Add dev utils

.github/dev/utils/DEBUGGING_FLAGS.patch

@@ -0,0 +1,61 @@
+diff --git a/config/compiler.gfortran.mk b/config/compiler.gfortran.mk
+index 007a335..3fdf8e4 100644
+--- a/config/compiler.gfortran.mk
++++ b/config/compiler.gfortran.mk
+@@ -24,7 +24,7 @@ endif
+
+ FMAKEDEP = $(SCRIPTS_DIR)/sfmakedepend
+ CPPFLAGS += -DCOMPILER_G95
+-FFLAGS = -g -cpp -fconvert=big-endian -O2 -fno-range-check -fallow-argument-mismatch
++FFLAGS = -g -cpp -fconvert=big-endian -O0 -Wall -fcheck=bounds -fcheck=do -fcheck=mem -fcheck=recursion -fbacktrace -fallow-argument-mismatch
+ F90FLAGS = $(FFLAGS) -ffree-line-length-none
+ LFLAGS =
+ ifeq ($(MP),YES)
+diff --git a/config/rules.mk b/config/rules.mk
+index d981c80..87ef4f2 100644
+--- a/config/rules.mk
++++ b/config/rules.mk
+@@ -62,7 +62,7 @@ I = I
+ # by default assume that fortran compiler can do cpp
+ EXTERNAL_CPP = NO
+ # assume that C compiler understands basic gcc flags
+-CFLAGS = -O2
++CFLAGS = -O0
+ # check if ABI was specified
+ ifneq ($(ABI),)
+   CFLAGS += -m$(ABI)
+@@ -430,7 +430,7 @@ endif
+ 	 $(CPP) $(CPPFLAGS) $< > $@
+
+ %.o: %.c
+-	$(CC) -c -O2 -m64 $<
++	$(CC) -c -O0 -Wall -fcheck=bounds -fcheck=do -fcheck=mem -fcheck=recursion -g -fbacktrace -fallow-argument-mismatch -m64 $<
+
+ %.f: %.m4f
+ 	-rm -f $@
+diff --git a/decks/Makefile b/decks/Makefile
+index 4d2791a..c167dc6 100644
+--- a/decks/Makefile
++++ b/decks/Makefile
+@@ -140,7 +140,7 @@ ifeq ($(GC),YES)
+ 		-DCMAKE_Fortran_COMPILER="$(F90)" \
+ 		-DCMAKE_Fortran_FLAGS="$(F90FLAGS)" \
+ 		-DCMAKE_EXE_LINKER_FLAGS="$(CTM_LFLAGS)"
+-	cd $(GC_BUILD_DIR) && make -j install
++	cd $(GC_BUILD_DIR) && make VERBOSE=1 -j install
+ 	cp $(GC_BUILD_DIR)/mod/*.mod $(MODEL_DIR)/mod/
+ 	cp $(GC_BUILD_DIR)/src/HEMCO/mod/*.mod $(MODEL_DIR)/mod/
+ 	cp $(GC_BUILD_DIR)/src/Cloud-J/mod/*.mod $(MODEL_DIR)/mod/
+diff --git a/modele-control.pyar b/modele-control.pyar
+index cf10239..1d78b27 100644
+--- a/modele-control.pyar
++++ b/modele-control.pyar
+@@ -3447,7 +3447,7 @@ macro(modele_set_flags)
+     add_definitions(-DCOMPILER_G95)
+     # This breaks if you try to wrap the long line in the obvious way.
+     set (CMAKE_Fortran_FLAGS_RELEASE "${CPPFLAGS} -O2 -g -fconvert=big-endian -fno-range-check -ffree-line-length-none")
+-    set (CMAKE_Fortran_FLAGS_DEBUG "${CPPFLAGS} -O -g -fbacktrace -fconvert=big-endian -fno-range-check -ffree-line-length-none -fcheck=bounds -fcheck=do -fcheck=mem -fcheck=recursion")
++    set (CMAKE_Fortran_FLAGS_DEBUG "${CPPFLAGS} -O0 -g -fbacktrace -fconvert=big-endian -fno-range-check -ffree-line-length-none -fcheck=bounds -fcheck=do -fcheck=mem -fcheck=recursion")
+
+
+     if (CMAKE_BUILD_TYPE MATCHES Release)

.github/dev/utils/build.sh

@@ -0,0 +1,106 @@
+#!/usr/bin/bash
+
+# Set up the environment used by GISS-GC
+# NOTE: Path may need to be edited for your system
+source ${HOME}/software/GISS-GC/setup.sh
+
+# Default values
+FRESH=false
+OPENMP=false
+GISS_ONLY=false
+DEBUG=false
+
+# Function to display help text
+show_help() {
+  echo "Usage: $0 [MP=YES|NO] [--openmp] [--giss-only] [-f] [--debug]"
+  echo
+  echo "Options:"
+  echo "  --help      Show this help message and exit."
+  echo "  --openmp    Compile with OpenMP enabled."
+  echo "  --giss-only Build without GEOS-Chem coupling."
+  echo "  -f          Fresh rebuild of the model."
+  echo "  --debug     Run with debugging turned on."
+}
+
+# Check for --help option
+if [ "$1" = "--help" ]; then
+  show_help
+  exit 0
+fi
+
+# Parse arguments
+for arg in "$@"; do
+  case $arg in
+  NP=*)
+    NP="${arg#*=}"
+    ;;
+  --openmp)
+    OPENMP=true
+    shift
+    ;;
+  -f)
+    FRESH=true
+    shift
+    ;;
+  --giss-only)
+    GISS_ONLY=true
+    shift
+    ;;
+  --debug)
+    DEBUG=true
+    shift
+    ;;
+  *)
+    echo "Unknown argument: $arg"
+    show_help
+    exit 1
+    ;;
+  esac
+done
+
+if [ "${GISS_ONLY}" = true ]; then
+  GC=NO
+  RUNID=GISS_ONLY
+else
+  GC=YES
+  RUNID=GISS_GC_14
+  # Copy over configuration files
+  HUGE_SPACE=${HOME}/data/giss-gc/huge_space/${RUNID}
+  PROD_RUNS=${HOME}/run/giss-gc/prod_runs/${RUNID}
+  for RUNDIR in ${HUGE_SPACE} ${PROD_RUNS}; do
+    ln -s -f ${GISS_HOME}/geoschem_config.yml ${RUNDIR}/geoschem_config.yml
+    ln -s -f ${GISS_HOME}/HEMCO_Config.rc ${RUNDIR}/HEMCO_Config.rc
+    ln -s -f ${GISS_HOME}/HEMCO_Diagn.rc ${RUNDIR}/HEMCO_Diagn.rc
+    ln -s -f ${GISS_HOME}/HISTORY.rc ${RUNDIR}/HISTORY.rc
+    ln -s -f ${GISS_HOME}/species_database.yml ${RUNDIR}/species_database.yml
+  done
+  # Create output directories
+  mkdir -p ${HUGE_SPACE}/OutputDir
+  mkdir -p ${PROD_RUNS}/OutputDir
+fi
+
+# Print the values for verification
+echo "NP=${NP}"
+echo "OPENMP=${OPENMP}"
+echo "GC=${GC}"
+echo "FRESH=${FRESH}"
+echo "DEBUG=${DEBUG}"
+
+# Conditionally fresh rebuild of the model
+cd ${GISS_HOME}/decks/
+cp ${GISS_HOME}/.github/rundecks/${RUNID}.R .
+if [ "${FRESH}" = true ]; then
+  make clean
+  make clean_all
+fi
+
+# Compile
+if [ "${DEBUG}" = true ]; then
+  git apply .github/utils/DEBUGGING_FLAGS.patch
+  make -j setup RUN=${RUNID} F90=mpif90 GC=${GC} MP=${OPENMP} MPI=YES MECH=carbon \
+    TYPE=Debug DEBUG=YES COMPILE_WITH_TRAPS=YES TRACEBACK=YES OVERWRITE=YES
+  git apply -R .github/utils/DEBUGGING_FLAGS.patch
+else
+  make -j setup RUN=${RUNID} F90=mpif90 GC=${GC} MP=${OPENMP} MPI=YES MECH=carbon \
+    TYPE=Release
+fi

.github/dev/utils/run.sh

@@ -0,0 +1,53 @@
+#!/usr/bin/sh
+
+# Default values
+NP=1
+GISS_ONLY=false
+
+# Function to display help text
+show_help() {
+  echo "Usage: $0 [NP=<integer>] [--giss-only]"
+  echo
+  echo "Arguments:"
+  echo "  NP          Set number of MPI processes (default: 1). Must be an integer."
+  echo
+  echo "Options:"
+  echo "  --help      Show this help message and exit."
+  echo "  --giss-only Build without GEOS-Chem coupling."
+}
+
+# Check for --help option
+if [ "$1" = "--help" ]; then
+  show_help
+  exit 0
+fi
+
+# Parse arguments
+for arg in "$@"; do
+  case $arg in
+  NP=*)
+    NP="${arg#*=}"
+    ;;
+  --giss-only)
+    GISS_ONLY=true
+    shift
+    ;;
+  *)
+    echo "Unknown argument: $arg"
+    show_help
+    exit 1
+    ;;
+  esac
+done
+
+# Set RUNID appropriately
+if [ "${GISS_ONLY}" = true ]; then
+  RUNID=GISS_ONLY
+else
+  RUNID=GISS_GC_14
+fi
+
+# Navigate to the run directory and run the model for one hour
+cd ~/run/giss-gc/prod_runs/${RUNID}
+./${RUNID}ln
+mpiexec -np ${NP} ./${RUNID}.exe -i I -cold-restart

.github/dev/utils/setup.sh

@@ -0,0 +1,42 @@
+#!/usr/bin/bash
+# ============================================================================ #
+# Activate the Python and spack environments used by GISS-GC.                  #
+# ============================================================================ #
+
+# Envronment variables for GISS modelE
+# NOTE: Path may need to be edited for your system
+export GISS_HOME=${SOFTWARE}/GISS-GC
+export ModelE_Support=${HOME}/run/giss-gc
+mkdir -p ${ModelE_Support}
+# Environment variables for compiler
+export CC=gcc
+export CXX=g++
+export FC=gfortran
+export F90=${FC}
+export F77=${FC}
+# Misc. enviroment variables
+export F_UFMTENDIAN=big
+export KMP_STACKSIZE=100000000
+export OMP_NUM_THREADS=1
+
+# Spack setup
+spack env activate -p giss-gc
+export MPI_ROOT=${HOME}/software/spack/opt/spack/linux-ubuntu22.04-skylake/gcc-11.4.0/openmpi-4.1.6-s3fu5gvaasgjy4jecnb6rvemx7oofexx
+
+# Environment variables for passing NetCDF-C paths to GEOS-Chem
+export NETCDF_HOME=$(nc-config --prefix)
+export GC_BIN=${NETCDF_HOME}/bin
+export GC_INCLUDE=${NETCDF_HOME}/include
+export GC_LIB=${NETCDF_HOME}/lib
+
+# Environment variables for passing NetCDF-Fortran paths to GEOS-Chem
+export NETCDF_F_HOME=$(nf-config --prefix)
+export GC_F_BIN=${NETCDF_F_HOME}/bin
+export GC_F_INCLUDE=${NETCDF_F_HOME}/include
+export GC_F_LIB=${NETCDF_F_HOME}/lib
+
+# GEOS-Chem input data
+export ROOT=${DATA}/gcclassic/ExtData/HEMCO/
+
+# Put tools in the path
+export PATH=${SOFTWARE}/tools/mk_diags:${PATH}