FAQ's & Troubleshooting

An active user forum is also available which is hosted on the AEMON website . Please consult this forum (and below) for FAQ’s and to ask questions and for support.

Where can I download some example simulations?

Example simulations and tutorials can be downloaded from the AED website at: Download Examples

Please NOTE: Different versions of the GLM model require slightly different configurations, as new features are added and older redundant features are removed. Example simulations that were downloaded for a previous version may not run with updated model binaries. As such, it is best to download the examples and model binaries at the same time.

Do I need to buy a license?

No. GLM is distributed under the GNU public release license, and is completely free of charge. GLM binaries downloaded from our website are provided pre-compiled with coupling to AED2 and FABM. For GLM version compiled with AED2+ you must get a registration, so please contact us

How do I turn on/off a particular module (WQ or ICE)?

Modules can be turned on or off by commenting out (!) ALL LINES that particular section of the glm2.nml file ( eg &wq_setup or &snow_ice ). e.g.

!&wq_setup !!-- Choose 'aed2' or 'fabm' (aed2 is the default) ! wq_lib = 'aed2' !! wq_nml_file = 'aed2.nml' ! ode_method = 1 ! split_factor = 1 ! bioshade_feedback = .true. ! repair_state = .true. !! mobility_off = .false. !! multi_ben = .true. ! benthic_mode = !/

When commenting or uncommenting the glm2.nml file take care to comment the entire section, including the “/”. Also, the glm2.nml will have comments in the file explaining what configurations options are available for each section. Please make sure not to uncomment these text blocks.

What software do you recommend to configure the model?

For windows users, we recommend Notepad++ for editing the nml files, and Microsoft excel for the timeseries csv files. However, Excel will automatically convert the time column to it’s default time format (as specified by the operating system). Each time you save and close the file you will need to convert the time format back to yyyy-mm-dd. Word processing software like word, wordpad and notepad can place hidden characters into a text file, which will crash the model.

How can I visualize the results?

GLM has an inbuilt visualization software (libplot) which is configured via the plots.nml file and executed at runtime via the command line argument --xdisp. GLM also produces a series of csv files that can be viewed in Excel and a netcdf containing all of the raw output data. We recommend either R or Matlab which post-processing the netcdf (see relevant sections). How do I configure the batch file? The simplest way to run the model in windows is via a batch file (*.bat). This batch file needs to be located in the same directory as the glm2.nml file. The batch file needs to contain the path to the GLM binary, and any additional flags. An example of the batch text is below:

..\..\glm-bin\x64\glm.exe --xdisp

Can I run the model on OSX?

GLM can be compiled for OSX, and configured to run from a shell script (*.sh). Unlike a batch file under windows, the shell script path is a little more complex as the glm binary is contained within the glm.app file. An example is below:

../../glm.app/Contents/MacOS/glm

How much disk space is required?

Although the GLM netcdf output is small compared to some of the 3D lake models, it can still be several GB is size. We recommend not running the model off a USB unless there is at least 10GB of space available.

My model ran, but now crashes?

Below are some of the most common causes that a previously running model may crash:

  • An output file is already open in Excel (eg lake.csv)
  • An input file has the wrong date format. Open the relevant bc files in a text editor like notepad++ which and see if the time format is correct. Remember Excel routinely changes date format to a default style which may not be compatible.
  • A section has been commented/uncommented incorrectly.
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