Slow loading of .mat files

Mark Drakesmith

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Jun 21, 2011, 10:34:04 AM6/21/11

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Hi.

I am experiencing a progressive slowing down of Matlab (r2010a on Windows 7 Pro x64) when loading variables form mat files.

I have a loop where I load a structure on each iteration. The variables are not too big (approx 2Mb). I find it gets slower loading the variables with each iteration, to the point where i have to terminate and restart the session.
I have used tic/toc to time how long it takes to load the files on each iterations. The time to load increases considerably:

Iteration Size (Mb) Time to load (s)
1 2.2201 6.7984
2 2.2541 9.5072
3 1.9966 12.5465
4 2.2100 11.5915
5 2.2003 18.5795
6 2.1955 15.7271
7 2.0191 14.071
8 2.1719 638.1973
9 2.0433 789.7458

I have loaded field iteratively (usually much larger ones than this) without experiencing this problem. I have restarted my computer a number of times (including a hard reset) and it has not helped. I am experiencing it on a number of scripts that load variables iteratively and it only started recently. I am at a loss as to how to fix this.

Any help you can offer would be appreciated.

Thanks

Mark

Mark Drakesmith

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Jun 23, 2011, 5:45:05 AM6/23/11

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Just to update on this. I have tried using profiler to find out what is happening during a load. The longest item on the summary was about 0.1s even though the load took over 5 minutes! I really don't know what is happening.

Any help that can be offered would be appreciated.

Many thanks

Mark

Sadik

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Jun 23, 2011, 6:51:02 AM6/23/11

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Hi Mark,

Can you post the part of your code that you are using to load the files?

Best.

Mark Drakesmith

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Jun 23, 2011, 8:10:20 AM6/23/11

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"Sadik " <sadik...@gmail.com> wrote in message <itv5qm$9ja$1...@newscl01ah.mathworks.com>...

> Hi Mark,
>
> Can you post the part of your code that you are using to load the files?
>
> Best.

Here is a simplified version of the loop I have been running. All i am doing on this version is loading the variables and then clearing them. Even on this version I still suffer the same problem.

Another thing I've noticed it only seems to effect structure variables. Double, single, etc.. variables seem to be OK.

Many thanks

Mark

------------------

load subj_params.mat subjcode eventcode

start_subj=[2:3 5:8 10:16];

selecttrials=[{1} {[2 3]} {[]} {[]} {5}];

for subj=start_subj;
subj
cd('..');
cd(subjcode(subj,:));

for event=[1 2 5]

v_name=[subjcode(subj,:) eventcode(event,:)];

load(['mne_pow_' v_name '.mat'],'source2'); % this is where the problem starts

clear source2

end

end

Sadik

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Jun 23, 2011, 7:35:23 PM6/23/11

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Sorry, no suggestions coming to my mind.

Kirill

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Jun 25, 2011, 12:24:58 PM6/25/11

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If MAT files are saved in Version 7.3, -v7, they are compressed by
default and it takes a lot of time to uncompress them on loading.

Try –v6 format if it is faster.

Kirill

Mark Drakesmith

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Jun 28, 2011, 12:01:04 PM6/28/11

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Kirill <kirill...@gmail.com> wrote in message <ea54e64b-7ae8-49eb...@d22g2000yqn.googlegroups.com>...

> If MAT files are saved in Version 7.3, -v7, they are compressed by
> default and it takes a lot of time to uncompress them on loading.
>

> Try –v6 format if it is faster.
>
> Kirill

Thanks for the advice, Kirill. Just re-saved my .mat files as v6 and it have improved the performance of my scripts substantially with no inexplicable slowing down.

Thanks very much!

Mark