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get working on derecho, save figures
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@adrifoster
adrifoster committed Apr 17, 2024
1 parent 98cb1a4 commit e5571ed
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Showing 2 changed files with 57 additions and 21 deletions.
17 changes: 13 additions & 4 deletions functional_unit_testing/build_fortran_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,13 +44,17 @@ def run_cmake(name, test_dir, pfunit_path, netcdf_c_path, netcdf_f_path, cmake_a
f"-DCIME_CMAKE_MODULE_DIRECTORY={cmake_module_dir}",
"-DCMAKE_BUILD_TYPE=CESM_DEBUG",
f"-DCMAKE_PREFIX_PATH={pfunit_path}",
f"-DNETCDF_C_PATH={netcdf_c_path}",
f"-DNETCDF_F_PATH={netcdf_f_path}",
"-DUSE_MPI_SERIAL=ON",
"-DENABLE_GENF90=ON",
f"-DCMAKE_PROGRAM_PATH={genf90_dir}"
]

if netcdf_c_path is not None:
cmake_command.append(f"-DNETCDF_C_PATH={netcdf_c_path}")

if netcdf_f_path is not None:
cmake_command.append(f"-DNETCDF_F_PATH={netcdf_f_path}")

cmake_command.extend(cmake_args.split(" "))

run_cmd_no_fail(" ".join(cmake_command), combine_output=True)
Expand Down Expand Up @@ -210,8 +214,13 @@ def build_unit_tests(build_dir, name, cmake_directory, make_j, clean=False):
# get cmake args and the pfunit and netcdf paths
cmake_args = get_extra_cmake_args(full_build_path, "mpi-serial")
pfunit_path = find_library(full_build_path, cmake_args, "PFUNIT_PATH")
netcdf_c_path = find_library(full_build_path, cmake_args, "NETCDF_C_PATH")
netcdf_f_path = find_library(full_build_path, cmake_args, "NETCDF_FORTRAN_PATH")

if not "NETCDF" in os.environ:
netcdf_c_path = find_library(full_build_path, cmake_args, "NETCDF_C_PATH")
netcdf_f_path = find_library(full_build_path, cmake_args, "NETCDF_FORTRAN_PATH")
else:
netcdf_c_path = None
netcdf_f_path = None

# change into the build dir
os.chdir(full_build_path)
Expand Down
61 changes: 44 additions & 17 deletions functional_unit_testing/run_fates_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,14 +72,16 @@ def get_color_pallete():
return colors


def plot_allometry_var(data, var, varname, units):
def plot_allometry_var(data, var, varname, units, save_fig, plot_dir=None):
"""Plot an allometry variable
Args:
data (xarray DataArray): the data array of the variable to plot
var (str): variable name (for data structure)
varname (str): variable name for plot labels
units (str): variable units for plot labels
save_fig (bool): whether or not to write out plot
plot_dir (str): if saving figure, where to write to
"""
df = pd.DataFrame({'dbh': np.tile(data.dbh, len(data.pft)),
'pft': np.repeat(data.pft, len(data.dbh)),
Expand Down Expand Up @@ -126,8 +128,12 @@ def plot_allometry_var(data, var, varname, units):
plt.title(f"Simulated {varname} for input parameter file", fontsize=11)
plt.legend(loc='upper left', title='PFT')

if save_fig:
fig_name = os.path.join(plot_dir, f"allometry_plot_{var}.png")
plt.savefig(fig_name)

def plot_total_biomass(data):

def plot_total_biomass(data, save_fig, plot_dir):
"""Plot two calculations of total biomass against each other
Args:
Expand Down Expand Up @@ -169,6 +175,10 @@ def plot_total_biomass(data):
plt.ylabel('Total biomass (kgC) from tissues', fontsize=11)
plt.title("Simulated total biomass for input parameter file", fontsize=11)
plt.legend(loc='upper left', title='PFT')

if save_fig:
fig_name = os.path.join(plot_dir, "allometry_plot_total_biomass_compare.png")
plt.savefig(fig_name)

def create_nc_file(cdl_path, run_dir):
"""Creates a netcdf file from a cdl file
Expand Down Expand Up @@ -235,7 +245,7 @@ def run_exectuables(build_dir, test_dir, test_exe, run_dir, args):
print(out)


def run_tests(clean, build, run, build_dir, run_dir, make_j, param_file):
def run_tests(clean, build, run, build_dir, run_dir, make_j, param_file, save_figs):
"""Builds and runs the fates tests
Args:
Expand All @@ -246,6 +256,7 @@ def run_tests(clean, build, run, build_dir, run_dir, make_j, param_file):
run_dir (str): run directory
make_j (int): number of processors for the build
param_file (str): input FATES parameter file
save_figs (bool): whether or not to write figures to file
Raises:
RuntimeError: Parameter file is not the correct file type
Expand All @@ -260,6 +271,13 @@ def run_tests(clean, build, run, build_dir, run_dir, make_j, param_file):
if not os.path.isdir(run_dir_path):
os.mkdir(run_dir_path)

if save_figs:
plot_dir = os.path.join(run_dir_path, 'plots')
if not os.path.isdir(plot_dir):
os.mkdir(plot_dir)
else:
plot_dir = None

if param_file is None:
print("Using default parameter file.")
param_file = DEFAULT_CDL_PATH
Expand All @@ -284,19 +302,19 @@ def run_tests(clean, build, run, build_dir, run_dir, make_j, param_file):
allometry_dat = xr.open_dataset(os.path.join(run_dir_path, out_file))

# plot allometry data
plot_allometry_var(allometry_dat.height, 'height', 'height', 'm')
plot_allometry_var(allometry_dat.bagw, 'bagw', 'aboveground biomass', 'kgC')
plot_allometry_var(allometry_dat.blmax, 'blmax', 'maximum leaf biomass', 'kgC')
plot_allometry_var(allometry_dat.crown_area, 'crown_area', 'crown area', 'm$^2$')
plot_allometry_var(allometry_dat.sapwood_area, 'sapwood_area', 'sapwood area', 'm$^2$')
plot_allometry_var(allometry_dat.bsap, 'bsap', 'sapwood biomass', 'kgC')
plot_allometry_var(allometry_dat.bbgw, 'bbgw', 'belowground biomass', 'kgC')
plot_allometry_var(allometry_dat.fineroot_biomass, 'fineroot_biomass', 'fineroot biomass', 'kgC')
plot_allometry_var(allometry_dat.bstore, 'bstore', 'storage biomass', 'kgC')
plot_allometry_var(allometry_dat.bdead, 'bdead', 'deadwood biomass', 'kgC')
plot_allometry_var(allometry_dat.total_biomass_parts, 'total_biomass_parts', 'total biomass (calculated from parts)', 'kgC')
plot_allometry_var(allometry_dat.total_biomass_tissues, 'total_biomass_tissues', 'total biomass (calculated from tissues)', 'kgC')
plot_total_biomass(allometry_dat)
plot_allometry_var(allometry_dat.height, 'height', 'height', 'm', save_figs, plot_dir)
plot_allometry_var(allometry_dat.bagw, 'bagw', 'aboveground biomass', 'kgC', save_figs, plot_dir)
plot_allometry_var(allometry_dat.blmax, 'blmax', 'maximum leaf biomass', 'kgC', save_figs, plot_dir)
plot_allometry_var(allometry_dat.crown_area, 'crown_area', 'crown area', 'm$^2$', save_figs, plot_dir)
plot_allometry_var(allometry_dat.sapwood_area, 'sapwood_area', 'sapwood area', 'm$^2$', save_figs, plot_dir)
plot_allometry_var(allometry_dat.bsap, 'bsap', 'sapwood biomass', 'kgC', save_figs, plot_dir)
plot_allometry_var(allometry_dat.bbgw, 'bbgw', 'belowground biomass', 'kgC', save_figs, plot_dir)
plot_allometry_var(allometry_dat.fineroot_biomass, 'fineroot_biomass', 'fineroot biomass', 'kgC', save_figs, plot_dir)
plot_allometry_var(allometry_dat.bstore, 'bstore', 'storage biomass', 'kgC', save_figs, plot_dir)
plot_allometry_var(allometry_dat.bdead, 'bdead', 'deadwood biomass', 'kgC', save_figs, plot_dir)
plot_allometry_var(allometry_dat.total_biomass_parts, 'total_biomass_parts', 'total biomass (calculated from parts)', 'kgC', save_figs, plot_dir)
plot_allometry_var(allometry_dat.total_biomass_tissues, 'total_biomass_tissues', 'total biomass (calculated from tissues)', 'kgC', save_figs, plot_dir)
plot_total_biomass(allometry_dat, save_figs, plot_dir)
plt.show()


Expand Down Expand Up @@ -373,6 +391,14 @@ def commandline_args():
"Script will check to make sure required output files are present.\n",
)

parser.add_argument(
"--save-figs",
action="store_true",
help="Write out generated figures to files.\n"
"Will be placed in run_dir/plots.\n"
"Should probably do this on remote machines.\n",
)

args = parser.parse_args()

check_arg_validity(args)
Expand Down Expand Up @@ -442,7 +468,8 @@ def main():
build = not args.skip_build
run = not args.skip_run

run_tests(args.clean, build, run, args.build_dir, args.run_dir, args.make_j, args.parameter_file)
run_tests(args.clean, build, run, args.build_dir, args.run_dir, args.make_j,
args.parameter_file, args.save_figs)

if __name__ == "__main__":

Expand Down

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