From @oko| @end|ng |rom |n@@-tou|ou@e@|r  Thu May  4 15:01:53 2023
From: @oko| @end|ng |rom |n@@-tou|ou@e@|r (Serguei Sokol)
Date: Thu, 4 May 2023 15:01:53 +0200
Subject: [Rd] save.image Non-responsive to Interrupt
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Message-ID: <18059965-1c70-a509-6ffb-81663d87e8f6@insa-toulouse.fr>

Le 03/05/2023 ? 01:25, Henrik Bengtsson a ?crit?:
> Along the lines of calling R_CheckUserInterrupt() only onces in a while:
>
>> OTOH, in the past we have had to *disable*  R_CheckUserInterrupt()
>> in parts of R's code because it was too expensive,
>> {see current src/main/{seq.c,unique.c}  for a series of commented-out
>> R_CheckUserInterrupt() for such speed-loss reasons}
> First, here are links to these two files viewable online:
>
>   * https://github.com/wch/r-source/blob/trunk/src/main/seq.c
>
>   * https://github.com/wch/r-source/blob/trunk/src/main/unique.c
>
> When not commented out, R_CheckUserInterrupt() would have been called
> every 1,000,000 times per:
>
>    /* interval at which to check interrupts */
>    #define NINTERRUPT 1000000
>
> and
>
>    if ((i+1) % NINTERRUPT == 0) R_CheckUserInterrupt()
>
> in each iteration. That '(i+1) % NINTERRUPT == 0' expression can be
> quite expensive too.
I vaguely remember a hack that was mentioned on this list as close to 
0-cost. It looked something like:

iint = NINTERRUPT;
for (...) {
 ?? if (--iint == 0) {
 ????? R_CheckUserInterrupt();
 ????? iint = NINTERRUPT;
 ? }
}

Best,
Serguei.

>    However, if we change the code to use NINTERRUPT
> = 2^k where k = {1, 2, ...}, say
>
>    #define NINTERRUPT 1048576
>
> the compiler would optimize the condition to use "the modulo of powers
> of 2 can alternatively be expressed as a bitwise AND operation"
> (Thomas Lumley, 2015-06-15).  The speedup is quite impressive, cf.
> <https://www.jottr.org/2015/06/05/checkuserinterrupt/>.
> Alternatively, one can increment a counter and reset to zero after
> calling R_CheckUserInterrupt(); I think that's equally performant.
>
> Regarding making serialize() / unserialize() interruptible: I think
> can be a good idea since we work with larger objects these days.
> However, if we implement this, we probably have to consider what
> happens when an interrupt happens. For example, transfers between a
> client and a server are no longer atomic at this level, which means we
> might end up in a corrupt state. This may, for instance, happen to
> database transactions, and PSOCK parallel worker communication.  A
> quick fix would be to use base::suspendInterrupts(), but better would
> of course be to handle interrupts gracefully.
>
> My $.02 + $0.02
>
> /Henrik
>
> On Tue, May 2, 2023 at 3:56?PM Jeroen Ooms <jeroenooms at gmail.com> wrote:
>> On Tue, May 2, 2023 at 3:29?PM Martin Maechler
>> <maechler at stat.math.ethz.ch> wrote:
>>>>>>>> Ivan Krylov
>>>>>>>>      on Tue, 2 May 2023 14:59:36 +0300 writes:
>>>      > ? Sat, 29 Apr 2023 00:00:02 +0000
>>>      > Dario Strbenac via R-devel <r-devel at r-project.org> ?????:
>>>
>>>      >> Could save.image() be redesigned so that it promptly responds to
>>>      >> Ctrl+C? It prevents the command line from being used for a number of
>>>      >> hours if the contents of the workspace are large.
>>>
>>>      > This is ultimately caused by serialize() being non-interruptible. A
>>>      > relatively simple way to hang an R session for a long-ish time would
>>>      > therefore be:
>>>
>>>      > f <- xzfile(nullfile(), 'a+b')
>>>      > x <- rep(0, 1e9) # approx. 8 gigabytes, adjust for your RAM size
>>>      > serialize(x, f)
>>>      > close(f)
>>>
>>>      > This means that calling R_CheckUserInterrupt() between saving
>>>      > individual objects is not enough: R also needs to check for interrupts
>>>      > while saving sufficiently long vectors.
>>>
>>>      > Since the serialize() infrastructure is carefully written to avoid
>>>      > resource leaks on allocation failures, it looks relatively safe to
>>>      > liberally sprinkle R_CheckUserInterrupt() where it makes sense to do
>>>      > so, i.e. once per WriteItem() (which calls itself recursively and
>>>      > non-recursively) and once per every downstream for loop iteration.
>>>      > Valgrind doesn't show any new leaks if I apply the patch, interrupt
>>>      > serialize() and then exit. R also passes make check after the applied
>>>      > patch.
>>>
>>>      > Do these changes make sense, or am I overlooking some other problem?
>>>
>>> Thank you, Ivan!
>>>
>>> They do make sense... but :
>>>
>>> OTOH, in the past we have had to *disable*  R_CheckUserInterrupt()
>>> in parts of R's code because it was too expensive,
>>> {see current src/main/{seq.c,unique.c}  for a series of commented-out
>>>   R_CheckUserInterrupt() for such speed-loss reasons}
>>>
>>> so  adding these may need a lot of care when we simultaneously
>>> want to remain  efficient for "morally valid" use of serialization...
>>> where we really don't want to pay too much of a premium.
>> Alternatively, one could consider making R throttle or debounce calls
>> to R_CheckUserInterrupt such that a repeated calls within x time are
>> ignored, cf: https://www.freecodecamp.org/news/javascript-debounce-example/
>>
>> The reasoning being that it may be difficult for (contributed) code to
>> determine when/where it is appropriate to check for interrupts, given
>> varying code paths and cpu speed. Maybe it makes more sense to call
>> R_CheckUserInterrupt frequently wherever it is safe to do so, and let
>> R decide if reasonable time has elapsed to actually run the (possibly
>> expensive) ui check again.
>>
>> Basic example: https://github.com/r-devel/r-svn/pull/125/files
>>
>>
>>
>>
>>> {{ saving the whole user workspace is not "valid" in that sense
>>>     in my view.  I tell all my (non-beginner) Rstudio-using
>>>     students they should turn *off* the automatic saving and
>>>     loading at session end / beginning; and for reproducibility
>>>     only saveRDS() [or save()] *explicitly* a few precious
>>>     objects ..
>>> }}
>>>
>>> Again, we don't want to punish people who know what they are
>>> doing, just because other R users manage to hang their R session
>>> by too little thinking ...
>>>
>>> Your patch adds 15 such interrupt checking calls which may
>>> really be too much -- I'm not claiming they are: with our
>>> recursive objects it's surely not very easy to determine the
>>> "minimally necessary" such calls.
>>>
>>> In addition, we may still consider adding an extra optional
>>> argument, say   `check.interrupt = TRUE`
>>> which we may default to TRUE when  save.image() is called
>>> but e.g., not when serialize() is called..
>>>
>>> Martin
>>>
>>>      > --
>>>      > Best regards,
>>>      > Ivan
>>>      > x[DELETED ATTACHMENT external: Rd_IvanKrylov_interrupt-serialize.patch, text/x-patch]
>>>      > ______________________________________________
>>>      > R-devel at r-project.org mailing list
>>>      > https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


-- 
Serguei Sokol
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[Rd] save.image Non-responsive to Interrupt
Serguei Sokol