wrfHydroScripts ============

Towards automating repetitive, time consuming, and error-prone tasks related to setting up and running WRF-Hydro.

These are bash scripts. To make these available at command line, you have to use bash as your shell because the individual scripts are sourced as functions of the same name (without ".sh" at the end) in to the shell environment. (You can't even define a function in csh, so you probably want to give up on it. Though you could call the full path to the scripts in csh, or put them in your $PATH. I.E. internally these scripts (should) use the full paths to the script files to call them)

Note this is a work in progress.

Setting up the scripts for your system is next. General usage tips are then given. Command usage is briefly shown after that..

Setup

These are listed in order from most critical to least critical.

~/.wrfHydroScripts

This file specifies the path to this repository on your computer (potentially other items to be added) and is assumed to be in this location with this name . E.g.

jamesmcc@hydro-c1:~> cat ~/.wrfHydroScripts  
wrfHydroScripts=/glade/u/home/jamesmcc/wrfHydroScripts
ncoScripts=/glade/u/home/jamesmcc/ncoScripts
wrf_hydro_model=/glade/u/home/jamesmcc/WRF_Hydro/wrf_hydro_model.

#bsubHeader: This regex is used to get the header from this file '^#BSUB'.
#            Variables available in bCleanRun: $nCores.
#            Double quotes must be escaped.
#BSUB -P P48500028                      # Project 99999999
#BSUB -x                                # exclusive use of node (not_shared)
#BSUB -n $nCores                            # number of total (MPI) tasks
#BSUB -R \"span[ptile=16]\"               # run a max of ptile tasks per node
#BSUB -J $jobName                       # job name
#BSUB -o $theDate.%J.stdout  # output filename
#BSUB -e $theDate.%J.stderr  # error filename
#BSUB -W $wallTime                      # wallclock time (hrs:mins)
#BSUB -q $queue                         # queue: small, economy, regular, premium
#BSUB -B                                # email when the job starts
#BSUB -N                                # email when the job finishes

sourceMe.sh (sourceMe.csh)

This file is meant to be sourced into a bash (or csh/tcsh) shell to make the scripts seemingly in your path commandline (with auto complete in bash)

jamesmcc@hydro-c1:~> source ~jamesmcc/wrfHydroScripts/sourceMe.sh 
(in csh: jamesmcc@hydro-c1:~> source ~jamesmcc/wrfHydroScripts/sourceMe.csh)

but better yet, put it in your /.bashrc (/.cshrc):

jamesmcc@hydro-c1:~> grep sourceMe ~/.bashrc  
source ~/wrfHydroScripts/sourceMe.sh  

For csh:

jamesmcc@hydro-c1:~> grep sourceMe ~/.cshrc  
source ~/wrfHydroScripts/sourceMe.csh  

Note you'll still have to source sourceMe.sh in qsub scripts when you want to pick these up (unless you perform other shenanigans).

~/.wrfHydroRegressionTests.txt

For regression testing only. This file specifies where regression test attempts are to be carried out and enumerates "canned" regression tests for interactive selection during the script.

jamesmcc@hydro-c1:~> cat ~/.wrfHydroRegressionTests.txt  
attemptDir = /home/jamesmcc/WRF_Hydro/TESTING/REGRESSION/ATTEMPTS  
  
*** Regression Tests Menu  
1: Boulder Creek 1D NHD Master = /home/jamesmcc/WRF_Hydro/TESTING/REGRESSION/TESTS/Boulder_Creek_NHD  
2: Boulder Creek NLDAS forcing 1D NHD Master = /home/jamesmcc/WRF_Hydro/TESTING/REGRESSION/TESTS/Boulder_Creek_NHD_NLDAS  
3: Front Range   4D NHD Master = /home/jamesmcc/WRF_Hydro/TESTING/REGRESSION/TESTS/FRNG_NHD  
4: Front Range   6H NHD Master = /home/jamesmcc/WRF_Hydro/TESTING/REGRESSION/TESTS/FRNG_NHD_6HR  
*** Regression Tests Menu   
  
    
*** testNLast Menu - currently this menu is to be comment selected, opt out = # at start  
1: testNaOutput   : fails if there are nans in any variable in the file  
2: testDiffOutput : test fails if there are non-zero differences with verification output  
*** testNLast Menu  

Usage tips

• One of the more complicated scripts that creates copies and/or links on your computer is linkToTestCase.
  The most important piece of advice for avoiding a rats nest of links and copied files is:
  In your namelists, never point to directories or files outside of the run directory.
  Use symlinks in to make all namelist references local to the run directory. For example, never use "../" or any other absolute path in your namelists.

Commands

Running WRF-Hydro

• cleanup [-r] [directoryToCleanupTo]
  Clean up a run directory. Option -r removes restart files. Specifying an existing directory cleansup to that directory.

• cleanRun [-cnpu] nCores [runDirectory] [binary]
  Run the model after cleaning up the run directory.
  Options, all passed to linkToTestCase.sh, used when specifying a runDirectory:
       -c copy files
       -n get nudging files
       -p write-protect
       -u un-write-protect

• qCleanRun [-cnpu] nCores [runDirectory] [binary]
  Submit cleanRun to qsub/torque job scheduler.
  Arguments identical to cleanRun. The header applied by this script can be tailored within.

• qHead

Setting up test cases

• linkToTestCase

Regression testing

• regTest [-q] binary

• testNLast

Compiling WRF-Hydro

• compileAll

• makeCheck

Setup wrfHydroScripts

• helpers

Plotting

• plotFrxst

Misc

• colorFormats Color coding sections/warnings/errors/etc in long, verbose outputs from complicated scripts is SUPER helpful. This is the color-coding cheat sheet.

• hgrep