How to use Command line

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I don't have a windows machine, so I'm not 100% sure the CLI is available on Windows or not, but I don't see any reason it wouldn't it's coded in C++ like the rest of E+ (CommandLineInterface.cc)

First, prior to v8.4 EnergyPlus uses to be run in command line using a batch file (the one you're using). This is no longer the case, and EnergyPlus now has a proper Command Line Interface (or 'cli'), which documentation can be found here.

If the energyplus isn't in your PATH, you'll need to use the full path (on mac that's /Applications/EnergyPlus-8-7-0/energyplus) or set your path correctly.

Display the help:

energyplus --help

Run a model test.idf in the current directory, with a weather file called weather.epw in the current directory as well, and output to a directory named out-test:

energyplus -w weather.epw -d out-test/ test.idf

By default it picks up the Energy+.idd from the same folder as where the energyplus executable is (so /Applications/EnergyPlus-8-7-0/Energy+.idd in my case). If you need to supply another one, use -i path_to_Energy+.idd (or --idd)

Obviously, all paths above can be made absolute if there aren't in current directory, or can be made relative. Here's a mixed example:

energyplus \
   --idd ~Software/Others/EnergyPlus-build/Products/Energy+.idd \ # Absolute path
   -w ../Weather/weather.epw \   # Relative path (one folder up, then inside Weather/)
   -d out-test/ \   # Current directory (relative path too)
   test.idf   # Current directory

If you really want to run Epl-run.bat, see the parameters its documentation here. If I decompose your query, I think the problem is that you're passing the idd as the first argument, when the first argument should be the input file without extension. The batch should will look for the .ini and .idd in the current directory.

c:\>EnergyPlusV8-7-0\Epl-run = Program to run
c:\EnergyyPlusV8-7-0\Energy+.idd = **Don't pass this!**
c:\EnergyPlusV8-7-0\ExampleFiles\5ZoneAirCooled = contains the file with full path and no extensions for input files
c:\EnergyPlusV8-7-0\ExampleFiles\5ZoneAirCooled = contains the file with full path and no extensions for output files
idf = extension of the input file
"C:\EnergyPlusV8-7-0\WeatherData\USA_VA_Sterling-Washington.Dulles.Intl.AP.724030_TMY3.epw" = contains the file with full path and extension for the weather file

EP = a weather file is used
N = no pause
nolimit = no 250 columns limit in readVarsESO
N = Don't call convertESOMTR
N = Don't call csvProc
0 = ??
Y = ??

Modelkit has an energyplus-run function that simplifies command line executions. Check out this video demonstrating modelkit commands, and the following video showing how to use a rakefile to automate these commands.