# Lesson 2 - Running WRF-Hydro¶

## Overview¶

In this lesson, we cover the basics of constructing and running a WRF-Hydro simulation using a prepared domain for the gridded routing configuration.

For a detailed description of model configurations see the Technical Description.

## Constructing a simulation with a prepared domain¶

In this section we describe the primary files needed to run a WRF-Hydro simulation.

A WRF-Hydro simulation consists of the following major components:

- executable/binary file
- parameter files
- domain files
- forcing files
- namelists

In this lesson we only cover basic descriptions of these elements. For a detailed description see the Technical Description.

The WRF-Hydro model code, compiled executable/binary, and associated parameter table files were described in Lesson 1.

If you have not already completed Lesson 1, please stop and do so now

Model run-time options are specified in two namelist files `hydro.namelist` and `namelist.hrldas`. These namelist files contain file path specifications, simulation duration, physics options, and output file selections, among others. We will cover many of these options in more depth in Lessons 4 and 5.

## Orientation to the example_case¶

This lesson will use a prepared domain located in the `~/wrf-hydro-training/example_case` directory. The structure of the `example_case` directory serves as a good example of how to organize your domain files. If using another domain with this lesson, such as one you may have created in the geospatial pre-processing tutorial, it is imperative that the file names and directory structure match those described below.

If using an official WRF-Hydro training example case, there will be a study area map and a readme file that describes the geographic setting, the directory, and the files.

First lets take a look at the study_map.png.

Now, lets view the readme file included with the domain for a brief description of the example case and its contents.

In [1]:

    cd ~/wrf-hydro-training/example_case
    cat README.txt

    # Overview

    This example case includes prepared geospatial data and input files for a
    sample domain (region of interest) and prepared forcing data.  This domain is
    a small region (22km x 28km) encompassing Tobyhanna Creek near Blakeslee, PA, USA
    (USGS stream gage 01447720) with forcing data for Hurricane Irene, extending from
    2011-08-27 to 2011-09-15.  The simulation begins with a restart from a spinup
    period of 2009-10-01 to 2011-08-27. The forcing data prepared for this example case
    is derived from the North American Land Data Assimilation System (NLDAS) hourly
    meteorological forcing data.

    There are 3 basic model configurations included in the test case: the National Water
    Model (NWM), Gridded, and NCAR Reach.

    See the WRF-Hydro V5 Technical Description located at
    https://ral.ucar.edu/projects/wrf_hydro for a more detailed description of model
    physics options, configurations, and input files. However, some non-standard
    files will be described below.

    # Directory contents

    example_case: directory containing all input files for the Tobyhanna, NY example case
            |
            - FORCING: Directory containing all NLDAS derived HRLDAS formatted hourly
            forcing data for the simulation period.

            - Gridded: Directory containing all files required for the gridded routing
            configuration with lakes included
                    |
                    - DOMAIN: Directory containing all geospatial data and input files for
                    the Gridded routing option.
                    - lake_shapes: directory containing shape files that define lakes
                    - RESTART: Directory containing model restart files for the Gridded
                    routing option
                    - hydro.namelist: Fortran namelist file for the hydro model
                    - namelist.hrldas: Fortran namelist file for the Noah-MP land surface
                    model.

            - Gridded_no_lakes: Directory containing all files required for the gridded routing
            configuration without lakes
                    |
                    - DOMAIN: Directory containing all geospatial data and input files for
                    the Gridded routing option
                    - RESTART: Directory containing model restart files for the Gridded
                    routing option
                    - hydro.namelist: Fortran namelist file for the hydro model
                    - namelist.hrldas: Fortran namelist file for the Noah-MP land surface
                    model

            - Reach: Directory containing all files required for the NCAR reach routing
            configuration
                    |
                    - DOMAIN: Directory containing all geospatial data and input files for
                    the NCAR reach routing option
                    - stream_network: directory containing files that define the stream
                    network
                    - RESTART: Directory containing model restart files for the NCAR reach
                    routing option
                    - hydro.namelist: Fortran namelist file for the hydro model
                    - namelist.hrldas: Fortran namelist file for the Noah-MP land surface
                    model

            - NWM: Directory containing all files required for the National Water Model
            (NWM) routing configuration
                    |
                    - DOMAIN: Directory containing all geospatial data and input files for
                    the NWM routing option.
                    - DOMAIN_LR: Directory containing all geospatial data and input files for
                    the NWM routing option for long-range forecasts. The primary difference is
                    that a number of the LR files are 1km grid cells instead of 250m.
                    - RESTART: Directory containing model restart files for the NWM routing
                    option.
                    - RESTART_LR: Directory containing model restart files for the NWM long
                    range routing option.
                    - hydro.namelist: Fortran namelist file for the hydro model.
                    - namelist.hrldas: Fortran namelist file for the Noah-MP land surface
                    model.

            - Supplemental: Directory containing supplemental files used to create the example
            case, including forcing files used for spinup
                    |
                    - supplemental_forcing.tar.gz: Tarball containing supplemental forcing data
                    - spinup_forcing_data.tar.gz: Tarball containing additional forcing
                    data for spinup
                    - namelist.wps: Reduced namelist.wps used to create the geogrid file using
                    the WRF-Hydro geogrid Docker utilitiy.

            - USGS_obs.csv: CSV file containing USGS streamflow data for gages in the domain.

            - study_map.png: Study area map.

Now lets take a look at the `example_case` directory.

In [2]:

    ls

    FORCING  Gridded_no_lakes  Reach       study_map.png  USGS_obs.csv
    Gridded  NWM               README.txt  supplemental

In this example case we have created several configurations for WRF-Hydro: National Water Model (NWM), Gridded, and Reach. For detailed descriptions of routing and physics configurations see the Technical Description. These model configurations have different geospatial data associated with them, and thus are represented by separate directories in the `~/wrf-hydro-training/example_case` directory.

### FORCING¶

This directory contains all of the forcing data for our simulation. Note that there is only one `FORCING` directory. The same forcing data can be used with all three configurations.

### The Gridded configuration directory¶

For this lesson, we will be running the Gridded configuration. Now we will explore the `~/wrf-hydro-training/example_case/Gridded` directory.

In [3]:

    ls Gridded

    DOMAIN  hydro.namelist  namelist.hrldas  RESTART

The contents of this directory are described briefly in the `README.txt` file that we viewed earlier, but we will discuss them again here. For a more detailed description of these files beyond what will be described below, see the Technical Description

DOMAIN: Directory containing all geospatial data and input files for the Gridded routing option with lakes included

In [4]:

    ls Gridded/DOMAIN

    Fulldom_hires.nc                     GWBUCKPARM.nc  soil_properties.nc
    geo_em.d01.nc                        hydro2dtbl.nc  wrfinput_d01.nc
    GEOGRID_LDASOUT_Spatial_Metadata.nc  LAKEPARM.nc
    GWBASINS.nc                          lake_shapes

Filename | Description | Source | Required
--- | --- | --- | ---
Fulldom_hires.nc | High resolution full domain file. Includes all fields specified on the routing grid. | WRF-Hydro GIS pre-processing toolkit | Yes
GWBASINS.nc | 2D file defining the locations of groundwater basins on a grid | WRF-Hydro GIS pre-processing toolkit | When the baseflow bucket model is turned on and user defined mapping is off
GWBUCKPARM.nc | Groundwater parameter table containing bucket model parameters for each basin | WRF-Hydro GIS pre-processing toolkit | When the baseflow bucket model is turned on
LAKEPARM.nc | Lake parameter table containing lake model parameters for each catchment | WRF-Hydro GIS pre-processing toolkit | When lake and reservoir routing is turned on
hydro2dtbl.nc | Spatially distributed parameter table for lateral flow routing within WRF-Hydro. | create_SoilProperties.R script (will also be automatically generated by WRF-Hydro) | When using spatially distributed terrain routing parameters
geo_em.d01.nc | The data required to define the domain and geospatial attributes of a spatially-distributed, or gridded, 1-dimensional (vertical) land surface model (LSM) | GEOGRID utility in the WRF preprocessing system (WPS) | Yes
wrfinput_d01.nc | file including all necessary fields for the Noah-MP land surface model, but with spatially uniform initial conditions. Users should be aware that the model will likely require additional spin-up time when initialized from this file. | create_Wrfinput.R script | Yes
soil_properties.nc | Spatially distributed land surface model parameters | create_SoilProperties.R script | If SPATIAL_SOIL compile-time option set to 1
GEOGRID_LDASOUT_Spatial_Metadata.nc | projection and coordinate information for the land surface model grid. | pre-processor | No, but allows for CF compliant outputs
lake_shapes/ | supplemental shape files that define lakes | pre-processor | No

RESTART: Directory containing model restart files

In [5]:

    ls Gridded/RESTART

    HYDRO_RST.2011-08-27_00:00_DOMAIN1  RESTART.2011082700_DOMAIN1

Restart files are an essential part of the WRF-Hydro modeling system. They are output on a fixed timestep specified by the user in the `namelist.hrldas` and `hydro.namelist` files, and represent a complete 'snapshot' of the model state at that time. These files can be used to restart a WRF-Hydro simulation from where the previous simulation terminated with all the model states intact.

When running a WRF-Hydro simulation, you may start your simulation with default initial conditions, referred to as a 'cold start'. When starting from a cold start, a model spinup period is needed to move the model state away from the default initial conditions to a more realistic, physically-based model state. Model output from the spinup period is generally not used for interpretation.

Restart files output at the end the spinup period can be used as the initial conditions for subsequent simulations, referred to as a 'warm start'. Simulations that start from a 'warm start' are generally the primary target for interpretation. 'Warm' and 'cold' starting the model will be discussed more in Lesson 4.

### Namelists¶

Namelists are another key component of the WRF-Hydro modeling system and are the primary means of specifying inputs, outputs, and run-time options. There are two namelist files used by WRF-Hydro: `hydro.namelist` for the routing and hydrologic model and `namelist.hrldas` for the land surface model.

NOTE: These filenames are hard-coded into the model and can not be changed.

For all official WRF-Hydro domains, namelists will be included with each of the model configurations. This is done so that a user can easily run each configuration with minimal setup, and they serve as a starting point for users to specify their own namelists for a given configuration.

There are different namelists for each configuration because certain namelist options are specific to the domain configuration used. We will cover the various namelist options in detail in Lesson 4, but for now we will simply view the namelist and use the default namelist provided with the Gridded configuration to construct our simulation.

Take a moment and read through the two namelists below and note how all filepaths are relative to the current directory containing the namelist. This is the recommended way of specifying filepaths.

In [6]:

    cat Gridded/hydro.namelist

    &HYDRO_nlist
    !!!! ---------------------- SYSTEM COUPLING ----------------------- !!!!

    ! Specify what is being coupled:  1=HRLDAS (offline Noah-LSM), 2=WRF, 3=NASA/LIS, 4=CLM
    sys_cpl = 1

    !!!! ------------------- MODEL INPUT DATA FILES ------------------- !!!!

    ! Specify land surface model gridded input data file (e.g.: "geo_em.d01.nc")
    GEO_STATIC_FLNM = "./DOMAIN/geo_em.d01.nc"

    ! Specify the high-resolution routing terrain input data file (e.g.: "Fulldom_hires.nc")
    GEO_FINEGRID_FLNM = "./DOMAIN/Fulldom_hires.nc"

    ! Specify the spatial hydro parameters file (e.g.: "hydro2dtbl.nc")
    ! If you specify a filename and the file does not exist, it will be created for you.
    HYDROTBL_F = "./DOMAIN/hydro2dtbl.nc"

    ! Specify spatial metadata file for land surface grid. (e.g.: "GEOGRID_LDASOUT_Spatial_Metadata.nc")
    LAND_SPATIAL_META_FLNM = "./DOMAIN/GEOGRID_LDASOUT_Spatial_Metadata.nc"

    ! Specify the name of the restart file if starting from restart...comment out with '!' if not...
    RESTART_FILE  = 'RESTART/HYDRO_RST.2011-08-27_00:00_DOMAIN1'

    !!!! --------------------- MODEL SETUP OPTIONS -------------------- !!!!

    ! Specify the domain or nest number identifier...(integer)
    IGRID = 1

    ! Specify the restart file write frequency...(minutes)
    ! A value of -99999 will output restarts on the first day of the month only.
    rst_dt = 1440

    ! Reset the LSM soil states from the high-res routing restart file (1=overwrite, 0=no overwrite)
    ! NOTE: Only turn this option on if overland or subsurface rotuing is active!
    rst_typ = 1

    ! Restart file format control
    rst_bi_in = 0       !0: use netcdf input restart file (default)
                        !1: use parallel io for reading multiple restart files, 1 per core
    rst_bi_out = 0      !0: use netcdf output restart file (default)
                        !1: use parallel io for outputting multiple restart files, 1 per core

    ! Restart switch to set restart accumulation variables to 0 (0=no reset, 1=yes reset to 0.0)
    RSTRT_SWC = 1

    ! Specify baseflow/bucket model initialization...(0=cold start from table, 1=restart file)
    GW_RESTART = 1

    !!!! -------------------- MODEL OUTPUT CONTROL -------------------- !!!!

    ! Specify the output file write frequency...(minutes)
    out_dt = 60

    ! Specify the number of output times to be contained within each output history file...(integer)
    !   SET = 1 WHEN RUNNING CHANNEL ROUTING ONLY/CALIBRATION SIMS!!!
    !   SET = 1 WHEN RUNNING COUPLED TO WRF!!!
    SPLIT_OUTPUT_COUNT = 1

    ! Specify the minimum stream order to output to netcdf point file...(integer)
    ! Note: lower value of stream order produces more output.
    order_to_write = 1

    ! Flag to turn on/off new I/O routines: 0 = deprecated output routines (use when running with Noah LSM),
    ! 1 = with scale/offset/compression, ! 2 = with scale/offset/NO compression,
    ! 3 = compression only, 4 = no scale/offset/compression (default)
    io_form_outputs = 4

    ! Realtime run configuration option:
    ! 0=all (default), 1=analysis, 2=short-range, 3=medium-range, 4=long-range, 5=retrospective,
    ! 6=diagnostic (includes all of 1-4 outputs combined)
    io_config_outputs = 5

    ! Option to write output files at time 0 (restart cold start time): 0=no, 1=yes (default)
    t0OutputFlag = 1

    ! Options to output channel & bucket influxes. Only active for UDMP_OPT=1.
    ! Nonzero choice requires that out_dt above matches NOAH_TIMESTEP in namelist.hrldas.
    ! 0=None (default), 1=channel influxes (qSfcLatRunoff, qBucket)
    ! 2=channel+bucket fluxes    (qSfcLatRunoff, qBucket, qBtmVertRunoff_toBucket)
    ! 3=channel accumulations    (accSfcLatRunoff, accBucket) *** NOT TESTED ***
    output_channelBucket_influx = 0

    ! Output netcdf file control
    CHRTOUT_DOMAIN = 0           ! Netcdf point timeseries output at all channel points (1d)
                                 !      0 = no output, 1 = output
    CHANOBS_DOMAIN = 1           ! Netcdf point timeseries at forecast points or gage points (defined in Routelink)
                                 !      0 = no output, 1 = output at forecast points or gage points.
    CHRTOUT_GRID = 0             ! Netcdf grid of channel streamflow values (2d)
                                 !      0 = no output, 1 = output
                                 !      NOTE: Not available with reach-based routing
    LSMOUT_DOMAIN = 0            ! Netcdf grid of variables passed between LSM and routing components (2d)
                                 !      0 = no output, 1 = output
                                 !      NOTE: No scale_factor/add_offset available
    RTOUT_DOMAIN = 0             ! Netcdf grid of terrain routing variables on routing grid (2d)
                                 !      0 = no output, 1 = output
    output_gw = 1                ! Netcdf GW output
                                 !      0 = no output, 1 = output
    outlake  = 1                 ! Netcdf grid of lake values (1d)
                                 !      0 = no output, 1 = output
    frxst_pts_out = 0            ! ASCII text file of forecast points or gage points (defined in Routelink)
                                 !      0 = no output, 1 = output

    !!!! ------------ PHYSICS OPTIONS AND RELATED SETTINGS ------------ !!!!

    ! Specify the number of soil layers (integer) and the depth of the bottom of each layer... (meters)
    ! Notes: In Version 1 of WRF-Hydro these must be the same as in the namelist.input file.
    !      Future versions will permit this to be different.
    NSOIL=4
    ZSOIL8(1) = -0.10
    ZSOIL8(2) = -0.40
    ZSOIL8(3) = -1.00
    ZSOIL8(4) = -2.00

    ! Specify the grid spacing of the terrain routing grid...(meters)
    DXRT = 250.0

    ! Specify the integer multiple between the land model grid and the terrain routing grid...(integer)
    AGGFACTRT = 4

    ! Specify the channel routing model timestep...(seconds)
    DTRT_CH = 10

    ! Specify the terrain routing model timestep...(seconds)
    DTRT_TER = 10

    ! Switch to activate subsurface routing...(0=no, 1=yes)
    SUBRTSWCRT = 1

    ! Switch to activate surface overland flow routing...(0=no, 1=yes)
    OVRTSWCRT = 1

    ! Specify overland flow routing option: 1=Seepest Descent (D8) 2=CASC2D (not active)
    ! NOTE: Currently subsurface flow is only steepest descent
    rt_option = 1

    ! Switch to activate channel routing...(0=no, 1=yes)
    CHANRTSWCRT = 1

    ! Specify channel routing option: 1=Muskingam-reach, 2=Musk.-Cunge-reach, 3=Diff.Wave-gridded
    channel_option = 3

    ! Specify the reach file for reach-based routing options (e.g.: "Route_Link.nc")
    !route_link_f = ""

    ! If using channel_option=2, activate the compound channel formulation? (Default=.FALSE.)
    ! This option is only supported if using reach-based routing with UDMP=1.
    compound_channel = .FALSE.

    ! Specify the lake parameter file (e.g.: "LAKEPARM.nc").
    ! Note REQUIRED if lakes are on.
    route_lake_f = "./DOMAIN/LAKEPARM.nc"

    ! Switch to activate baseflow bucket model...(0=none, 1=exp. bucket, 2=pass-through)
    GWBASESWCRT = 1

    ! Groundwater/baseflow 2d mask specified on land surface model grid (e.g.: "GWBASINS.nc")
    !Note: Only required if baseflow  model is active (1 or 2) and UDMP_OPT=0.
    gwbasmskfil = "./DOMAIN/GWBASINS.nc"

    ! Groundwater bucket parameter file (e.g.: "GWBUCKPARM.nc")
    GWBUCKPARM_file = "./DOMAIN/GWBUCKPARM.nc"

    ! User defined mapping, such NHDPlus: 0=no (default), 1=yes
    UDMP_OPT = 0

    ! If on, specify the user-defined mapping file (e.g.: "spatialweights.nc")
    !udmap_file = ""

    /

    &NUDGING_nlist

    /

In [7]:

    cat Gridded/namelist.hrldas

    &NOAHLSM_OFFLINE

    HRLDAS_SETUP_FILE = "./DOMAIN/wrfinput_d01.nc"
    INDIR = "./FORCING"
    SPATIAL_FILENAME = "./DOMAIN/soil_properties.nc"
    OUTDIR = "./"

    START_YEAR  = 2011
    START_MONTH = 08
    START_DAY   = 27
    START_HOUR  = 00
    START_MIN   = 00

    RESTART_FILENAME_REQUESTED = "RESTART/RESTART.2011082700_DOMAIN1"

    ! Specification of simulation length in days OR hours
    ! KDAY = 7
    KHOUR = 455

    ! Physics options (see the documentation for details)
    DYNAMIC_VEG_OPTION                = 4
    CANOPY_STOMATAL_RESISTANCE_OPTION = 1
    BTR_OPTION                        = 1
    RUNOFF_OPTION                     = 3
    SURFACE_DRAG_OPTION               = 1
    FROZEN_SOIL_OPTION                = 1
    SUPERCOOLED_WATER_OPTION          = 1
    RADIATIVE_TRANSFER_OPTION         = 3
    SNOW_ALBEDO_OPTION                = 2
    PCP_PARTITION_OPTION              = 1
    TBOT_OPTION                       = 2
    TEMP_TIME_SCHEME_OPTION           = 3
    GLACIER_OPTION                    = 2
    SURFACE_RESISTANCE_OPTION         = 4

    ! Timesteps in units of seconds
    FORCING_TIMESTEP = 3600
    NOAH_TIMESTEP    = 3600
    OUTPUT_TIMESTEP  = 86400

    ! Land surface model restart file write frequency
    RESTART_FREQUENCY_HOURS = 24

    ! Split output after split_output_count output times.
    SPLIT_OUTPUT_COUNT = 1

    ! Soil layer specification
    NSOIL=4
    soil_thick_input(1) = 0.10
    soil_thick_input(2) = 0.30
    soil_thick_input(3) = 0.60
    soil_thick_input(4) = 1.00

    ! Forcing data measurement height for winds, temp, humidity
    ZLVL = 10.0

    ! Restart file format options
    rst_bi_in = 0      !0: use netcdf input restart file
                       !1: use parallel io for reading multiple restart files (1 per core)
    rst_bi_out = 0     !0: use netcdf output restart file
                       !1: use parallel io for outputting multiple restart files (1 per core)
    /

    &WRF_HYDRO_OFFLINE

    ! Specification of forcing data:  1=HRLDAS-hr format, 2=HRLDAS-min format, 3=WRF,
    !    4=Idealized, 5=Ideal w/ Spec.Precip.,
    !    6=HRLDAS-hrl y fomat w/ Spec. Precip., 7=WRF w/ Spec. Precip.,
    !    9=Channel-only forcing, see hydro.namelist output_channelBucket_influxes
    !    10=Channel+Bucket only forcing, see hydro.namelist output_channelBucket_influxes
    FORC_TYP = 1

    /

## Creating a simulation directory¶

Now that we have covered the major functional elements that constitute a simulation, we will combine these elements and construct a simulation. This is done by placing the `FORCING`, `Gridded/DOMAIN`, `trunk/NDHMS/Run` directories and `namelist.hrldas` and `hydro.namelist` files together in a directory that will be our simulation directory. However, to save disk space it is often preferable to create symbolic links rather than copying the actual files.

NOTE: We will only use symbolic links with files that we will NOT be editing

In the following steps, we will construct our simulation directory.

Step 1. Create simulation directory

We will create a directory for our simulation

In [8]:

    mkdir -p ~/wrf-hydro-training/output/lesson2/run_gridded_default
    cd ~/wrf-hydro-training/output/lesson2/run_gridded_default

Step 2. Copy model run files

We will copy the required model run files from the ~/wrf-hydro-training/wrf_hydro_nwm_public/trunk/NDHMS/Run directory. These files are small so we will make actual copies rather than symbolic links in this case. Additionally, copies are preferred in this case because a user may want to edit the *.TBL files and as stated previously symbolic links should not be used with files that we may edit.

In [9]:

    cp ~/wrf-hydro-training/wrf_hydro_nwm_public/trunk/NDHMS/Run/*.TBL .
    cp ~/wrf-hydro-training/wrf_hydro_nwm_public/trunk/NDHMS/Run/wrf_hydro.exe .

    ls

    CHANPARM.TBL  GENPARM.TBL  HYDRO.TBL  MPTABLE.TBL  SOILPARM.TBL  wrf_hydro.exe

Step 3. Symlink DOMAIN files

We will create symbolic links to the required domain files from the `~/wrf-hydro-training/DOMAIN/Gridded` directory. These files can be large so we will make symbolic links rather than copying the actual files.

In [10]:

    ln -sf ~/wrf-hydro-training/example_case/FORCING .
    ln -sf ~/wrf-hydro-training/example_case/Gridded/DOMAIN .
    ln -sf ~/wrf-hydro-training/example_case/Gridded/RESTART .

    ls

    CHANPARM.TBL  FORCING      HYDRO.TBL    RESTART       wrf_hydro.exe
    DOMAIN        GENPARM.TBL  MPTABLE.TBL  SOILPARM.TBL

Step 4. Copy namelist files

Because we are using the default prepared namelists from the example WRF-Hydro domain, we will copy those in as well. If you were using your own namelists, they would likely be edited and copied from elsewhere. These are small text files so we will make actual copies rather than symbolic links.

In [11]:

    cp ~/wrf-hydro-training/example_case/Gridded/namelist.hrldas .
    cp ~/wrf-hydro-training/example_case/Gridded/hydro.namelist .

    ls

    CHANPARM.TBL  GENPARM.TBL     MPTABLE.TBL      SOILPARM.TBL
    DOMAIN        hydro.namelist  namelist.hrldas  wrf_hydro.exe
    FORCING       HYDRO.TBL       RESTART

We have now constructed our simulation directory with all the requisite files.

In the next section we will run the simulation.

## Running WRF-Hydro using default run-time options¶

Now that we have constructed our simulation directory, we can run our simulation. For this we will be using the `mpirun` command, which has a number of arguments. For this simple case, we only need to supply one argument, the number of cores. This is done with the `-np` argument, and we will set it to 2 cores.

We will pipe the output to a log file because running a simulation can generate a lot of standard output in the terminal.

In [12]:

    mpirun -np 2 ./wrf_hydro.exe >> run.log 2>&1

If your simulation ran successfully, there should now be a large number of output files in the `~/wrf-hydro-training/output/lesson2/run_gridded_default`. We will describe these output files in more depth in Lesson 4. Additionally, detailed descriptions of the output files can be found in the Technical Description.

List the contents of the run directory.

In [13]:

    ls

    201108270000.LDASOUT_DOMAIN1  201109052000.LAKEOUT_DOMAIN1
    201108270100.CHANOBS_DOMAIN1  201109052100.CHANOBS_DOMAIN1
    201108270100.GWOUT_DOMAIN1    201109052100.GWOUT_DOMAIN1
    201108270100.LAKEOUT_DOMAIN1  201109052100.LAKEOUT_DOMAIN1
    201108270200.CHANOBS_DOMAIN1  201109052200.CHANOBS_DOMAIN1
    201108270200.GWOUT_DOMAIN1    201109052200.GWOUT_DOMAIN1
    201108270200.LAKEOUT_DOMAIN1  201109052200.LAKEOUT_DOMAIN1
    201108270300.CHANOBS_DOMAIN1  201109052300.CHANOBS_DOMAIN1
    201108270300.GWOUT_DOMAIN1    201109052300.GWOUT_DOMAIN1
    201108270300.LAKEOUT_DOMAIN1  201109052300.LAKEOUT_DOMAIN1
    201108270400.CHANOBS_DOMAIN1  201109060000.CHANOBS_DOMAIN1
    201108270400.GWOUT_DOMAIN1    201109060000.GWOUT_DOMAIN1
    201108270400.LAKEOUT_DOMAIN1  201109060000.LAKEOUT_DOMAIN1
    201108270500.CHANOBS_DOMAIN1  201109060000.LDASOUT_DOMAIN1
    201108270500.GWOUT_DOMAIN1    201109060100.CHANOBS_DOMAIN1
    201108270500.LAKEOUT_DOMAIN1  201109060100.GWOUT_DOMAIN1
    201108270600.CHANOBS_DOMAIN1  201109060100.LAKEOUT_DOMAIN1
    201108270600.GWOUT_DOMAIN1    201109060200.CHANOBS_DOMAIN1
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    201109032100.GWOUT_DOMAIN1    201109131700.CHANOBS_DOMAIN1
    201109032100.LAKEOUT_DOMAIN1  201109131700.GWOUT_DOMAIN1
    201109032200.CHANOBS_DOMAIN1  201109131700.LAKEOUT_DOMAIN1
    201109032200.GWOUT_DOMAIN1    201109131800.CHANOBS_DOMAIN1
    201109032200.LAKEOUT_DOMAIN1  201109131800.GWOUT_DOMAIN1
    201109032300.CHANOBS_DOMAIN1  201109131800.LAKEOUT_DOMAIN1
    201109032300.GWOUT_DOMAIN1    201109131900.CHANOBS_DOMAIN1
    201109032300.LAKEOUT_DOMAIN1  201109131900.GWOUT_DOMAIN1
    201109040000.CHANOBS_DOMAIN1  201109131900.LAKEOUT_DOMAIN1
    201109040000.GWOUT_DOMAIN1    201109132000.CHANOBS_DOMAIN1
    201109040000.LAKEOUT_DOMAIN1  201109132000.GWOUT_DOMAIN1
    201109040000.LDASOUT_DOMAIN1  201109132000.LAKEOUT_DOMAIN1
    201109040100.CHANOBS_DOMAIN1  201109132100.CHANOBS_DOMAIN1
    201109040100.GWOUT_DOMAIN1    201109132100.GWOUT_DOMAIN1
    201109040100.LAKEOUT_DOMAIN1  201109132100.LAKEOUT_DOMAIN1
    201109040200.CHANOBS_DOMAIN1  201109132200.CHANOBS_DOMAIN1
    201109040200.GWOUT_DOMAIN1    201109132200.GWOUT_DOMAIN1
    201109040200.LAKEOUT_DOMAIN1  201109132200.LAKEOUT_DOMAIN1
    201109040300.CHANOBS_DOMAIN1  201109132300.CHANOBS_DOMAIN1
    201109040300.GWOUT_DOMAIN1    201109132300.GWOUT_DOMAIN1
    201109040300.LAKEOUT_DOMAIN1  201109132300.LAKEOUT_DOMAIN1
    201109040400.CHANOBS_DOMAIN1  201109140000.CHANOBS_DOMAIN1
    201109040400.GWOUT_DOMAIN1    201109140000.GWOUT_DOMAIN1
    201109040400.LAKEOUT_DOMAIN1  201109140000.LAKEOUT_DOMAIN1
    201109040500.CHANOBS_DOMAIN1  201109140000.LDASOUT_DOMAIN1
    201109040500.GWOUT_DOMAIN1    201109140100.CHANOBS_DOMAIN1
    201109040500.LAKEOUT_DOMAIN1  201109140100.GWOUT_DOMAIN1
    201109040600.CHANOBS_DOMAIN1  201109140100.LAKEOUT_DOMAIN1
    201109040600.GWOUT_DOMAIN1    201109140200.CHANOBS_DOMAIN1
    201109040600.LAKEOUT_DOMAIN1  201109140200.GWOUT_DOMAIN1
    201109040700.CHANOBS_DOMAIN1  201109140200.LAKEOUT_DOMAIN1
    201109040700.GWOUT_DOMAIN1    201109140300.CHANOBS_DOMAIN1
    201109040700.LAKEOUT_DOMAIN1  201109140300.GWOUT_DOMAIN1
    201109040800.CHANOBS_DOMAIN1  201109140300.LAKEOUT_DOMAIN1
    201109040800.GWOUT_DOMAIN1    201109140400.CHANOBS_DOMAIN1
    201109040800.LAKEOUT_DOMAIN1  201109140400.GWOUT_DOMAIN1
    201109040900.CHANOBS_DOMAIN1  201109140400.LAKEOUT_DOMAIN1
    201109040900.GWOUT_DOMAIN1    201109140500.CHANOBS_DOMAIN1
    201109040900.LAKEOUT_DOMAIN1  201109140500.GWOUT_DOMAIN1
    201109041000.CHANOBS_DOMAIN1  201109140500.LAKEOUT_DOMAIN1
    201109041000.GWOUT_DOMAIN1    201109140600.CHANOBS_DOMAIN1
    201109041000.LAKEOUT_DOMAIN1  201109140600.GWOUT_DOMAIN1
    201109041100.CHANOBS_DOMAIN1  201109140600.LAKEOUT_DOMAIN1
    201109041100.GWOUT_DOMAIN1    201109140700.CHANOBS_DOMAIN1
    201109041100.LAKEOUT_DOMAIN1  201109140700.GWOUT_DOMAIN1
    201109041200.CHANOBS_DOMAIN1  201109140700.LAKEOUT_DOMAIN1
    201109041200.GWOUT_DOMAIN1    201109140800.CHANOBS_DOMAIN1
    201109041200.LAKEOUT_DOMAIN1  201109140800.GWOUT_DOMAIN1
    201109041300.CHANOBS_DOMAIN1  201109140800.LAKEOUT_DOMAIN1
    201109041300.GWOUT_DOMAIN1    201109140900.CHANOBS_DOMAIN1
    201109041300.LAKEOUT_DOMAIN1  201109140900.GWOUT_DOMAIN1
    201109041400.CHANOBS_DOMAIN1  201109140900.LAKEOUT_DOMAIN1
    201109041400.GWOUT_DOMAIN1    201109141000.CHANOBS_DOMAIN1
    201109041400.LAKEOUT_DOMAIN1  201109141000.GWOUT_DOMAIN1
    201109041500.CHANOBS_DOMAIN1  201109141000.LAKEOUT_DOMAIN1
    201109041500.GWOUT_DOMAIN1    201109141100.CHANOBS_DOMAIN1
    201109041500.LAKEOUT_DOMAIN1  201109141100.GWOUT_DOMAIN1
    201109041600.CHANOBS_DOMAIN1  201109141100.LAKEOUT_DOMAIN1
    201109041600.GWOUT_DOMAIN1    201109141200.CHANOBS_DOMAIN1
    201109041600.LAKEOUT_DOMAIN1  201109141200.GWOUT_DOMAIN1
    201109041700.CHANOBS_DOMAIN1  201109141200.LAKEOUT_DOMAIN1
    201109041700.GWOUT_DOMAIN1    201109141300.CHANOBS_DOMAIN1
    201109041700.LAKEOUT_DOMAIN1  201109141300.GWOUT_DOMAIN1
    201109041800.CHANOBS_DOMAIN1  201109141300.LAKEOUT_DOMAIN1
    201109041800.GWOUT_DOMAIN1    201109141400.CHANOBS_DOMAIN1
    201109041800.LAKEOUT_DOMAIN1  201109141400.GWOUT_DOMAIN1
    201109041900.CHANOBS_DOMAIN1  201109141400.LAKEOUT_DOMAIN1
    201109041900.GWOUT_DOMAIN1    201109141500.CHANOBS_DOMAIN1
    201109041900.LAKEOUT_DOMAIN1  201109141500.GWOUT_DOMAIN1
    201109042000.CHANOBS_DOMAIN1  201109141500.LAKEOUT_DOMAIN1
    201109042000.GWOUT_DOMAIN1    201109141600.CHANOBS_DOMAIN1
    201109042000.LAKEOUT_DOMAIN1  201109141600.GWOUT_DOMAIN1
    201109042100.CHANOBS_DOMAIN1  201109141600.LAKEOUT_DOMAIN1
    201109042100.GWOUT_DOMAIN1    201109141700.CHANOBS_DOMAIN1
    201109042100.LAKEOUT_DOMAIN1  201109141700.GWOUT_DOMAIN1
    201109042200.CHANOBS_DOMAIN1  201109141700.LAKEOUT_DOMAIN1
    201109042200.GWOUT_DOMAIN1    201109141800.CHANOBS_DOMAIN1
    201109042200.LAKEOUT_DOMAIN1  201109141800.GWOUT_DOMAIN1
    201109042300.CHANOBS_DOMAIN1  201109141800.LAKEOUT_DOMAIN1
    201109042300.GWOUT_DOMAIN1    201109141900.CHANOBS_DOMAIN1
    201109042300.LAKEOUT_DOMAIN1  201109141900.GWOUT_DOMAIN1
    201109050000.CHANOBS_DOMAIN1  201109141900.LAKEOUT_DOMAIN1
    201109050000.GWOUT_DOMAIN1    201109142000.CHANOBS_DOMAIN1
    201109050000.LAKEOUT_DOMAIN1  201109142000.GWOUT_DOMAIN1
    201109050000.LDASOUT_DOMAIN1  201109142000.LAKEOUT_DOMAIN1
    201109050100.CHANOBS_DOMAIN1  201109142100.CHANOBS_DOMAIN1
    201109050100.GWOUT_DOMAIN1    201109142100.GWOUT_DOMAIN1
    201109050100.LAKEOUT_DOMAIN1  201109142100.LAKEOUT_DOMAIN1
    201109050200.CHANOBS_DOMAIN1  201109142200.CHANOBS_DOMAIN1
    201109050200.GWOUT_DOMAIN1    201109142200.GWOUT_DOMAIN1
    201109050200.LAKEOUT_DOMAIN1  201109142200.LAKEOUT_DOMAIN1
    201109050300.CHANOBS_DOMAIN1  201109142300.CHANOBS_DOMAIN1
    201109050300.GWOUT_DOMAIN1    201109142300.GWOUT_DOMAIN1
    201109050300.LAKEOUT_DOMAIN1  201109142300.LAKEOUT_DOMAIN1
    201109050400.CHANOBS_DOMAIN1  CHANPARM.TBL
    201109050400.GWOUT_DOMAIN1    diag_hydro.00000
    201109050400.LAKEOUT_DOMAIN1  diag_hydro.00001
    201109050500.CHANOBS_DOMAIN1  DOMAIN
    201109050500.GWOUT_DOMAIN1    FORCING
    201109050500.LAKEOUT_DOMAIN1  GENPARM.TBL
    201109050600.CHANOBS_DOMAIN1  hydro.namelist
    201109050600.GWOUT_DOMAIN1    HYDRO_RST.2011-08-28_00:00_DOMAIN1
    201109050600.LAKEOUT_DOMAIN1  HYDRO_RST.2011-08-29_00:00_DOMAIN1
    201109050700.CHANOBS_DOMAIN1  HYDRO_RST.2011-08-30_00:00_DOMAIN1
    201109050700.GWOUT_DOMAIN1    HYDRO_RST.2011-08-31_00:00_DOMAIN1
    201109050700.LAKEOUT_DOMAIN1  HYDRO_RST.2011-09-01_00:00_DOMAIN1
    201109050800.CHANOBS_DOMAIN1  HYDRO_RST.2011-09-02_00:00_DOMAIN1
    201109050800.GWOUT_DOMAIN1    HYDRO_RST.2011-09-03_00:00_DOMAIN1
    201109050800.LAKEOUT_DOMAIN1  HYDRO_RST.2011-09-04_00:00_DOMAIN1
    201109050900.CHANOBS_DOMAIN1  HYDRO_RST.2011-09-05_00:00_DOMAIN1
    201109050900.GWOUT_DOMAIN1    HYDRO_RST.2011-09-06_00:00_DOMAIN1
    201109050900.LAKEOUT_DOMAIN1  HYDRO_RST.2011-09-07_00:00_DOMAIN1
    201109051000.CHANOBS_DOMAIN1  HYDRO_RST.2011-09-08_00:00_DOMAIN1
    201109051000.GWOUT_DOMAIN1    HYDRO_RST.2011-09-09_00:00_DOMAIN1
    201109051000.LAKEOUT_DOMAIN1  HYDRO_RST.2011-09-10_00:00_DOMAIN1
    201109051100.CHANOBS_DOMAIN1  HYDRO_RST.2011-09-11_00:00_DOMAIN1
    201109051100.GWOUT_DOMAIN1    HYDRO_RST.2011-09-12_00:00_DOMAIN1
    201109051100.LAKEOUT_DOMAIN1  HYDRO_RST.2011-09-13_00:00_DOMAIN1
    201109051200.CHANOBS_DOMAIN1  HYDRO_RST.2011-09-14_00:00_DOMAIN1
    201109051200.GWOUT_DOMAIN1    HYDRO.TBL
    201109051200.LAKEOUT_DOMAIN1  MPTABLE.TBL
    201109051300.CHANOBS_DOMAIN1  namelist.hrldas
    201109051300.GWOUT_DOMAIN1    RESTART
    201109051300.LAKEOUT_DOMAIN1  RESTART.2011082800_DOMAIN1
    201109051400.CHANOBS_DOMAIN1  RESTART.2011082900_DOMAIN1
    201109051400.GWOUT_DOMAIN1    RESTART.2011083000_DOMAIN1
    201109051400.LAKEOUT_DOMAIN1  RESTART.2011083100_DOMAIN1
    201109051500.CHANOBS_DOMAIN1  RESTART.2011090100_DOMAIN1
    201109051500.GWOUT_DOMAIN1    RESTART.2011090200_DOMAIN1
    201109051500.LAKEOUT_DOMAIN1  RESTART.2011090300_DOMAIN1
    201109051600.CHANOBS_DOMAIN1  RESTART.2011090400_DOMAIN1
    201109051600.GWOUT_DOMAIN1    RESTART.2011090500_DOMAIN1
    201109051600.LAKEOUT_DOMAIN1  RESTART.2011090600_DOMAIN1
    201109051700.CHANOBS_DOMAIN1  RESTART.2011090700_DOMAIN1
    201109051700.GWOUT_DOMAIN1    RESTART.2011090800_DOMAIN1
    201109051700.LAKEOUT_DOMAIN1  RESTART.2011090900_DOMAIN1
    201109051800.CHANOBS_DOMAIN1  RESTART.2011091000_DOMAIN1
    201109051800.GWOUT_DOMAIN1    RESTART.2011091100_DOMAIN1
    201109051800.LAKEOUT_DOMAIN1  RESTART.2011091200_DOMAIN1
    201109051900.CHANOBS_DOMAIN1  RESTART.2011091300_DOMAIN1
    201109051900.GWOUT_DOMAIN1    RESTART.2011091400_DOMAIN1
    201109051900.LAKEOUT_DOMAIN1  run.log
    201109052000.CHANOBS_DOMAIN1  SOILPARM.TBL
    201109052000.GWOUT_DOMAIN1    wrf_hydro.exe

There are also four important files for determining the success or failure of the run, diag_hydro.0000*. The number of diag files is equal to the number of cores used for the run. These diag_hydro.0000* files contain logs and diagnostics on the simulation run.

You can check that your simulation ran successfully by examining the last line of the diag files, which should read `The model finished successfully........`

In [14]:

    tail -1 diag_hydro.00000

     The model finished successfully.......

# Next up - Basics of working with WRF-Hydro outputs¶

This concludes Lesson 2. In the next lesson, we will briefly discuss working with some of the output files. The output files from WRF-Hydro are standard netCDF4 files, and thus there are many way to work with these data. We simply cover a few Python libraries and commands that are needed for later lessons in this tutorial.

Lesson 3 is by no means a comprehensive guide to working with netCDF files.

IT IS BEST TO EITHER SHUTDOWN THIS LESSON OR CLOSE IT BEFORE PROCEEDING TO THE NEXT LESSON TO AVOID POSSIBLY EXCEEDING ALLOCATED MEMORY. Shutdown the lesson be either closing the browser tab for the lesson or selecting `Kernel -> Shut Down Kernel` in JupyterLab.

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