Run Summa model on HPC

Structure for Unifying Multiple Modeling Alternative (SUMMA) is a hydrologic modeling approach that is built on a common set of conservation equations and a common numerical solver, which together constitute the structural core of the model. Different modeling approaches can then be implemented within the structural core, enabling a controlled and systematic analysis of alternative modeling options, and providing insight for future model development.

This notebook demonstrates how to harmonize different libraries and tools provided in the CyberGIS-Jupyter environment to run SUMMA model with a High Performance Computer (HPC) resource (Lyu 2019). The SUMMA Model instance used is a part of the Clark et al., (2015) study, and explored the impact of different stomatal resistance parameterizations on total evapotranspiration (ET) in the Reynolds Mountain East catchment in southwestern Idaho.

Lyu, F., Yin, D., Padmanabhan, A., Choi, Y., Goodall, J. L., Castronova, A., Tarboton, D., Wang, S. (2019) “Bridging Reproducible Hydrological Modeling with CyberGIS-Jupyter: A Case Study on SUMMA”. In: Proceedings of Practice and Experience in Advanced Research Computing (PEARC19), July 28-August 1, 2019, Chicago, IL, USA. https://dl.acm.org/citation.cfm?id=3333052

Clark, M. P., B. Nijssen, J. Lundquist, D. Kavetski, D. Rupp, R. Woods, E. Gutmann, A. Wood, D. Gochis, R. Rasmussen, D. Tarboton, V. Mahat, G. Flerchinger, and D. Marks, 2015: A unified approach for process-based hydrologic modeling: Part 2. Model implementation and example applications. Water Resources Research, 51, doi: 10.1002/2015WR017200

Retrieve a Summa model instance resource from HydroShare

In [1]:
resource_id = '1f3f310af8364d2aa3e6a9459152a21c'
import json
import os
from hs_restclient import HydroShare, HydroShareAuthBasic
auth = HydroShareAuthBasic("cybergis", "demo")
hs = HydroShare(auth=auth)
base_dir = os.path.abspath('/home/jovyan/work')
download_dir = os.path.join(base_dir, 'Downloads')
!mkdir -p {download_dir}
hs.getResource(resource_id, destination=download_dir, unzip=True)

Unzip model instance package

In [2]:
import os
#Unzip model file
model_folder_name = "SummaModel_ReynoldsAspenStand_StomatalResistance_sopron"
content_folder = os.path.join(download_dir ,"{}/{}/data/contents".format(resource_id, resource_id))
file_manger_rel_path = "settings/summa_fileManager_riparianAspenSimpleResistance.txt"
import tempfile
workspace_dir = os.path.join(base_dir, 'workspace')
!mkdir -p {workspace_dir}
unzip_dir = tempfile.mkdtemp(dir=workspace_dir)
!cd {content_folder} && unzip -o {model_folder_name}.zip -d {unzip_dir}
print("Unzipping Done")
Archive:  SummaModel_ReynoldsAspenStand_StomatalResistance_sopron.zip
   creating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/
   creating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/data/
   creating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/data/forcingData/
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/data/forcingData/forcing_above_aspen.nc  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/data/reynolds_geojson_latlon.geojson  
   creating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/data/validationData/
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/data/validationData/ReynoldsCreek_eddyFlux.nc  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/installTestCases_local.sh  
   creating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/output/
   creating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/GENPARM.TBL  
   creating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/dos2unix.sh  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/Model_Output.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zBasinModelVarMeta.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zBasinParamMeta.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zCategoryMeta.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zForceMeta.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zLocalAttributeMeta.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zLocalModelIndexMeta.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zLocalModelVarMeta.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zLocalParamMeta.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zModelIndexMeta.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zParamMeta.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zTimeMeta.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/var_lookup.f90  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/MPTABLE.TBL  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/SOILPARM.TBL  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_fileManager_riparianAspenSimpleResistance.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zBasinParamInfo.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zDecisions_riparianAspenSimpleResistance.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zForcingFileList_riparianAspen.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zForcingInfo_riparianAspen.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zInitialCond.nc  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zLocalAttributes_riparianAspen.nc  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zLocalParamInfo.txt  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zParamTrial_riparianAspen.nc  
  inflating: /home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/VEGPARM.TBL  
Unzipping Done

"Install" SUMMA model on Jupyter server (fix broken path in summa file_manager)

In [3]:
model_source_folder_path = os.path.join(unzip_dir, model_folder_name)
!cd {model_source_folder_path} && chmod +x ./installTestCases_local.sh
!cd {model_source_folder_path} && ./installTestCases_local.sh
TestCases installed

Use PySumma to configure model parameters

In [4]:
from pysumma import Simulation

# path to the SUMMA filemanager file on Jupyter
file_manager = os.path.join(model_source_folder_path, file_manger_rel_path)

# Create pySUMMA Simulation Object
executable = ""
S = Simulation(executable, file_manager)

# Configure the model
S.decisions['simulStart'].value = "2006-07-01 00:00"
S.decisions['simulFinsh'].value = "2007-08-20 00:00"
S.decisions['stomResist'].value = 'BallBerry'
# Save configiuration to disk
S._write_configuration()
print(S)
Executable path: 
Simulation status: Initialized
File manager configuration:
'SUMMA_FILE_MANAGER_V1.0'    ! filemanager_version
'/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/'    ! settings_path
'/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/data/forcingData/'    ! input_path
'/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/output/'    ! output_path
'summa_zDecisions_riparianAspenSimpleResistance.txt'    ! decisions_path
'meta/summa_zTimeMeta.txt'    ! meta_time
'meta/summa_zLocalAttributeMeta.txt'    ! meta_attr
'meta/summa_zCategoryMeta.txt'    ! meta_type
'meta/summa_zForceMeta.txt'    ! meta_force
'meta/summa_zLocalParamMeta.txt'    ! meta_localparam
'meta/Model_Output.txt'    ! output_control
'meta/summa_zLocalModelIndexMeta.txt'    ! meta_localindex
'meta/summa_zBasinParamMeta.txt'    ! meta_basinparam
'meta/summa_zBasinModelVarMeta.txt'    ! meta_basinmvar
'summa_zLocalAttributes_riparianAspen.nc'    ! local_attributes
'summa_zLocalParamInfo.txt'    ! local_param_info
'summa_zBasinParamInfo.txt'    ! basin_param_info
'summa_zForcingFileList_riparianAspen.txt'    ! forcing_file_list
'summa_zInitialCond.nc'    ! model_init_cond
'summa_zParamTrial_riparianAspen.nc'    ! parameter_trial
'vegImpactsTranspire'    ! output_prefix

Submit model to XSEDE Comet HPC using CyberGIS-Jupyter tool

In [5]:
from cybergis import summaUI

s = summaUI(model_source_folder_path, file_manger_rel_path, 
            workspace_dir)
In [6]:
s.runSumma()
Out[6]:
In [9]:
job_dir = os.path.join(workspace_dir, 
                            "{}/output".format(s.job_local_id))
summa_output = os.path.join(job_dir, 
                            "vegImpactsTranspire_output_test_timestep.nc")
print(summa_output)
/home/jovyan/work/workspace/Summa_1576878880_63aeeb23/output/vegImpactsTranspire_output_test_timestep.nc

Check model output -- NetCDF file

In [10]:
import xarray as xr
output_info = xr.open_dataset(summa_output)
output_info
Out[10]:
<xarray.Dataset>
Dimensions:                    (gru: 1, hru: 1, ifcSoil: 9, ifcToto: 14, midSoil: 8, midToto: 13, time: 9961)
Coordinates:
  * time                       (time) datetime64[ns] 2006-07-01 ... 2007-08-20
  * hru                        (hru) int32 1
Dimensions without coordinates: gru, ifcSoil, ifcToto, midSoil, midToto
Data variables:
    pptrate                    (time, hru) float64 ...
    airtemp                    (time, hru) float64 ...
    hruId                      (hru) int32 ...
    basin__SurfaceRunoff       (time, gru) float64 ...
    basin__ColumnOutflow       (time, gru) float64 ...
    basin__AquiferStorage      (time, gru) float64 ...
    basin__AquiferRecharge     (time, gru) float64 ...
    basin__AquiferBaseflow     (time, gru) float64 ...
    basin__AquiferTranspire    (time, gru) float64 ...
    averageInstantRunoff       (time, gru) float64 ...
    averageRoutedRunoff        (time, gru) float64 ...
    nSnow                      (time, hru) int32 ...
    nSoil                      (time, hru) int32 ...
    nLayers                    (time, hru) int32 ...
    scalarSWE                  (time, hru) float64 ...
    mLayerTemp                 (time, midToto, hru) float64 ...
    mLayerVolFracIce           (time, midToto, hru) float64 ...
    mLayerVolFracLiq           (time, midToto, hru) float64 ...
    mLayerVolFracWat           (time, midToto, hru) float64 ...
    mLayerMatricHead           (time, midSoil, hru) float64 ...
    scalarSurfaceTemp          (time, hru) float64 ...
    mLayerDepth                (time, midToto, hru) float64 ...
    iLayerHeight               (time, ifcToto, hru) float64 ...
    scalarSenHeatTotal         (time, hru) float64 ...
    scalarLatHeatTotal         (time, hru) float64 ...
    scalarSnowSublimation      (time, hru) float64 ...
    scalarCanopyTranspiration  (time, hru) float64 ...
    scalarCanopyEvaporation    (time, hru) float64 ...
    scalarGroundEvaporation    (time, hru) float64 ...
    scalarThroughfallSnow      (time, hru) float64 ...
    scalarThroughfallRain      (time, hru) float64 ...
    scalarRainPlusMelt         (time, hru) float64 ...
    scalarInfiltration         (time, hru) float64 ...
    scalarExfiltration         (time, hru) float64 ...
    scalarSurfaceRunoff        (time, hru) float64 ...
    iLayerLiqFluxSoil          (time, ifcSoil, hru) float64 ...
    mLayerLiqFluxSoil          (time, midSoil, hru) float64 ...
Attributes:
    summaVersion:     v2.0.0
    buildTime:        Fri Aug 30 16:04:07 UTC 2019
    gitBranch:        sopron_2018-0-gf18270c
    gitHash:          f18270c2ce5f2b5004c2b3e1799bd0969612bb68
    soilStress:       NoahType
    stomResist:       BallBerry
    num_method:       itertive
    fDerivMeth:       analytic
    LAI_method:       specified
    notPopulatedYet:  notPopulatedYet
    f_Richards:       mixdform
    groundwatr:       noXplict
    hc_profile:       constant
    bcUpprTdyn:       nrg_flux
    bcLowrTdyn:       zeroFlux
    bcUpprSoiH:       liq_flux
    bcLowrSoiH:       drainage
    veg_traits:       CM_QJRMS1988
    canopyEmis:       difTrans
    snowIncept:       lightSnow
    windPrfile:       logBelowCanopy
    astability:       louisinv
    canopySrad:       BeersLaw
    alb_method:       varDecay
    snowLayers:       CLM_2010
    compaction:       anderson
    thCondSnow:       jrdn1991
    thCondSoil:       mixConstit
    spatial_gw:       localColumn
    subRouting:       timeDlay

Plot time series for total evapotranspiration

In [11]:
%matplotlib inline
import matplotlib.pyplot as plt
from pandas.plotting import register_matplotlib_converters
register_matplotlib_converters()
x = output_info['time']
y = (output_info['scalarCanopyTranspiration'] + \
     output_info['scalarCanopyEvaporation'] + \
     output_info['scalarGroundEvaporation'])*3600

plt.figure(figsize=(15, 5))
plt.plot(x, y, color='grey', linestyle='solid', markersize=0)

    # Get the current axis of the plot and
    # set the x and y-axis labels
ax = plt.gca()
ax.set_ylabel("Total ET (kg m-2 h-1)")
ax.set_xlabel('Date')
ax.grid(True)

ax.set_title('SUMMA Plot for Total ET')
output_info.close()

Cleanup

In [12]:
! rm -rvf {unzip_dir} {job_dir}
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/data/forcingData/forcing_above_aspen.nc'
rm: cannot remove '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/data/forcingData': Directory not empty
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/data/reynolds_geojson_latlon.geojson'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/data/validationData/ReynoldsCreek_eddyFlux.nc'
removed directory '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/data/validationData'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/installTestCases_local.sh'
removed directory '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/output'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/GENPARM.TBL'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/dos2unix.sh'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/Model_Output.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zBasinModelVarMeta.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zBasinParamMeta.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zCategoryMeta.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zForceMeta.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zLocalAttributeMeta.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zLocalModelIndexMeta.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zLocalModelVarMeta.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zLocalParamMeta.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zModelIndexMeta.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zParamMeta.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/summa_zTimeMeta.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta/var_lookup.f90'
removed directory '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/meta'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/MPTABLE.TBL'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/SOILPARM.TBL'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_fileManager_riparianAspenSimpleResistance.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zBasinParamInfo.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zDecisions_riparianAspenSimpleResistance.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zForcingFileList_riparianAspen.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zForcingInfo_riparianAspen.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zInitialCond.nc'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zLocalAttributes_riparianAspen.nc'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zLocalParamInfo.txt'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/summa_zParamTrial_riparianAspen.nc'
removed '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings/VEGPARM.TBL'
rm: cannot remove '/home/jovyan/work/workspace/tmp69sut9ru/SummaModel_ReynoldsAspenStand_StomatalResistance_sopron/settings': Directory not empty
removed '/home/jovyan/work/workspace/Summa_1576878880_63aeeb23/output/runinfo.txt'
removed '/home/jovyan/work/workspace/Summa_1576878880_63aeeb23/output/vegImpactsTranspire_output_test_timestep.nc'
removed directory '/home/jovyan/work/workspace/Summa_1576878880_63aeeb23/output'

Done