From schattenpflanze at arcor.de  Mon Apr 25 19:44:34 2011
From: schattenpflanze at arcor.de (schattenpflanze at arcor.de)
Date: Mon, 25 Apr 2011 19:44:34 +0200
Subject: [Rd] Interrupting C++ code execution
In-Reply-To: <F1EAEEC8-7828-403F-BF2D-10A4F925B4E6@r-project.org>
References: <4DB53D47.7060903@arcor.de>
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	<4DB58E94.8050304@arcor.de>
	<85607CA7-D76F-4210-9C6E-F3E9F26F7D0E@r-project.org>
	<F1EAEEC8-7828-403F-BF2D-10A4F925B4E6@r-project.org>
Message-ID: <4DB5B302.9090800@arcor.de>

Dear Simon,

thanks again for your explanations. Your previous e-mail clarified 
several points for me.

> Actually, it just came to me that there is a hack you could use. [...]
That actually looks quite nice. At least when compared to my currently 
only alternative of not interrupting at all. I will test it, in 
particular with respect to computational speed. Perhaps I can at least 
call it once per second.

Best regards,
Peter


> The
> problem with it is that it will eat all errors, even if they were not
> yours (e.g. those resulting from events triggered the event loop), so
> I would not recommend it for general use. But here we go:
>
> static void chkIntFn(void *dummy) { R_CheckUserInterrupt(); }
>
> // this will call the above in a top-level context so it won't
> longjmp-out of your context bool checkInterrupt() { return
> (R_ToplevelExec(chkIntFn, NULL) == FALSE); }
>
> // your code somewhere ... if (checkInterrupt()) { // user
> interrupted ... }
>
> You must call it on the main thread and you should be prepared that
> it may take some time and may interact with the OS...
>
> Cheers, Simon
>
>
> On Apr 25, 2011, at 12:23 PM, Simon Urbanek wrote:
>
>>
>> On Apr 25, 2011, at 11:09 AM, schattenpflanze at arcor.de wrote:
>>
>>> Thank you for your response, Simon.
>>>
>>>>> 1. Calling R_CheckUserInterrupt() interrupts immediately, so
>>>>> I have no possibility to exit my code gracefully. In
>>>>> particular, I suppose that objects created on the heap (e.g.,
>>>>> STL containers) are not destructed properly.
>>>> In general, you're responsible for the cleanup. See R-devel
>>>> archives for discussion on the interactions of C++ and R error
>>>> handling. Generally, you should not use local objects and you
>>>> should use on.exit to make sure you clean up.
>>> I am using Rcpp (Rcpp-modules, to be precise). This means, I do
>>> actually not write any R code. Moreover, the C++ code does not
>>> use the R API. My C++ functions are 'exposed' to R via Rcpp,
>>> which creates suitable S4 classes. Rcpp does the exception
>>> handling. In particular, there is no obvious possibility for me
>>> to add an 'on.exit' statement to a particular exposed C++
>>> method.
>>>
>>>> Generally, you should not use local objects
>>> We are talking about large amounts of code, dozens of nested
>>> function calls, and even external libraries. So "not using local
>>> objects" is definitely no option.
>>>
>>
>> But that would imply that the library calls R! Note that we're
>> talking about the stack at the point of R API call, so you can do
>> what you want until you cal R API. At the moment you touch R API
>> you should have no local C++ objects on the stack (all the way
>> down) - that's what I meant.
>>
>>
>>>>> 2. Calling R_CheckUserInterrupt() within a parallel OpenMP
>>>>> loop causes memory corruptions. Even if I do so within a
>>>>> critical section, it usually results in segfaults, crashes,
>>>>> or invalid variable contents afterwards. I suppose this is
>>>>> due to the threads not being destroyed properly. Since most
>>>>> of the time critical computations are done in parallel, this
>>>>> means I can hardly interrupt anything.
>>>> As you know R is not thread-safe so you cannot call any R API
>>>> from a thread - including OMP threads - so obviously you can't
>>>> call R_CheckUserInterrupt().
>>> That is very interesting. Not being thread safe does not
>>> necessarily imply that a function cannot be called from within a
>>> thread (as long as it is not done concurrently from several
>>> threads). In particular, the main program itself is also a
>>> thread, isn't it?
>>
>> Yes, but each thread has a separate stack, and you can only enter R
>> with the same stack you left (because the stack will be restored to
>> the state of the calling context).
>>
>>
>>> Since no cleanup is done, however, it is now clear that calling
>>> R_CheckUserInterrupt() _anywhere_ in my program, parallel section
>>> or not, is a bad idea.
>>>
>>>> Since you're using threads the safe way is to perform your
>>>> computations on a separate thread and let R handle events so
>>>> that you can abort your computation thread as part of on.exit.
>>> Starting the computations in a separate thread is a nice idea. I
>>> could then call R_CheckUserInterrupt() every x milliseconds in
>>> the function which dispatches the worker thread. Unfortunately, I
>>> see no obvious way of adding an "on.exit" statement to an Rcpp
>>> module method. So I would probably have to call an R function
>>> from C++ (e.g., using RInside) which contains the on.exit
>>> statement, which in turn calls again a C++ function setting a
>>> global 'abort' flag and waits for the threads to be terminated.
>>> Hmmm.
>>>
>>> How does on.exit work?
>>
>> It sets the conexit object of the current context structure to the
>> closure to be evaluated when the context is left. endcontext() then
>> simply evaluates that closure when the context is left.
>>
>>
>>> Could I mimic that behaviour directly in C++?
>>>
>>
>> Unfortunately there is no C-level onexit hook and the internal
>> structure of RCNTXT is not revealed to packages. So AFAICS the
>> closest you can get is to use eval to call on.exit().
>>
>> However, I think it would be useful to have a provision for
>> creating a context with a C-level hook - the question is whether
>> the others have the feeling that it's going to a too low level ...
>>
>>
>>>>> Having a function similar to R_CheckUserInterrupt() but
>>>>> returning a boolean variable (has an interrupt occurred or
>>>>> not?) would solve these problems. Is there a way to find out
>>>>> about user interrupt requests (the user pressing ctrl+c or
>>>>> maybe a different set of keys) without interrupting
>>>>> immediately?
>>>> Checking for interrupts may involve running the OS event loop
>>>> (to allow the user to interact with R) and thus is not
>>>> guaranteed to return.
>>> I see.
>>>
>>>> There is no general solution - if you're worried only about
>>>> your, local code, then on unix, for example, you could use
>>>> custom signal handlers to set a flag and co-operatively
>>>> interrupt your program. On Windows there is the UserBreak flag
>>>> which can be set by a separate thread and thus you may check on
>>>> it. That said, all this is very much platform-specific.
>>> Being able to set a flag is all I need and would be the perfect
>>> solution imho. However, I do not yet see how I could achieve
>>> that.
>>>
>>
>> It is GUI-specific, unfortunately. AFAIR the Windows GUI does that
>> because it's running on a separate thread. I think the X11-based
>> GUIs use fds so the are synchronous and on OS X runs the OS loop
>> inside the R event loop - so, again, synchronous.
>>
>>
>>> How can I write a signal handler within C++ code which does not
>>> create a GUI and has no dedicated event dispatching thread?
>>
>> That's simple just use signal() to register your handler.
>>
>>
>>> Would it be possible to use, e.g., a Qt keyboard event handler
>>> within the C++ code? Would a keyboard event be visible to such an
>>> event handler? Is it not intercepted by R / the terminal window /
>>> the OS?
>>>
>>
>> Meshing R's loop, GUI loop and your own code will be a nightmare.
>> For example, one problem is that if you are running the GUI loop
>> and it triggers an event that R would otherwise handle (e.g.
>> resizing plot window) you're in trouble since you can't let R do
>> anything...
>>
>>
>>> Does any existing R package contain signal handlers?
>>>
>>
>> I'm not sure - I would definitely not recommend that to be used in
>> packages since it's platform-dependent and changes the semantics of
>> signals defined by R. But you can play with it ;).
>>
>> Cheers, Simo



[Rd] Interrupting C++ code execution
schattenpflanze at arcor.de