How do I use save with a parfor loop using Parallel Computing Toolbox?

I would like to save some variables to .mat files from inside a parfor loop. However I get an error:

ERROR: ??? Error using ==> parallel_function at 598
Error in ==> parallel_function>make_general_channel/channel_general at 894
Transparency violation error.
See Parallel Computing Toolbox documentation about Transparency.

Answer 1

[MathWorks Support Team]

Transparency is violated by the save command because in general MATLAB cannot determine which variables from the workspace will be saved to a file.

Pre-R2024a

The solution is to move the call to save to a separate function and to call that function from inside the parfor loop. Pass any variables that are to be saved as arguments to the function. That way MATLAB can determine which ones will be saved and transparency is not violated.

For example:

Save the following as "parsave.m":

function parsave(fname, x,y)
  save(fname, 'x', 'y')
end

Then run it with:

parfor ii = 1:4
  x = rand(10,10);
  y = ones(1,3);
  parsave(sprintf('output%d.mat', ii), x, y);
end

R2024a Onwards

MATLAB now supports calling save within a parfor loop when the -fromstruct option is used. 

The following documentation example demonstrates how to collect your variables into a struct and then save inside the parfor loop.

www.mathworks.com/help/parallel-computing/save-variables-in-parfor-loop.html

[Walter Roberson]

Notice Alex Shaw's discussion, below

Answer 2

[Daniel]

A nice alternative to implement your own save function is using the built-in matfile function:

parfor ii = 1:4
m=matfile(sprintf('output%d.mat', ii),'writable',true)
x = rand(10,10);
y = ones(1,3);
m.x=x;
m.y=y;
end

Here the parser has no issue understanding which variables are used.