Matlab Tips - labordynamicsinstitute/replicability-training GitHub Wiki

Tips and tricks for working with other people's Matlab programs

Adjusting paths globally in a Matlab program

Many authors don't do this, but 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 (see below how to run Matlab jobs)
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.

Saving a figure

See saveas

saveas(fig,filename)

For instance

bar(x);
saveas(gcf,'Barchart.png')

(for the report, always save as PNG, as it is easier to integrate into the report)

Making a Directory

If you an encounter an error that stems from the code attempting to write to a directory that does not exist, use the mkdir function. For example, to create a new folder called "newFolder":

[status, msg] = mkdir('newFolder')

This will create the new folder. If the operation succeeds in the folder creation, it will show the following (if it fails you will get a 0):

status = logical
   1

More info on this function can be found here.

I am running a Matlab program, but nothing has happened for an hour?

First, check that Matlab is currently busy. Look in the bottom left corner of the Matlab window for text that says "Busy". If it is there, wait! Matlab replications tend to take longer than Stata replications, and can run for 1 or 2 days without signs of progress. The wait time varies heavily for different programs, but if it runs for several days with no signs of progress, ask Lars or Flavio.

I get an error `Undefined function or variable 'xyz'`?

Check the following for information on 'xyz'.

readme file
article
google

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:

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 = "S:\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 = "S:\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).

Redirecting Matlab temporary directories

Matlab may write to temporary directories. If the filesystem is not large enough, it can be redirected.

#Create a job specific temp directory to avoid this
mkdir -p ~/matlabtmp/$PBS_JOBID
export MATLABWORKDIR=~/matlabtmp/$PBS_JOBID

Running MATLAB without the desktop GUI

Linux

matlab -nodisplay -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).

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