Matlab hangs when I am trying to generate a mex-file. When I run the program like normal everything works and when I try to generate a mex-file matlab gets to the end of the code but nothing happens after that. I have understood that it might have something to do with the figures. I read somewhere that it calls mclWaitForFiguresToDie but I have not understood how to fix it.
One figure should be displayed but it is not displayed while generating the mex-code.
Related
I know it's possible to forward any output from a remote machine to a local one by using the X11 forwarding remote tunnelling, so that when you run a MATLAB command it will display all the graphical outputs back to the machine you've connected from.
My question is:
Is there any MATLAB command to just output the figures (e.g., plot,surf,etc.) without displaying any other graphical object (i.e., the main interface)?
In practice, I would like to interact with MATLAB by using the command line (as shown below) and forward back only the figures.
MATLAB cannot display figures without its own figure-GUI, so the answer to your question would be no.
However: there is a workaround: create an invisible figure using f=figure('visible', 'off'), then plot your data, and finally use saveas(f,filename,fileextention). Don't forget to close(f) your figure after saving, to free the RAM. You'll now have a figure in your file directory, which you can display using your favourite visualising tool, which might even be possible through a call to system, although I have never tested that.
BUG: I used cell-arrays in the underlying functions, bad!
I cannot understand why restarting Matlab result sometimes into more verbose error messages that help me to actually solve problems. Now I am trying to find a command that makes Matlab showing as much information as possible. For example the below index-exceed-dimension error is totally useless with my recursive algorithm -- this is the specific algorithm where Matlab have once revealed the specific line but now for some reason only telling the vacuously the name of the algorithm
Index exceeds matrix dimensions.
Error in Dij (line 65)
Dij_=Dij(ii,jj,[II,k],[r,q_(k)]);
where you can see that I am running the algorithm Dij failing on the line running the algorithm Dij again.
How can I get more information about the error? Or how can I get inside any point in the recursive algorithm? -Linebreak and trying to get inside that point just fires the error.
Add a try catch block on your recursive algorithm, print the information you think it would be valid and then rethrow an error that will terminate your other callbacks silently.
You may use the keyboard matlab function to check the matlab workspace as the recursive function goes on. You can choose to add it just before your error message, so it will be called every time it goes deeper in the recursive level, so that you can check what is going on, or you can add it when the error occurs (on the catch).
This is just a draft, it may contain errors, adapt it into your needs:
try
% recursive routine
catch ext
if strcmp(ext.identifier,'MyPackage:MyRecursiveRoutine:TerminateSilently'))
% Do nothing
else
% Display useful information, you edit it to add information you think would be valid, i.e.:
disp(ext.getReport)
disp(yourVariable)
% get dbstack size, to see how many recursive functions, i.e:
theStack = dbstack;
recursiveCalls=sum(strcmp({theStack.name},'MyRecursiveFcnName'))
% You may even add the keyboard function here, so that you can inspect your workspace:
keyboard
throw(MExcept('MyPackage:MyRecursiveRoutine:TerminateSilently',''));
end
end
Run dbstop if error before running your code to drop to the debugger exactly at the point of error. From there you can inspect the variables, including whatever variable you've carried along to ID the level. You can also run dbstack to see the full call stack.
It is not evident in the description where the bug is because it does not show with which tools I programmed the underlying functions: I used cellarrays and for some reason Matlab returns far worse error messages with cellarrays than with Matrices so:
my genuine recommendation is avoid cellarrays and use matrices -- and if you need to play with a lot of zero cases, use the ready sparse functionalities because they have far better debugging verbosity!
Instead of wasting too much time to debugging, choose the right tools and Matlab is excellent with Matrices and you can see it in the quality of error messages.
This question already has an answer here:
How to abort a running program in MATLAB?
(1 answer)
Closed 7 years ago.
I write a long running script in Matlab, e.g.
tic;
d = rand(5000);
[a,b,c] = svd(d);
toc;
It seems running forever. Becasue I press F5 in the editor window. So I cannot press C-Break to stop in the Matlab console.
I just want to know how to stop the script. I am current use Task Manager to kill Matlab, which is really silly.
Thanks.
Matlab help says this-
For M-files that run a long time, or that call built-ins or MEX-files that run a long time, Ctrl+C does not always effectively stop execution. Typically, this happens on Microsoft Windows platforms rather than UNIX[1] platforms. If you experience this problem, you can help MATLAB break execution by including a drawnow, pause, or getframe function in your M-file, for example, within a large loop. Note that Ctrl+C might be less responsive if you started MATLAB with the -nodesktop option.
So I don't think any option exist. This happens with many matlab functions that are complex. Either we have to wait or don't use them!.
If ctrl+c doesn't respond right away because your script is too long/complex, hold it.
The break command doesn't run when matlab is executing some of its deeper scripts, and either it won't log a ctrl sequence in the buffer, or it clears the buffer just before or just after it completes those pieces of code. In either case, when matlab returns to execute more of your script, it will recognize that you are holding ctrl+c and terminate.
For longer running programs, I usually try to find a good place to provide a status update and I always accompany that with some measure of time using tic and toc. Depending on what I am doing, I might use run time, segment time, some kind of average, etc...
For really long running programs, I found this to be exceptionally useful
http://www.mathworks.com/matlabcentral/fileexchange/16649-send-text-message-to-cell-phone/content/send_text_message.m
but it looks like they have some newer functions for this too.
MATLAB doesn't respond to Ctrl-C while executing a mex implemented function such as svd. Also when MATLAB is allocating big chunk of memory it doesn't respond. A good practice is to always run your functions for small amount of data, and when all test passes run it for actual scale. When time is an issue, you would want to analyze how much time each segment of code runs as well as their rough time complexity.
Consider having multiple matlab sessions. Keep the main session window (the pretty one with all the colours, file manager, command history, workspace, editor etc.) for running stuff that you know will terminate.
Stuff that you are experimenting with, say you are messing with ode suite and you get lots of warnings: matrix singular, because you altered some parameter and didn't predict what would happen, run in a separate session:
dos('matlab -automation -r &')
You can kill that without having to restart the whole of Matlab.
One solution I adopted--for use with java code, but the concept is the same with mexFunctions, just messier--is to return a FutureValue and then loop while FutureValue.finished() or whatever returns true. The actual code executes in another thread/process. Wrapping a try,catch around that and a FutureValue.cancel() in the catch block works for me.
In the case of mex functions, you will need to return somesort of pointer (as an int) that points to a struct/object that has all the data you need (native thread handler, bool for complete etc). In the case of a built in mexFunction, your mexFunction will most likely need to call that mexFunction in the separate thread. Mex functions are just DLLs/shared objects after all.
PseudoCode
FV = mexLongProcessInAnotherThread();
try
while ~mexIsDone(FV);
java.lang.Thread.sleep(100); %pause has a memory leak
drawnow; %allow stdout/err from mex to display in command window
end
catch
mexCancel(FV);
end
Since you mentioned Task Manager, I'll guess you're using Windows. Assuming you're running your script within the editor, if you aren't opposed to quitting the editor at the same time as quitting the running program, the keyboard shortcut to end a process is:
Alt + F4
(By which I mean press the 'Alt' and 'F4' keys on your keyboard simultaneously.)
Alternatively, as mentioned in other answers,
Ctrl + C
should also work, but will not quit the editor.
if you are running your matlab on linux, you can terminate the matlab by command in linux consule.
first you should find the PID number of matlab by this code:
top
then you can use this code to kill matlab:
kill
example:
kill 58056
To add on:
you can insert a time check within a loop with intensive or possible deadlock, ie.
:
section_toc_conditionalBreakOff;
:
where within this section
if (toc > timeRequiredToBreakOff) % time conditional break off
return;
% other options may be:
% 1. display intermediate values with pause;
% 2. exit; % in some cases, extreme : kill/ quit matlab
end
I would like to run a program called QuantiSNP that used Matlab in its code. I am not familiar with Matlab at all. I got the below error message and no output. Any idea how to fix it? FYI, I don't have access to source code of the program....
??? Error using ==> chol Matrix must be positive definite.
MATLAB:posdef
Highly appreciate your help
Jean
It's very hard trying to answer your question without seeing any code but here is some general info about the problem you are facing:
What you see is a Matlab error message. I assume QuantiSNP is a compiled Matlab program so you probably can't debug it. In short it says that at some point the program is trying to calculate the Cholesky factorization using chol() function, but the matrix inside is not positive definite. Most of the time the problem happens because the matrix is actually zero, which in turn is [potentially] caused by an invalid input parameter
Check to see if the parameters you are using (1) are valid and (2) match your environment. If there is an input CSV or TXT file, make sure the path is correct. Make sure numbers make sense. Are there any zeros or extra lines somewhere that should not be there?
Depending on which version of QuantiSNP you have, you may have access to the --verbose switch. Add --verbose to the end of your command (for example quantisnp2.exe firstparam secondparam --verbose) to see some messages on the screen as the program runs through the data. See if you can figure out where it's failing and if it's related to your input parameters.
Take a look the QuantiSNP how-to page to make sure you understand the required parameters and the formatting of the input file.
I have built a GUI with some text boxes and a pushbutton. When I execute the GUI from MATLAB, it produces the desired plot on a separate window. The plot is created by a function that is stored in the same directory and is called in the callback function of pushbutton.
When I package it with the .m file of the GUI as the main file, I get an exe. When this exe runs, it normally takes data from data source (sqlserver) but then does not give the plot in a separate window as within matlab (also not in the same GUI window). There is a sound and from the behaviour it seems that the plots appears and vanishes in a very short time. But this is my perception and may be wrong, maybe it is some error message that is suppressed.
What can I do to solve this?
You've run into the problem discussed here in this post
Once the code is finished evaluating it cleans up, including closing the window you created. One solution would be to pause your script right after plotting.
Here's a discussion of many functions that can be used to pause execution with a GUI.