IMPORTANT UPDATE
I just made the discovery that after restarting Matlab and the computer, this simplified code no longer reproduces the problem for me either... I am so sorry for taking up your time with a script that didn't work. However, the old problem still persists in my original script if I save anything in any folder (that I have tried) in the inner 'for' loop. For my purposes, I have worked around it by simply not make this save unless I absolutely need it. The original script has the following structure in terms of for loops and use of save or load:
load() % .mat files, size 365x92x240
for day = 1:365
load() % .mat files, size 8x92x240
for type = 1:17
load() % .mat files size 17x92x240
load() % .mat files size 92x240
for step 1:8
%only calculations
end
save() % .mat files size 8x92x240
end
save() % .mat files, size 8x92x240
end
% the load and saves outside the are in for loops too, but do not seem to affect the described behavior in the above script
load() % .mat files size 8x92x240
save() % .mat files size 2920x92x240
load()
save() % .mat files size 365x92x240
load()
save() % .mat files size 12x92x240
If run in full, the script saves approx. 10 Gb and loads approx. 2Gb of data.
The entire script is rather lengthy and makes a lot of saves and loads. It would be rather impractical too share all here before I have managed to reproduce the problem in a reduced version, unfortunately. As I frustratingly discovered that the very same code could behave differently from to time to time, it immediately got more tedious than anticipated to find a simplification that consistently reproduces the behavior. I will get back as soon as I am sure about a manageable code that produces the problem.
PREVIOUS PROBLEM DESCRIPTION
(NB. The code below does not for sure reproduce the described problem.):
I just learnt the hard way that, in Matlab, you can't name a saving folder to temp in a for loop without slowing down data loading in the next round of the loop. My question is why?
If you are interested in reproducing the problem yourself, please see the code below. To run it, you will also need a matfile called anyData.mat to load and two folders for saving, one called temp and the other called temporary.
clear all;clc;close all;profile off;
profile on
tT= zeros(1,endDay+1);
tTD= zeros(1,endDay+1);
for day = 0:2;
tic
T = importdata('anyData.mat')
tT(day+1)=toc; %loading time in seconds
tic
TD = importdata('anyData.mat')
tTD(day+1)=toc;
for type = 0:1
saveFile = ones(92,240);
save('AnyFolder\temporary\saveFile.mat', 'saveFile') % leads to fast data loading
%save('AnyFolder\temp\saveFile.mat', 'saveFile') %leads to slow data loading
end % end of type
end% end of day
profile off
profile report
plot(tT)
You will see in y-axis of the plot that data loading takes significantly longer time when you in the later for loop save to temp rather than temporary. Is there anyone out there who knows why this occurs?
There are two things here
Storage during a for loop is an expensive operation as it usually opens a file stream and closes it before it moves on. You might not be able to avoid this.
Second thing is speed of storage and its cache speed. Most likely programs use temp folder for its own temporary files and have a garbage collector or software looking after these to clean them. If you start opening and closing file stream to this folder you have to send a request to get exclusive write access to the folder. This again adds to the time.
If you are doing image processing operations and you have multiple images you can run into a bottle neck with writing to hard drive due to its speed, cache and current memory available to MATLAB.
I can't reproduce the problem, suspect it's system and data-size specific. But some general comments which could help you out of the predicament:
As pointed out by commenters and the above answers, file i/o within a double for loop can be extremely parasitic, especially in cases where you only need to access part of the data in the file, where other system operations delay the process, or where the data files are large enough to require virtual memory (windows) / swap space (linux) to even load them. In the latter case, you could be in a situation where you're moving a file from one part of the hard disk to another when you open it!
I assume that you're loading/saving because you don't have c.10GB of ram to hold everything in memory for computation. The actual problem is not described, so I can't be certain, but think you might find that the matfile class to be useful... TMW documentation. This is used to map directly to/from a mat file. This:
reduces file stream opening and closing IOPS
allows arbitrarily large variable sizes (governed by disk size, not memory)
allows you to read/write partially (i.e. write only some elements of an array without loading the whole file)
in the case that your mat file is too large to be held in memory, avoids loading it into swap space which would be extremely cumbersome.
Hope this helps.
Tom
Related
After a long time searching for an answer and not having found one, my last resort is asking a new question. I create multiple (N=1000) -mat v-6 files that are each about 100 MB in size and contain a single matrix. In a separate part of my code, I need to load in each file. The problem I'm running into is that loading the files in suddenly becomes very time consuming around file number 600 and I'm not sure why its happening. Thanks in advance for any suggestions.
I'm using Matlab R2014b on a Mac with 16GB of ram.
Sample code
c=nan(1,1000)
for h=1:1000
tic
filename=[basefilename,'_',num2str(h),'.mat'];
transition=load(filename,'P')
c(h)=toc;
end
Here is an image of the recorded loading times using the exact code above
I am getting some readings off an accelerometer connected to an Arduino which is in turn connected to MATLAB through serial communication. I would like to write the readings into a text file. A 10 second reading will write around 1000 entries that make the text file size around 1 kbyte.
I will be using the following code:
%%%%%// Communication %%%%%
arduino=serial('COM6','BaudRate',9600);
fopen(arduino);
fileID = fopen('Readings.txt','w');
%%%%%// Reading from Serial %%%%%
for i=1:Samples
scan = fscanf(arduino,'%f');
if isfloat(scan),
vib = [vib;scan];
fprintf(fileID,'%0.3f\r\n',scan);
end
end
Any suggestions on improving this code ? Will this have a time or Size limit? This code is to be run for 3 days.
Do not use text files, use binary files. 42718123229.123123 is 18 bytes in ASCII, 4 bytes in a binary file. Don't waste space unnecessarily. If your data is going to be used later in MATLAB, then I just suggest you save in .mat files
Do not use a single file! Choose a reasonable file size (e.g. 100Mb) and make sure that when you get to that many amount of data you switch to another file. You could do this by e.g. saving a file per hour. This way you minimize the possible errors that may happen if the software crashes 2 minutes before finishing.
Now knowing the real dimensions of your problem, writing a text file is totally fine, nothing special is required to process such small data. But there is a problem with your code. You are writing a variable vid which increases over time. That may cause bad performance because you are not using preallocation and it may consume a lot of memory. I strongly recommend not to keep this variable, and if you need the dater read it afterwards.
Another thing you should consider is verification of your data. What do you do when you receive less samples than you expect? Include timestamps! Be aware that these timestamps are not precise because you add them afterwards, but it allows you to identify if just some random samples are missing (may be interpolated afterwards) or some consecutive series of maybe 100 samples is missing.
I have a memory issue with a simple Matlab code I am running. When I run the following loop with the function listed, Matlab can go up to image 50 and after that it runs out of memory and ends. I need to run about 400 images and save them as a file on my hard drive for inspection. As you see in the function I am trying to clear everything but the memory still continues to grow. I have tried this Code with Matlab 13a and Matlab 14a and I have the same problem.
Here is the function (image is a jp2 image)
function plot1(image,boundary)
image1=imread(image)
h=figure
imshow(image1)
rectangle('Position',boundary)
saveas(h,[image '_newimage.jpg'],'jpg)
clear image1;clear h;cla reset;clear classes;
clear all;close all;
end
The above function is simple enough and I do not understand why the memory keeps increasing since I have cleared everything.
The program that calls this function looks like this (the image list and the xmin,xmax,width,height have been read from a list before in the program in a different loop):
for k=1:nf
boundary=[xmin(k) ymin(k) width(k) height(k)]
plot1(image{k},boundary)
end
Does anyone have any ideas about what is causing the memory increase?
Thank you for your time.
Is it any way in matlab that after program is finished to run, find the memory and time?
Also, if the workplace is saved and then it is loaded again, is it possible to see the time and memory for it ?
Thanks.
For the time consumption, would the profiler work? It slows the execution a bit, but is nice for debugging. Otherwise try to enclose the section you want to time with tic-toc.
And for memory consumption there were, and still is I think, no really convenient way to do this, however, something may have happened here. This is how mathworks answered a few years ago. You can try whos, but that one only works inside the current scope. Also memory can be used to see matlabs total memory consumption.
The time taken for loading a file should be possible to see by enclosing it with the usual tic-toc command. The size of a saved file on disk can be seen using dir on the file, but the size could be different in matlab. I guess that the safest way is to check the size before saving if it will be loaded under the same execution and otherwise it may be convenient to log the size somehow.
Don't know if i got your question correctly, but if you need to trace the time your function takes there are two ways:
the functions
tic;
t=toc
work like a stopwatch, tic starts the counting and toc tells you how long passed since last tic.
if you need to do more in depth analysis of the times matlab also offers a profile function.
i suggest you go through matlab documentation on how to use it...
hope i helped.
S.
For execution time between code lines use:
tic;
toc;
t = toc;
disp(['Execution time: ' num2str(t)])
To know and show memory usage of variables you can use whos
whos
S = whos; % type struct variable containing all the info of the actual workspace
S.bytes
To calculate the total storage, you can make a loop
Memory = 0;
S = whos;
for k = 1:length(S)
Memory = Memory + S(k).bytes;
end
disp(['Total memory used by variables in storage (Bytes): ' num2str(Memory)])
You might prefer to see whos page in mathworks
As in my previous question I have the following problem. I have a matrix P nxn which elements are matrices P{i,j} which are also nxn. So the total amount of elements is n^4. For n=100 there is an error about the lack of memory. I calculate this matrix only one time and then operate with it. Could you advise me, how to store matrices P{i,j} on the HDD?
I mean that maybe it is possible to store each of them in a file like "data_i_j.dat" and then load it while doing computations in a loop for i and j?
The save function will write data to a file, and the load function will read it back again. save(filename,varname,varname,varname...), followed by S = load(filename) and referring to S.varname (there's also a version of load that just dumps stuff into your current workspace, but that seems like poor practice).