Re: [R] some general advice sought on the use of gctorture()
On 04/24/2015 06:49 AM, Franckx Laurent wrote: Dear all I have bumped into the dreaded 'segfault' error type when running some C++ code using .Call(). segfaults often involve invalid memory access at the C level that are best discovered via valgrind or similar rather than gctorture. A good way to spot these is to (a) come up with a _minimal_ reproducible script test.R that takes just a few seconds to run and that tickles, at least some times, the segfault (b) make sure that your package is compiled without optimizations and with debugging symbols, e.g., in ~/.R/Makevars add the lines CFLAGS=-ggdb -O0 CXXFLAGS=-ggdb -O0 (c) run the code under 'valgrind' R -d valgrind -f test.r Look especially for 'invalid read' or 'invalid write' messages, and isolate _your_ code in the callback that the message produces. There is a 'worked example' at http://bioconductor.org/developers/how-to/c-debugging/#case-study Of course this might lead to nothing, and then you'll be back to your original question about using gctorture or other strategies. Martin Morgan I have already undertaken several attempts to debug the C++ code with gdb(), but until now I have been unable to pinpoint the origin of the problem. There are two elements that I think are puzzling (a) this .Call() has worked fine for about three years, for a variety of data (b) the actual crash occurs at random points during the execution of the function (well, random from a human eye's point of view). From what I understand in the R extensions manual, the actual problem may have been around for a while before the actual call to the C++ code. As recommended in the manual, I am now using gctorture() to try to pinpoint the origins of the problem. I can, alas, only confirm that gctorture() has an enormous impact on execution time, even for operations that are normally executed within the blink of an eye. From what I have seen until now, executing all the R code before the crash with gctorture(TRUE) could take months. I suppose then that the best way to proceed would be to proceed backward from the point where the crash occurs when gctorture(FALSE). I have tried to find some concrete examples of good practices in the use of gctorture() to identify memory problems in R, but most of what I have found on the web is simply a copy of the help page. Does anybody know more concrete and elaborated examples that could give an indication on how to best proceed further? Laurent Franckx, PhD Senior researcher sustainable mobility VITO NV | Boeretang 200 | 2400 Mol Tel. ++ 32 14 33 58 22| mob. +32 479 25 59 07 | Skype: laurent.franckx | laurent.fran...@vito.be | Twitter @LaurentFranckx VITO Disclaimer: http://www.vito.be/e-maildisclaimer __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] some general advice sought on the use of gctorture()
This is very off-topic here. My suggestion would be to do as the Posting Guide says and ask this on R-devel, or perhaps even a gdb forum. From what little I know, valgrind might help also. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On April 24, 2015 6:49:31 AM PDT, Franckx Laurent laurent.fran...@vito.be wrote: Dear all I have bumped into the dreaded 'segfault' error type when running some C++ code using .Call(). I have already undertaken several attempts to debug the C++ code with gdb(), but until now I have been unable to pinpoint the origin of the problem. There are two elements that I think are puzzling (a) this .Call() has worked fine for about three years, for a variety of data (b) the actual crash occurs at random points during the execution of the function (well, random from a human eye's point of view). From what I understand in the R extensions manual, the actual problem may have been around for a while before the actual call to the C++ code. As recommended in the manual, I am now using gctorture() to try to pinpoint the origins of the problem. I can, alas, only confirm that gctorture() has an enormous impact on execution time, even for operations that are normally executed within the blink of an eye. From what I have seen until now, executing all the R code before the crash with gctorture(TRUE) could take months. I suppose then that the best way to proceed would be to proceed backward from the point where the crash occurs when gctorture(FALSE). I have tried to find some concrete examples of good practices in the use of gctorture() to identify memory problems in R, but most of what I have found on the web is simply a copy of the help page. Does anybody know more concrete and elaborated examples that could give an indication on how to best proceed further? Laurent Franckx, PhD Senior researcher sustainable mobility VITO NV | Boeretang 200 | 2400 Mol Tel. ++ 32 14 33 58 22| mob. +32 479 25 59 07 | Skype: laurent.franckx | laurent.fran...@vito.be | Twitter @LaurentFranckx VITO Disclaimer: http://www.vito.be/e-maildisclaimer __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] some general advice sought on the use of gctorture()
Dear all I have bumped into the dreaded 'segfault' error type when running some C++ code using .Call(). I have already undertaken several attempts to debug the C++ code with gdb(), but until now I have been unable to pinpoint the origin of the problem. There are two elements that I think are puzzling (a) this .Call() has worked fine for about three years, for a variety of data (b) the actual crash occurs at random points during the execution of the function (well, random from a human eye's point of view). From what I understand in the R extensions manual, the actual problem may have been around for a while before the actual call to the C++ code. As recommended in the manual, I am now using gctorture() to try to pinpoint the origins of the problem. I can, alas, only confirm that gctorture() has an enormous impact on execution time, even for operations that are normally executed within the blink of an eye. From what I have seen until now, executing all the R code before the crash with gctorture(TRUE) could take months. I suppose then that the best way to proceed would be to proceed backward from the point where the crash occurs when gctorture(FALSE). I have tried to find some concrete examples of good practices in the use of gctorture() to identify memory problems in R, but most of what I have found on the web is simply a copy of the help page. Does anybody know more concrete and elaborated examples that could give an indication on how to best proceed further? Laurent Franckx, PhD Senior researcher sustainable mobility VITO NV | Boeretang 200 | 2400 Mol Tel. ++ 32 14 33 58 22| mob. +32 479 25 59 07 | Skype: laurent.franckx | laurent.fran...@vito.be | Twitter @LaurentFranckx VITO Disclaimer: http://www.vito.be/e-maildisclaimer __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
