Henrik Bengtsson
2016-Oct-26 19:54 UTC
[Rd] BUG?: On Linux setTimeLimit() fails to propagate timeout error when it occurs (works on Windows)
Thank you for the feedback and confirmations. Interesting to see that
it's also reproducible on macOS expect for Spencer; that might
indicate a difference in builds.
BTW, my original post suggested that timeout error was for sure
detected while running Sys.sleep(10). However, it could of course
also be that it is only detected after it finishes.
For troubleshooting, the help("setTimeLimit", package =
"base") says that:
* "Time limits are checked whenever a user interrupt could occur. This
will happen frequently in R code and during Sys.sleep, but only at
points in compiled C and Fortran code identified by the code author."
The example here uses Sys.sleep(), which supports and detects user interrupts.
The timeout error message is thrown by the R_ProcessEvents(void)
function as defined in:
* src/unix/sys-unix.c
(https://github.com/wch/r-source/blob/trunk/src/unix/sys-unix.c#L421-L453)
* src/gnuwin32/system.c
(https://github.com/wch/r-source/blob/trunk/src/gnuwin32/system.c#L110-L140)
So, they're clearly different implementations on Windows and Unix.
Also, for the Unix implementation, the code differ based on
preprocessing directive HAVE_AQUA, which could explain why Spencer
observes a different behavior than Peter and Berend (all on macOS).
Whenever the R_CheckUserInterrupt() function is called it in turn
always calls R_ProcessEvents(). At the end, there is a code snippet -
if (R_interrupts_pending) onintr(); - which is Windows specific and
could be another important difference between Windows and Unix. This
function is defined in:
* src/main/errors.c
(https://github.com/wch/r-source/blob/trunk/src/main/errors.c#L114-L134)
The do_setTimeLimit() function controls global variables cpuLimitValue
and elapsedLimitValue, which are checked in R_ProcessEvents(), but
other than setting the timeout limits I don't think it's involved in
the runtime checks. The do_setTimeLimit() is defined in:
* src/main/sysutils.c
(https://github.com/wch/r-source/blob/trunk/src/main/sysutils.c#L1692-L1736)
Unfortunately, right now, I've got little extra time to troubleshoot
this further.
/Henrik
On Wed, Oct 26, 2016 at 2:22 AM, Berend Hasselman <bhh at xs4all.nl>
wrote:>
>> On 26 Oct 2016, at 04:44, Henrik Bengtsson <henrik.bengtsson at
gmail.com> wrote:
>> .......
>> This looks like a bug to me. Can anyone on macOS confirm whether this
>> is also a problem there or not?
>>
>
>
> Tried it on macOS El Capitan and got this (running in R.app with R version
3.3.2 RC (2016-10-23 r71574):
>
>> setTimeLimit(elapsed=1)
>> system.time({ Sys.sleep(10); message("done") })
> Error in Sys.sleep(10) : reached elapsed time limit
> Timing stopped at: 0.113 0.042 10.038
>
> Berend
>
peter dalgaard
2016-Oct-26 20:34 UTC
[Rd] BUG?: On Linux setTimeLimit() fails to propagate timeout error when it occurs (works on Windows)
Spencer also had tools and rsconnect loaded (via a namespace) but it doesn't seem to make a difference for me if I load them. It also doesn't seem to matter for me whether it is CRAN R, locally built R, Terminal, R.app. However, RStudio differs> setTimeLimit(elapsed=1)Error: reached elapsed time limit> setTimeLimit(elapsed=1)Error: reached elapsed time limit> setTimeLimit(elapsed=1); system.time({Sys.sleep(10);message("done")})Error in Sys.sleep(10) : reached elapsed time limit Timing stopped at: 0.003 0.003 0.733 -pd> On 26 Oct 2016, at 21:54 , Henrik Bengtsson <henrik.bengtsson at gmail.com> wrote: > > Thank you for the feedback and confirmations. Interesting to see that > it's also reproducible on macOS expect for Spencer; that might > indicate a difference in builds. > > BTW, my original post suggested that timeout error was for sure > detected while running Sys.sleep(10). However, it could of course > also be that it is only detected after it finishes. > > > For troubleshooting, the help("setTimeLimit", package = "base") says that: > > * "Time limits are checked whenever a user interrupt could occur. This > will happen frequently in R code and during Sys.sleep, but only at > points in compiled C and Fortran code identified by the code author." > > The example here uses Sys.sleep(), which supports and detects user interrupts. > > > The timeout error message is thrown by the R_ProcessEvents(void) > function as defined in: > > * src/unix/sys-unix.c > (https://github.com/wch/r-source/blob/trunk/src/unix/sys-unix.c#L421-L453) > * src/gnuwin32/system.c > (https://github.com/wch/r-source/blob/trunk/src/gnuwin32/system.c#L110-L140) > > So, they're clearly different implementations on Windows and Unix. > Also, for the Unix implementation, the code differ based on > preprocessing directive HAVE_AQUA, which could explain why Spencer > observes a different behavior than Peter and Berend (all on macOS). > > > Whenever the R_CheckUserInterrupt() function is called it in turn > always calls R_ProcessEvents(). At the end, there is a code snippet - > if (R_interrupts_pending) onintr(); - which is Windows specific and > could be another important difference between Windows and Unix. This > function is defined in: > > * src/main/errors.c > (https://github.com/wch/r-source/blob/trunk/src/main/errors.c#L114-L134) > > > The do_setTimeLimit() function controls global variables cpuLimitValue > and elapsedLimitValue, which are checked in R_ProcessEvents(), but > other than setting the timeout limits I don't think it's involved in > the runtime checks. The do_setTimeLimit() is defined in: > > * src/main/sysutils.c > (https://github.com/wch/r-source/blob/trunk/src/main/sysutils.c#L1692-L1736) > > > Unfortunately, right now, I've got little extra time to troubleshoot > this further. > > /Henrik > > On Wed, Oct 26, 2016 at 2:22 AM, Berend Hasselman <bhh at xs4all.nl> wrote: >> >>> On 26 Oct 2016, at 04:44, Henrik Bengtsson <henrik.bengtsson at gmail.com> wrote: >>> ....... >>> This looks like a bug to me. Can anyone on macOS confirm whether this >>> is also a problem there or not? >>> >> >> >> Tried it on macOS El Capitan and got this (running in R.app with R version 3.3.2 RC (2016-10-23 r71574): >> >>> setTimeLimit(elapsed=1) >>> system.time({ Sys.sleep(10); message("done") }) >> Error in Sys.sleep(10) : reached elapsed time limit >> Timing stopped at: 0.113 0.042 10.038 >> >> Berend >> > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel-- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
Spencer Graves
2016-Oct-26 21:04 UTC
[Rd] BUG?: On Linux setTimeLimit() fails to propagate timeout error when it occurs (works on Windows)
I was using RStudio 0.99.902. Spencer On 10/26/2016 3:34 PM, peter dalgaard wrote:> Spencer also had tools and rsconnect loaded (via a namespace) but it doesn't seem to make a difference for me if I load them. It also doesn't seem to matter for me whether it is CRAN R, locally built R, Terminal, R.app. However, RStudio differs > >> setTimeLimit(elapsed=1) > Error: reached elapsed time limit >> setTimeLimit(elapsed=1) > Error: reached elapsed time limit >> setTimeLimit(elapsed=1); system.time({Sys.sleep(10);message("done")}) > Error in Sys.sleep(10) : reached elapsed time limit > Timing stopped at: 0.003 0.003 0.733 > > -pd > > >> On 26 Oct 2016, at 21:54 , Henrik Bengtsson <henrik.bengtsson at gmail.com> wrote: >> >> Thank you for the feedback and confirmations. Interesting to see that >> it's also reproducible on macOS expect for Spencer; that might >> indicate a difference in builds. >> >> BTW, my original post suggested that timeout error was for sure >> detected while running Sys.sleep(10). However, it could of course >> also be that it is only detected after it finishes. >> >> >> For troubleshooting, the help("setTimeLimit", package = "base") says that: >> >> * "Time limits are checked whenever a user interrupt could occur. This >> will happen frequently in R code and during Sys.sleep, but only at >> points in compiled C and Fortran code identified by the code author." >> >> The example here uses Sys.sleep(), which supports and detects user interrupts. >> >> >> The timeout error message is thrown by the R_ProcessEvents(void) >> function as defined in: >> >> * src/unix/sys-unix.c >> (https://github.com/wch/r-source/blob/trunk/src/unix/sys-unix.c#L421-L453) >> * src/gnuwin32/system.c >> (https://github.com/wch/r-source/blob/trunk/src/gnuwin32/system.c#L110-L140) >> >> So, they're clearly different implementations on Windows and Unix. >> Also, for the Unix implementation, the code differ based on >> preprocessing directive HAVE_AQUA, which could explain why Spencer >> observes a different behavior than Peter and Berend (all on macOS). >> >> >> Whenever the R_CheckUserInterrupt() function is called it in turn >> always calls R_ProcessEvents(). At the end, there is a code snippet - >> if (R_interrupts_pending) onintr(); - which is Windows specific and >> could be another important difference between Windows and Unix. This >> function is defined in: >> >> * src/main/errors.c >> (https://github.com/wch/r-source/blob/trunk/src/main/errors.c#L114-L134) >> >> >> The do_setTimeLimit() function controls global variables cpuLimitValue >> and elapsedLimitValue, which are checked in R_ProcessEvents(), but >> other than setting the timeout limits I don't think it's involved in >> the runtime checks. The do_setTimeLimit() is defined in: >> >> * src/main/sysutils.c >> (https://github.com/wch/r-source/blob/trunk/src/main/sysutils.c#L1692-L1736) >> >> >> Unfortunately, right now, I've got little extra time to troubleshoot >> this further. >> >> /Henrik >> >> On Wed, Oct 26, 2016 at 2:22 AM, Berend Hasselman <bhh at xs4all.nl> wrote: >>>> On 26 Oct 2016, at 04:44, Henrik Bengtsson <henrik.bengtsson at gmail.com> wrote: >>>> ....... >>>> This looks like a bug to me. Can anyone on macOS confirm whether this >>>> is also a problem there or not? >>>> >>> >>> Tried it on macOS El Capitan and got this (running in R.app with R version 3.3.2 RC (2016-10-23 r71574): >>> >>>> setTimeLimit(elapsed=1) >>>> system.time({ Sys.sleep(10); message("done") }) >>> Error in Sys.sleep(10) : reached elapsed time limit >>> Timing stopped at: 0.113 0.042 10.038 >>> >>> Berend >>> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel
luke-tierney at uiowa.edu
2016-Oct-27 16:26 UTC
[Rd] BUG?: On Linux setTimeLimit() fails to propagate timeout error when it occurs (works on Windows)
On unix, unless event polling is enabled Sys.sleep just waits in a select() call (with a SIGINT handler in place) so the elapsed time isn't checked until after the select call is complete. Rstudio uses event polling, and in particular sets R_wait_usec to 10000, which means event and interrupt checks happen during a Sys.seep call. The R GUI on macOS doesn't seem to do this (but my lldb skills aren't up to checking). Now that we have this elapsed time limit mechanism it might be a good idea to set the default for R_wait_usec to something reasonable on unix in general. 100000 might be a good value. A more worrying thing I noticed while looking at this is that blocking reads on fifos and pipes and probably sockets are not interruptable -- that should probably be looked into. Best, luke On Wed, 26 Oct 2016, peter dalgaard wrote:> Spencer also had tools and rsconnect loaded (via a namespace) but it doesn't seem to make a difference for me if I load them. It also doesn't seem to matter for me whether it is CRAN R, locally built R, Terminal, R.app. However, RStudio differs > >> setTimeLimit(elapsed=1) > Error: reached elapsed time limit >> setTimeLimit(elapsed=1) > Error: reached elapsed time limit >> setTimeLimit(elapsed=1); system.time({Sys.sleep(10);message("done")}) > Error in Sys.sleep(10) : reached elapsed time limit > Timing stopped at: 0.003 0.003 0.733 > > -pd > > >> On 26 Oct 2016, at 21:54 , Henrik Bengtsson <henrik.bengtsson at gmail.com> wrote: >> >> Thank you for the feedback and confirmations. Interesting to see that >> it's also reproducible on macOS expect for Spencer; that might >> indicate a difference in builds. >> >> BTW, my original post suggested that timeout error was for sure >> detected while running Sys.sleep(10). However, it could of course >> also be that it is only detected after it finishes. >> >> >> For troubleshooting, the help("setTimeLimit", package = "base") says that: >> >> * "Time limits are checked whenever a user interrupt could occur. This >> will happen frequently in R code and during Sys.sleep, but only at >> points in compiled C and Fortran code identified by the code author." >> >> The example here uses Sys.sleep(), which supports and detects user interrupts. >> >> >> The timeout error message is thrown by the R_ProcessEvents(void) >> function as defined in: >> >> * src/unix/sys-unix.c >> (https://github.com/wch/r-source/blob/trunk/src/unix/sys-unix.c#L421-L453) >> * src/gnuwin32/system.c >> (https://github.com/wch/r-source/blob/trunk/src/gnuwin32/system.c#L110-L140) >> >> So, they're clearly different implementations on Windows and Unix. >> Also, for the Unix implementation, the code differ based on >> preprocessing directive HAVE_AQUA, which could explain why Spencer >> observes a different behavior than Peter and Berend (all on macOS). >> >> >> Whenever the R_CheckUserInterrupt() function is called it in turn >> always calls R_ProcessEvents(). At the end, there is a code snippet - >> if (R_interrupts_pending) onintr(); - which is Windows specific and >> could be another important difference between Windows and Unix. This >> function is defined in: >> >> * src/main/errors.c >> (https://github.com/wch/r-source/blob/trunk/src/main/errors.c#L114-L134) >> >> >> The do_setTimeLimit() function controls global variables cpuLimitValue >> and elapsedLimitValue, which are checked in R_ProcessEvents(), but >> other than setting the timeout limits I don't think it's involved in >> the runtime checks. The do_setTimeLimit() is defined in: >> >> * src/main/sysutils.c >> (https://github.com/wch/r-source/blob/trunk/src/main/sysutils.c#L1692-L1736) >> >> >> Unfortunately, right now, I've got little extra time to troubleshoot >> this further. >> >> /Henrik >> >> On Wed, Oct 26, 2016 at 2:22 AM, Berend Hasselman <bhh at xs4all.nl> wrote: >>> >>>> On 26 Oct 2016, at 04:44, Henrik Bengtsson <henrik.bengtsson at gmail.com> wrote: >>>> ....... >>>> This looks like a bug to me. Can anyone on macOS confirm whether this >>>> is also a problem there or not? >>>> >>> >>> >>> Tried it on macOS El Capitan and got this (running in R.app with R version 3.3.2 RC (2016-10-23 r71574): >>> >>>> setTimeLimit(elapsed=1) >>>> system.time({ Sys.sleep(10); message("done") }) >>> Error in Sys.sleep(10) : reached elapsed time limit >>> Timing stopped at: 0.113 0.042 10.038 >>> >>> Berend >>> >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel > >-- Luke Tierney Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics and Fax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: luke-tierney at uiowa.edu Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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