c $*.F90
+.F90.s:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -S $*.F90
+.F90.x:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -o $*.x $*.F90 *.o $(LDFLAGS)