MATLAB-related procedures

MATLAB-related procedures#

In this section, we will show you a few things related specifically to running code reproducibly with MATLAB. For more general debugging tips for MATLAB and other computer languages, see our wiki.

Adding `config.m` to MATLAB and path names#

When you replace hard-coded filepaths in Matlab, please do the following:

Say the author has code like

xlsread('C:\Users\me\submission\AEJMacro\yesterday\data.xlsx')

You should do the following:

Copy template-config.m to the directory of the Matlab script you are running, and call it config.m.
Adjust the options.
Add the line config to the main Matlab script.

Then

% Add this ONCE at the top of the program. Do NOT repeat it.
config
% wherever the hard-coded path appears, replace with
xlsread(fullfile(rootdir,'data.xlsx')

This works on any platform.

Running MATLAB without the desktop GUI and with log file#

Windows

See these instructions for finding the Matlab binary on the system. However, this should work “out of the box” on CCSS-managed systems from the Bash prompt.

start matlab -nosplash  -minimize -r  "addpath(genpath('.'));main"  -logfile matlab.log

where main.m is the Matlab program you want to run (you omit the .m when calling it).

Note

This will still open a Matlab window in the background (check your taskbar).

Linux

Assuming MATLAB is in your path (check with matlab), the following will generate a logfile.

time matlab -nodisplay -r "addpath(genpath('.')); main" -logfile matlab-$(date +%F_%H-%M-%S).log

where main.m is the Matlab program you want to run (you omit the .m when calling it).

If you do not have matlab in your path, check with system admins. For BioHPC, as long as you are on the ECCO nodes, you should have access. See BioHPC ECCO page for some details.

The .m program is using a software extension to MATLAB called “Dynare”#

Do not attempt to install Dynare on CCSS or BioHPC computers.

However, it is not necessary to install Dynare, it is sufficient to unpack the ZIP files. Try the information below first:

Warning

Use the precise version of Dynare specified by the authors. If that version is not located on L:\common, then talk to your supervisor.

Be sure to include the config.m file as outlined above!
Inspect the last part of the config.m, it should have code much like the following:

%%% Dynare settings
%
% The following are possible Dynare settings. Uncomment the one you need.

% dynarepath = "/Applications/Dynare/4.6.1/matlab"
% dynarepath = "L:\LDILab\dynare\dynare-4.5.7\matlab"
%dynarepath = "L:\common\dynare-4.5.7\matlab"

% 
% Then uncomment the following line:
%
%addpath(genpath(dynarepath))

You will want the path for the system you are working on. If CCSS Cloud, use the L: path. If on BioHPC, you will need to add a path like /home/ecco_lv39/common/dynare.
Then uncomment the addpath() statement at the end.

Your modified config.m should look somewhat like this:

%%% Dynare settings
%
% The following are possible Dynare settings. Uncomment the one you need.

% dynarepath = "/Applications/Dynare/4.6.1/matlab"
% dynarepath = "L:\LDILab\dynare\dynare-4.5.7\matlab"

dynarepath = "L:\common\dynare-4.5.7\matlab"

% 
% Then uncomment the following line:
%

addpath(genpath(dynarepath))

The Matlab program should now run, and call out to the Dynare software as needed.

If a specific version is mentioned and is not there, download it from the Dynare website - choose the ZIP version. Then unzip it to the L: drive (move it around if necessary so you get the same structure as in the example above, i.e. L:\common\dynare\(SOME VERSION)\matlab). Then include the addpath command as before.

If you don’t have access to the L drive yet, contact us.

Mention of MEX programs, what do I do?#

(or: MEX files provided for Linux/MacOS, but you need to run on Windows)

There should be .cpp files provided - if not, they should be requested from the author
From within Matlab, run mex name_of_file.cpp (though this should also be provided by the author).

MATLAB complains about a missing Toolbox#

Check that the Path includes said Toolbox, see https://it.mathworks.com/help/matlab/ref/pathtool.html. It may also be that we are not licensed to use that Toolbox. Make a note of the error in the replication report.