I'm running a real-time data assimilation program written in Matlab, and there seems to be a slow memory leak. Over the course of about 16 days, the average memory usage has increased by about 40% (see the figure below) from about 1.1GB to 1.5GB. The program loops every 15 minutes, and there is a peak in memory usage for about 30 seconds during the data assimilation step (visible in the figure).
At the end of each 15 minute cycle, I'm saving the names, sizes, and types of all variables in the currently active workspace to a .mat file using the whos function. There are just over 100 variables, and after running the code for about 16 days, there is no clear trend in the amount of memory used by any of the variables.
Some variables are cleared at the end of each cycle, but some of them are not. I'm also calling close all to make sure there are no figures sitting in memory, and I made sure that when I'm writing ASCII files, I always fclose(fileID) the file.
I'm stumped...I'm wondering if anyone here has any suggestions about things I should look for or tools that could help track down the issue. Thanks in advance!
Edit, system info:
RHEL 6.8
Matlab R2014b
I figured out the problem. It turns out that the figure handles were hidden, and close('all') only works on figures that are visible. I assume they're hidden because the figures are created outside the scope of where I was trying to close the figures. The solution was to replace close('all') with close all hidden, which closes all figures including those with hidden handles.
I'll go ahead and restate what #John and #horchler mentioned in their comments, in case their suggestions can help people with similar issues:
Reusing existing figures can increase performance and reduce the potential for memory leaks.
Matlab has an undocumented memory profiler that could help debug performance related issues.
For processes that are running indefinitely, it's good practice to separate data collection/processing and product generation (figures etc). The first reads in and processes the data and saves it to a DB or file. The second allows you to "view/access/query" the data.
If you are calling compiled mex functions in your code, the memory leak could be coming from the Fortran or C/C++ code. Not cleaning up a single variable could cause a leak, and would explain linear memory growth.
The Matlab function whos is great for looking at the size in memory of each variable in the workspace. This can be useful for tracking down which variable is the culprit of a memory leak.
Thanks #John and #horchler!
Related
I have a memory intensive Matlab script.
What puzzles me is that if I run this code it will leak memory at the very first iteration (out of the 46 expected). The leak will eventually become so big that it will require forcing Matlab to quit:
Trying to find the leak point, I set a breakpoint at the first line in the loop but as I hit "Continue" the execution ran through the first loop and stopped again at the breakpoint and produced no leak. Removing the breakpoint and continuing from that point reintroduces the leak.
Using the breakpoint to execute the code one loop at the time avoids the leak and the code terminates with no issues (fig.2).
Now, I would like to:
1) understand whether this leak is due to something I introduced or whether it could be a Matlab specific issue,
2) get an idea of how to find the leak (I cannot use the debugger as it removes the problem).
I would love to provide the code but it is quite a big chunk (>100 lines), so my question is more about the general approach than the actual debugging of the specific issue.
Thanks for the suggestions.
My approach has been to isolate the portion of code that was causing the problem with printouts above each line of code so that before the leaky crash I could see where the execution stopped.
The culprit was a zeros(100k) line where I tried to pre-allocate a big matrix.
I tried executing the same line on a newer version of Matlab (2015b vs 2014b) and found that while the older version lets you instantiate big matrices (over ~ 50k by 50k) and freezes when it sucks all the memory, the newer version returns the following error:
Error using zeros
Requested 50000x50000 (18.6GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time and cause MATLAB to become unresponsive.
See array size limit or preference panel for more
information.
In my case the limits for a NxN matrix are:
N > ~60000 on Matlab2014b on 16GB RAM
N >= 46341 on Matlab2015b on 12GB RAM
With the difference that my 2014 version lets me at least try to create them and collapses when they are too big and the 2015 version prevented me from trying at all.
The puzzling bit is that, on the 2014b version, if I debug the code the compilers lets the zeros(100k) line run and everything works just fine.
The problem appears again if I try to visualise the contents of the matrix in Matlab Variables Tab.
I am batch processing a bunch of files (~200) on MATLAB, in essence
for i = 1:n, process(i); end
where process(i) opens a file, reads it and writes out the output to another file. (I am not posting details about process here because it is hundreds of lines long and I readily admit I don't fully understand the code, having obtained it from someone else).
This runs out of memory after every dozen of files or so. Of course, on Linux, the memory function is not available so we have to figure it out "by hand". Well, I thought there is some memory leak, so let's issue a clear all after every run, i.e.
for i = 1:n, process(i); clear all; end
No luck, this still runs out of memory. At the point where this happens, who says there's just two small arrays in memory (<100 elements). Note that quitting MATLAB and restarting solves the problem, so the computer certainly has enough memory to process a single item.
Any ideas to help me detect where the error comes from would be welcome.
This is probable not the solution you are hoping for but as a workaround you could have a shell script that loops over several calls to Matlab.
I use MATLAB for programming some meta-heuristics. Recently, I have been working on an algorithm for solving an industrial engineering problem. My problem with MATLAB is getting "out of memory" errors. Now I'm trying some suggestions from Mathworks and Stackoverflow (Hope they will work). However, there is one thing I did not understand.
During the run of the algorithm in MATLAB (it takes 4000-5000 cpu sec for a medium sized problem), even though I preallocate variables, code does not demand dynamic array resizing and does not add new variables, I observe that the memory usage of the algorithm grows continuously. The main function calls some other functions written by me. What could be the reason of increase of the memory usage?
The computer I use for the running of the algorithm has 8GBs of memory and win8 64bit installed.
The only way to figure this out is to see where the memory is going.
I think you may accidentally store results that you don't need, or that you underestimate the size of your output/intermediate variables.
Here is how I would proceed:
Turn on dbstop if error
Run the code till you get the out of memory error
See how much memory is being used (make sure to check all work spaces)
Probably you now know where the extra memory is going. If you don't find much memory being used, continue with this:
Check the memory command to see how much memory is still available
Carefully look at the line being executed, perhaps you actually need a huge amount of memory for it
If all else fails share your findings here and others can help you look for it.
The reason of memory usage growth is CPlex. I tried many alternatives but I couldn't find any other useful solution than increasing virtual memory to several hundred GBs. If you don't have special reasons to insist on CPlex (commercial usage, licensing etc.), I would suggest anyone, who encounter this problem, to use GUROBI. It is free and unlimited for academic usage, totally integrable with MATLAB. That's the solution I have found for my problem with Cplex. I hope this solution works for everybody.
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
I'm running a simulation of a diffusion-reaction equation in MATLAB, and I pre-allocate the memory for all of my vectors beforehand, however, during the loop, in which I solve a system of equations using BICG, the amount of memory that MATLAB uses is increasing.
For example:
concentration = zeros(N, iterations);
for t = 1:iterations
concentration(:,t+1) = bicg(matrix, concentration(:,t));
end
As the program runs, the amount of memory MATLAB is using increases, which seems to suggest that the matrix, concentration, is increasing in size as the program continues, even though I pre-allocated the space. Is this because the elements in the matrix are becoming doubles instead of zeros? Is there a better way to pre-allocate the memory for this matrix, so that all of the memory the program requires will be pre-allocated at the start? It would be easier for me that way, because then I would know from the start how much memory the program will require and if the simulation will crash the computer or not.
Thanks for all your help, guys. I did some searching around and didn't find an answer, so I hope I'm not repeating a question.
EDIT:
Thanks Amro and stardt for your help guys. I tried running 'memory' in MATLAB, but the interpreter said that command is not supported for my system type. I re-ran the simulation though with 'whos concentration' displayed every 10 iterations, and the allocation size of the matrix wasn't changing with time. However, I did notice that the size of the matrix was about 1.5 GB. Even though that was the case, system monitor was only showing MATLAB as using 300 MB (but it increased steadily to reach a little over 1 GB by the end of the simulation). So I'm guessing that MATLAB pre-allocated the memory just fine and there are no memory leaks, but system monitor doesn't count the memory as in use until MATLAB starts writing values to it in the loop. I don't know why that would be, as I would imagine that writing zeros would trigger the system monitor to see that memory as 'in use,' but I guess that's not the case here.
Anyway, I appreciate your help with this. I would vote both of your answers up as I found them both helpful, but I don't have enough reputation points to do that. Thanks guys!
I really doubt it's a memory leak, since most "objects" in MATLAB clean after themselves once they go out of scope. AFAIK, MATLAB does not use a GC per se, but a deterministic approach to managing memory.
Therefore I suspect the issue is more likely to be caused by memory fragmentation: when MATLAB allocates memory for a matrix, it has to be contiguous. Thus when the function is repeatedly called, creating and deleting matrices, and over time, the fragmentation becomes a noticeable problem...
One thing that might help you debug is using the undocumented: profile on -memory which will track allocation in the MATLAB profiler. Check out the monitoring tool by Joe Conti as well. Also this page has some useful information.
I am assuming that you are watching the memory usage of matlab in, for example, the task manager on windows. The memory usage is probably increasing due to the execution of bicg() and variables that have not been garbage collected after it ends. The memory allocated to the concentration matrix stays the same. You can type
whos concentration
before and after your "for" loop to see how much memory is allocated to that variable.