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SarahAlidoostSarahAlidoost
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re-run nbs on snellius
1 parent a266471 commit 6393fef

2 files changed

Lines changed: 78 additions & 85 deletions

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‎notebooks/run_model_in_notebook.ipynb‎

Lines changed: 51 additions & 44 deletions
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@@ -88,29 +88,29 @@
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"execution_count": 5,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"{'WorkDir': '/home/sarah/temp/ecoextreml/test/',\n",
98-
" 'SoilPropertyPath': '/home/sarah/temp/ecoextreml/data/model_parameters/soil_property/',\n",
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" 'ForcingPath': '/home/sarah/temp/ecoextreml/data/forcing/plumber2_data/',\n",
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" 'ForcingFileName': 'AR-SLu_2010-2010_FLUXNET2015_Met.nc',\n",
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" 'directional': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/directional/',\n",
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" 'fluspect_parameters': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/fluspect_parameters/',\n",
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" 'leafangles': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/leafangles/',\n",
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" 'radiationdata': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/radiationdata/',\n",
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" 'soil_spectrum': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/soil_spectrum/',\n",
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" 'InitialConditionPath': '/home/sarah/temp/ecoextreml/soil_initialcondition/',\n",
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" 'input_data': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/input_data.xlsx',\n",
97+
"{'WorkDir': '/scratch-shared/ecoextreml/stemmus_scope/',\n",
98+
" 'SoilPropertyPath': '/projects/0/einf2480/model_parameters/soil_property/',\n",
99+
" 'ForcingPath': '/projects/0/einf2480/forcing/plumber2_data/',\n",
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" 'ForcingFileName': 'FI-Hyy_1996-2014_FLUXNET2015_Met.nc',\n",
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" 'directional': '/projects/0/einf2480/model_parameters/vegetation_property/directional/',\n",
102+
" 'fluspect_parameters': '/projects/0/einf2480/model_parameters/vegetation_property/fluspect_parameters/',\n",
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" 'leafangles': '/projects/0/einf2480/model_parameters/vegetation_property/leafangles/',\n",
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" 'radiationdata': '/projects/0/einf2480/model_parameters/vegetation_property/radiationdata/',\n",
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" 'soil_spectrum': '/projects/0/einf2480/model_parameters/vegetation_property/soil_spectrum/',\n",
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" 'input_data': '/projects/0/einf2480/model_parameters/vegetation_property/input_data.xlsx',\n",
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" 'InitialConditionPath': '/projects/0/einf2480/soil_initialcondition/',\n",
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" 'NumberOfTimeSteps': '5',\n",
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" 'InputPath': '/will_be_created_under_WorkDir/input/AU-DaS_2022-05-11-1705/',\n",
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" 'OutputPath': '/home/sarah/temp/ecoextreml/output/AR-SLu_2022-07-29-1451/'}"
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" 'InputPath': '',\n",
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" 'OutputPath': ''}"
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]
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},
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"execution_count": 9,
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"execution_count": 5,
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"metadata": {},
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"output_type": "execute_result"
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}
@@ -125,14 +125,14 @@
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"execution_count": 6,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"/home/sarah/temp/ecoextreml/test/input/ZA-Kru_2022-08-03-1537/ZA-Kru_2022-08-03-1537_config.txt\n"
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"/gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/ZA-Kru_2022-08-08-1439/ZA-Kru_2022-08-08-1439_config.txt\n"
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]
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}
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],
@@ -147,29 +147,29 @@
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"execution_count": 7,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"{'WorkDir': '/home/sarah/temp/ecoextreml/test/',\n",
157-
" 'SoilPropertyPath': '/home/sarah/temp/ecoextreml/data/model_parameters/soil_property/',\n",
158-
" 'ForcingPath': '/home/sarah/temp/ecoextreml/data/forcing/plumber2_data/',\n",
156+
"{'WorkDir': '/scratch-shared/ecoextreml/stemmus_scope/',\n",
157+
" 'SoilPropertyPath': '/projects/0/einf2480/model_parameters/soil_property/',\n",
158+
" 'ForcingPath': '/projects/0/einf2480/forcing/plumber2_data/',\n",
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" 'ForcingFileName': 'ZA-Kru_2000-2002_FLUXNET2015_Met.nc',\n",
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" 'directional': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/directional/',\n",
161-
" 'fluspect_parameters': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/fluspect_parameters/',\n",
162-
" 'leafangles': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/leafangles/',\n",
163-
" 'radiationdata': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/radiationdata/',\n",
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" 'soil_spectrum': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/soil_spectrum/',\n",
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" 'InitialConditionPath': '/home/sarah/temp/ecoextreml/soil_initialcondition/',\n",
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" 'input_data': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/input_data.xlsx',\n",
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" 'directional': '/projects/0/einf2480/model_parameters/vegetation_property/directional/',\n",
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" 'fluspect_parameters': '/projects/0/einf2480/model_parameters/vegetation_property/fluspect_parameters/',\n",
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" 'leafangles': '/projects/0/einf2480/model_parameters/vegetation_property/leafangles/',\n",
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" 'radiationdata': '/projects/0/einf2480/model_parameters/vegetation_property/radiationdata/',\n",
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" 'soil_spectrum': '/projects/0/einf2480/model_parameters/vegetation_property/soil_spectrum/',\n",
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" 'input_data': '/projects/0/einf2480/model_parameters/vegetation_property/input_data.xlsx',\n",
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" 'InitialConditionPath': '/projects/0/einf2480/soil_initialcondition/',\n",
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" 'NumberOfTimeSteps': '10',\n",
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" 'InputPath': '/home/sarah/temp/ecoextreml/test/input/ZA-Kru_2022-08-03-1537/',\n",
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" 'OutputPath': '/home/sarah/temp/ecoextreml/test/output/ZA-Kru_2022-08-03-1537/'}"
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" 'InputPath': '/gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/ZA-Kru_2022-08-08-1439/',\n",
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" 'OutputPath': '/gpfs/scratch1/shared/ecoextreml/stemmus_scope/output/ZA-Kru_2022-08-08-1439/'}"
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]
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},
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"execution_count": 11,
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"execution_count": 7,
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"metadata": {},
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"output_type": "execute_result"
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}
@@ -181,16 +181,16 @@
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},
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{
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"cell_type": "code",
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"execution_count": 12,
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"execution_count": 8,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"b'Reading config from /home/sarah/temp/ecoextreml/test/input/ZA-Kru_2022-08-03-1537/ZA-Kru_2022-08-03-1537_config.txt\\n\\n The calculations start now \\r\\n The calculations end now \\r'"
190+
"b'Opening log file: /gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/ZA-Kru_2022-08-08-1439//java.log.51183\\nReading config from /gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/ZA-Kru_2022-08-08-1439/ZA-Kru_2022-08-08-1439_config.txt\\nThe calculations start now\\nThe calculations end now\\n'"
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]
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},
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"execution_count": 12,
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"execution_count": 8,
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"metadata": {},
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"output_type": "execute_result"
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}
@@ -203,21 +203,21 @@
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},
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{
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"cell_type": "code",
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"execution_count": 14,
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"execution_count": 9,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"/home/sarah/temp/ecoextreml/test/output/ZA-Kru_2022-08-03-1537/ZA-Kru_2022-08-03-1537_STEMMUS_SCOPE.nc\n"
213+
"/gpfs/scratch1/shared/ecoextreml/stemmus_scope/output/ZA-Kru_2022-08-08-1439/ZA-Kru_2022-08-08-1439_STEMMUS_SCOPE.nc\n"
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]
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}
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],
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"source": [
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"# save output in netcdf format\n",
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"variables_will_be_in_NetCDF_file = \"./STEMMUS_SCOPE/utils/csv_to_nc/required_netcdf_variables.csv\"\n",
220-
"nc_file_name = save.to_netcdf(model.config, variables_will_be_in_NetCDF_file)\n",
219+
"required_netcdf_variables = \"./required_netcdf_variables.csv\"\n",
220+
"nc_file_name = save.to_netcdf(model.config, required_netcdf_variables)\n",
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"print(nc_file_name)"
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]
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},
@@ -230,17 +230,17 @@
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},
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{
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"cell_type": "code",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"b'Reading config from /home/sarah/temp/ecoextreml/test/input/ZA-Kru_2022-08-03-1541/ZA-Kru_2022-08-03-1541_config.txt\\n\\n The calculations start now \\r\\n The calculations end now \\r'\n",
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"/home/sarah/temp/ecoextreml/test/output/ZA-Kru_2022-08-03-1541/ZA-Kru_2022-08-03-1541_STEMMUS_SCOPE.nc\n",
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"b'Reading config from /home/sarah/temp/ecoextreml/test/input/AR-SLu_2022-08-03-1541/AR-SLu_2022-08-03-1541_config.txt\\n\\n The calculations start now \\r\\n The calculations end now \\r'\n",
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"/home/sarah/temp/ecoextreml/test/output/AR-SLu_2022-08-03-1541/AR-SLu_2022-08-03-1541_STEMMUS_SCOPE.nc\n"
240+
"b'Opening log file: /gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/ZA-Kru_2022-08-08-1442//java.log.63885\\nReading config from /gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/ZA-Kru_2022-08-08-1442/ZA-Kru_2022-08-08-1442_config.txt\\nThe calculations start now\\nThe calculations end now\\n'\n",
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"/gpfs/scratch1/shared/ecoextreml/stemmus_scope/output/ZA-Kru_2022-08-08-1442/ZA-Kru_2022-08-08-1442_STEMMUS_SCOPE.nc\n",
242+
"b'Opening log file: /gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/AR-SLu_2022-08-08-1442//java.log.403\\nReading config from /gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/AR-SLu_2022-08-08-1442/AR-SLu_2022-08-08-1442_config.txt\\nThe calculations start now\\nThe calculations end now\\n'\n",
243+
"/gpfs/scratch1/shared/ecoextreml/stemmus_scope/output/AR-SLu_2022-08-08-1442/AR-SLu_2022-08-08-1442_STEMMUS_SCOPE.nc\n"
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]
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}
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],
@@ -266,10 +266,17 @@
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" print(result)\n",
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" \n",
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" # save results in a netcdf file\n",
269-
" nc_file_name = save.to_netcdf(model.config, variables_will_be_in_NetCDF_file)\n",
269+
" nc_file_name = save.to_netcdf(model.config, required_netcdf_variables)\n",
270270
" print(nc_file_name)\n",
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" "
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {

‎notebooks/run_model_in_notebook_dev.ipynb‎

Lines changed: 27 additions & 41 deletions
Original file line numberDiff line numberDiff line change
@@ -10,14 +10,15 @@
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": 9,
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"metadata": {},
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"outputs": [],
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"source": [
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"import os\n",
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"from pathlib import Path\n",
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"import subprocess\n",
20-
"from PyStemmusScope import StemmusScope"
20+
"from PyStemmusScope import StemmusScope\n",
21+
"from PyStemmusScope import save"
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]
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},
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{
@@ -48,31 +49,9 @@
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},
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{
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"cell_type": "code",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Already on 'python-compliant'\n",
59-
"Your branch is up to date with 'origin/python-compliant'.\n",
60-
"On branch python-compliant\n",
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"Your branch is up to date with 'origin/python-compliant'.\n",
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"\n",
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"Untracked files:\n",
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" (use \"git add <file>...\" to include in what will be committed)\n",
65-
"\t\u001b[31mexe/mccExcludedFiles.log\u001b[m\n",
66-
"\t\u001b[31mexe/readme.txt\u001b[m\n",
67-
"\t\u001b[31mexe/requiredMCRProducts.txt\u001b[m\n",
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"\t\u001b[31mexe/run_STEMMUS_SCOPE.sh\u001b[m\n",
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"\t\u001b[31mexe/unresolvedSymbols.txt\u001b[m\n",
70-
"\t\u001b[31mslurm_1224932.out\u001b[m\n",
71-
"\n",
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"nothing added to commit but untracked files present (use \"git add\" to track)\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"dev_branch = \"python-compliant\"\n",
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"!git -C {path_to_model} checkout {dev_branch}\n",
@@ -105,9 +84,9 @@
10584
" 'soil_spectrum': '/projects/0/einf2480/model_parameters/vegetation_property/soil_spectrum/',\n",
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" 'input_data': '/projects/0/einf2480/model_parameters/vegetation_property/input_data.xlsx',\n",
10786
" 'InitialConditionPath': '/projects/0/einf2480/soil_initialcondition/',\n",
108-
" 'NumberOfTimeSteps': '17520',\n",
109-
" 'InputPath': '/scratch-shared/ecoextreml/stemmus_scope/input/FI-Hyy_2022-05-11-1705/',\n",
110-
" 'OutputPath': '/scratch-shared/ecoextreml/stemmus_scope/output/FI-Hyy_2022-05-11-1705/'}"
87+
" 'NumberOfTimeSteps': '5',\n",
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" 'InputPath': '',\n",
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" 'OutputPath': ''}"
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]
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},
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"execution_count": 4,
@@ -137,7 +116,7 @@
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"/gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/ZA-Kru_2022-07-18-1651/ZA-Kru_2022-07-18-1651_config.txt\n"
119+
"/gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/ZA-Kru_2022-08-08-1446/ZA-Kru_2022-08-08-1446_config.txt\n"
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]
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}
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],
@@ -170,8 +149,8 @@
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" 'input_data': '/projects/0/einf2480/model_parameters/vegetation_property/input_data.xlsx',\n",
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" 'InitialConditionPath': '/projects/0/einf2480/soil_initialcondition/',\n",
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" 'NumberOfTimeSteps': '5',\n",
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" 'InputPath': '/gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/ZA-Kru_2022-07-18-1651/',\n",
174-
" 'OutputPath': '/gpfs/scratch1/shared/ecoextreml/stemmus_scope/output/ZA-Kru_2022-07-18-1651/'}"
152+
" 'InputPath': '/gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/ZA-Kru_2022-08-08-1446/',\n",
153+
" 'OutputPath': '/gpfs/scratch1/shared/ecoextreml/stemmus_scope/output/ZA-Kru_2022-08-08-1446/'}"
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]
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},
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"execution_count": 6,
@@ -203,7 +182,7 @@
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"output_type": "stream",
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"text": [
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"MATLAB is selecting SOFTWARE OPENGL rendering.\n",
206-
"Opening log file: /gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/ZA-Kru_2022-07-18-1651//java.log.35508\n",
185+
"Opening log file: /gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/ZA-Kru_2022-08-08-1446//java.log.32841\n",
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"\n",
208187
" < M A T L A B (R) >\n",
209188
" Copyright 1984-2021 The MathWorks, Inc.\n",
@@ -214,10 +193,9 @@
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"To get started, type doc.\n",
215194
"For product information, visit www.mathworks.com.\n",
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" \n",
217-
"Reading config from /gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/ZA-Kru_2022-07-18-1651/ZA-Kru_2022-07-18-1651_config.txt\n",
218-
"\n",
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" The calculations start now \n",
220-
" The calculations end now \r"
196+
"Reading config from /gpfs/scratch1/shared/ecoextreml/stemmus_scope/input/ZA-Kru_2022-08-08-1446/ZA-Kru_2022-08-08-1446_config.txt\n",
197+
"The calculations start now\n",
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"The calculations end now\n"
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]
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}
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],
@@ -244,12 +222,20 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 10,
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"metadata": {},
249-
"outputs": [],
227+
"outputs": [
228+
{
229+
"name": "stdout",
230+
"output_type": "stream",
231+
"text": [
232+
"/gpfs/scratch1/shared/ecoextreml/stemmus_scope/output/ZA-Kru_2022-08-08-1446/ZA-Kru_2022-08-08-1446_STEMMUS_SCOPE.nc\n"
233+
]
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}
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],
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"source": [
251-
"variables_will_be_in_NetCDF_file = path_to_model / \"utils\" / \"csv_to_nc\" / \"required_netcdf_variables.csv\"\n",
252-
"nc_file_name = save.to_netcdf(model.config, variables_will_be_in_NetCDF_file)\n",
237+
"required_netcdf_variables = path_to_model / \"utils\" / \"csv_to_nc\" / \"required_netcdf_variables.csv\"\n",
238+
"nc_file_name = save.to_netcdf(model.config, required_netcdf_variables)\n",
253239
"print(nc_file_name)"
254240
]
255241
},

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