Error with parallel toolbox

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Alexander Holmes
Alexander Holmes on 23 Aug 2018
Commented: Sean de Wolski on 28 Aug 2018
I tried running code on a cluster using batch which I fills a 10000 by 10000 matrix with random numbers.
I have a script runTest:
job = batch('test');
wait(job);
load(job);
save("A","A",'-v7.3');
where test.m is the following:
parfor i=1:10000
for j=1:10000
A(i,j) = rand;
end
end
However, when I run this on a cluster, it says 'Error using batch (line 179). Reference to non-existent field 'AlternativeConstructorIndex'.
How do I go about fixing this? It runs fine in my own machine, and runs fine on the cluster when I don't go via the batch function (but then won't run in parallel, and seems to just ignore the parfor loop, or perform the same thing on each processor rather than splitting the tasks between them). The parallel computing toolbox is definitely installed (I checked via an interactive session).

Answers (1)

OCDER
OCDER on 27 Aug 2018
Edited: OCDER on 27 Aug 2018
Do not use batch and scripts if not needed.
"but then won't run in parallel, and seems to just ignore the parfor loop, or perform the same thing on each processor rather than splitting the tasks between them)"
This indicates the cluster default setting for parallel computing is to NOT autocreate a parpool when encountering a parfor statement for the first time. To check the setting on the cluster try this:
ps = parallel.Settings
ps.Pool.AutoCreate
= 0 %will not start parpool automatically
= 1 %will start pool automatically when encountering parfor
%You can set it to true:
if ~ps.Pool.AutoCreate
ps.Pool.AutoCreate = true; %But this isn't a good practice. See below
end
To ensure the Matlab starts parpool, use the parpool command explicitly. https://www.mathworks.com/help/distcomp/parpool.html
Pool = gcp('nocreate');
if isempty(Pool)
parpool();
end
A = test();
save('A.mat','A','-v7.3');
%test.m is this:
function A = test()
parfor i=1:10000
for j=1:10000
A(i,j) = rand;
end
end
I try to avoid using scripts in parallel computing, as it seems there are unique debugging issues.
  5 Comments
OCDER
OCDER on 28 Aug 2018
Is that the error you are receiving? seems like a matlab installation/configuration issue on the cluster. One fix is in that answer link.
Sean de Wolski
Sean de Wolski on 28 Aug 2018
I'd contact support. Either way that sounds like a bug.

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