bert: you are right, sorry for not cc-ing the list. thanks also for the hint. I wanted to bring this up here again, emphasising that we do find in at least one case *a very large difference* in the p value, using the same scripts and data on a windows versus mac machine (see reproducible example in the gitlab link posted below). I have now come across several instances in which results of (g)lmer models don?t agree on windows vs unix-based machines, which I find a bit disturbing. any ideas where non-negligible differences could come from? thanks, nico> On 30. May 2019, at 16:58, Bert Gunter <bgunter.4567 at gmail.com> wrote: > > > Unless there us good reason not to, always cc the list. I have done so here. > > The R Installation manual has some info on how to use different BLASes I believe, but someone with expertise (I have none) needs to respond to your queries. > > On Thu, May 30, 2019 at 7:50 AM Nicolas Schuck <nico.schuck at gmail.com <mailto:nico.schuck at gmail.com>> wrote: > I know that it is in use on the Mac, see sessionInfo below. I have to check on the Win system. Why would that make such a difference and how could I make the Win get the same results as the Unix Systems? > > R version 3.6.0 (2019-04-26) > Platform: x86_64-apple-darwin15.6.0 (64-bit) > Running under: macOS Mojave 10.14.5 > Matrix products: default > BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib > LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib > Random number generation: > RNG: Mersenne-Twister > Normal: Inversion Sample: Rounding > locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > attached base packages: [1] stats graphics grDevices utils datasets methods base > Thanks, Nico > On 30. May 2019, at 16:34, Bert Gunter <bgunter.4567 at gmail.com <mailto:bgunter.4567 at gmail.com>> wrote: > >> The BLAS in use on each? >> >> Bert Gunter >> >> "The trouble with having an open mind is that people keep coming along and sticking things into it." >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) >> >> >> On Thu, May 30, 2019 at 5:27 AM Nicolas Schuck <nico.schuck at gmail.com <mailto:nico.schuck at gmail.com>> wrote: >> Dear fellow R coders, >> >> I am observing differences in results obtained using glmer when using a Mac or Linux computer versus a PC. Specifically, I am talking about a relatively complex glmer model with a nested random effects structure. The model is set up in the following way: >> gcctrl = glmerControl(optimizer=c('nloptwrap'), optCtrl = list(maxfun = 500000), calc.derivs = FALSE) >> >> glmer_pre_instr1 = glmer( >> formula = cbind(FREQ, NSAMP-FREQ) ~ FDIST_minz + poly(RFREQ,2) + ROI + (1 + FDIST_minz + RFREQ + ROI|ID/COL), >> data = cdf_pre_instr, >> family = binomial, >> control = gcctrl) >> >> Code and data of an example for which I find reproducible, non-negligible differences between Mac/Win can be found here: https://gitlab.com/nschuck/glmer_sandbox/tree/master <https://gitlab.com/nschuck/glmer_sandbox/tree/master> <https://gitlab.com/nschuck/glmer_sandbox/tree/master <https://gitlab.com/nschuck/glmer_sandbox/tree/master>> >> The differences between the fitted models seem to be most pronounced regarding the estimated correlation structure of the random effects terms. Mac and Linux yield very similar results, but Windows deviates quite a bit in some cases. This has a large impact on p values obtained when performing model comparisons. I have tried this on Mac OS 10.14, Windows 10 and Ubuntu and Debian. All systems I have tried are using lme 1.1.21 and R 3.5+. >> >> Does anyone have an idea what the underlying cause might be? >> >> Thanks, >> Nico >> >> >> >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help at r-project.org <mailto:R-help at r-project.org> mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help <https://stat.ethz.ch/mailman/listinfo/r-help> >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html <http://www.r-project.org/posting-guide.html> >> and provide commented, minimal, self-contained, reproducible code.[[alternative HTML version deleted]]
Hi, 32bit vs. 64bit systems? Another thing I would look at would be how the windows machine will read the data file. Though issues should probably only arise with respect to text data, I've often experienced problems with reading unicode csv files on windows computers compared with unix-based computers. No guarantee though, just suggestions... Olivier. On Wed, 5 Jun 2019 12:15:53 +0200 Nicolas Schuck <nico.schuck at gmail.com> wrote:> bert: you are right, sorry for not cc-ing the list. thanks also for > the hint. > > I wanted to bring this up here again, emphasising that we do find in > at least one case *a very large difference* in the p value, using the > same scripts and data on a windows versus mac machine (see > reproducible example in the gitlab link posted below). I have now > come across several instances in which results of (g)lmer models > don?t agree on windows vs unix-based machines, which I find a bit > disturbing. any ideas where non-negligible differences could come > from? > > thanks, > nico > > > > On 30. May 2019, at 16:58, Bert Gunter <bgunter.4567 at gmail.com> > > wrote: > > > > > > Unless there us good reason not to, always cc the list. I have done > > so here. > > > > The R Installation manual has some info on how to use different > > BLASes I believe, but someone with expertise (I have none) needs to > > respond to your queries. > > > > On Thu, May 30, 2019 at 7:50 AM Nicolas Schuck > > <nico.schuck at gmail.com <mailto:nico.schuck at gmail.com>> wrote: I > > know that it is in use on the Mac, see sessionInfo below. I have to > > check on the Win system. Why would that make such a difference and > > how could I make the Win get the same results as the Unix Systems? > > > > R version 3.6.0 (2019-04-26) > > Platform: x86_64-apple-darwin15.6.0 (64-bit) > > Running under: macOS Mojave 10.14.5 > > Matrix products: default > > BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib > > LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib > > Random number generation: > > RNG: Mersenne-Twister > > Normal: Inversion Sample: Rounding > > locale: [1] > > en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: [1] stats graphics grDevices utils > > datasets methods base Thanks, Nico On 30. May 2019, at 16:34, > > Bert Gunter <bgunter.4567 at gmail.com > > <mailto:bgunter.4567 at gmail.com>> wrote: > > > >> The BLAS in use on each? > >> > >> Bert Gunter > >> > >> "The trouble with having an open mind is that people keep coming > >> along and sticking things into it." > >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > >> > >> > >> On Thu, May 30, 2019 at 5:27 AM Nicolas Schuck > >> <nico.schuck at gmail.com <mailto:nico.schuck at gmail.com>> wrote: Dear > >> fellow R coders, > >> > >> I am observing differences in results obtained using glmer when > >> using a Mac or Linux computer versus a PC. Specifically, I am > >> talking about a relatively complex glmer model with a nested > >> random effects structure. The model is set up in the following > >> way: gcctrl = glmerControl(optimizer=c('nloptwrap'), optCtrl = list > >> (maxfun = 500000), calc.derivs = FALSE) > >> > >> glmer_pre_instr1 = glmer( > >> formula = cbind(FREQ, NSAMP-FREQ) ~ FDIST_minz + poly > >> (RFREQ,2) + ROI + (1 + FDIST_minz + RFREQ + ROI|ID/COL), data > >> cdf_pre_instr, family = binomial, > >> control = gcctrl) > >> > >> Code and data of an example for which I find reproducible, > >> non-negligible differences between Mac/Win can be found here: > >> https://gitlab.com/nschuck/glmer_sandbox/tree/master > >> <https://gitlab.com/nschuck/glmer_sandbox/tree/master> > >> <https://gitlab.com/nschuck/glmer_sandbox/tree/master > >> <https://gitlab.com/nschuck/glmer_sandbox/tree/master>> The > >> differences between the fitted models seem to be most pronounced > >> regarding the estimated correlation structure of the random > >> effects terms. Mac and Linux yield very similar results, but > >> Windows deviates quite a bit in some cases. This has a large > >> impact on p values obtained when performing model comparisons. I > >> have tried this on Mac OS 10.14, Windows 10 and Ubuntu and Debian. > >> All systems I have tried are using lme 1.1.21 and R 3.5+. > >> > >> Does anyone have an idea what the underlying cause might be? > >> > >> Thanks, > >> Nico > >> > >> > >> > >> > >> [[alternative HTML version deleted]] > >> > >> ______________________________________________ > >> R-help at r-project.org <mailto:R-help at r-project.org> mailing list -- > >> To UNSUBSCRIBE and more, see > >> https://stat.ethz.ch/mailman/listinfo/r-help > >> <https://stat.ethz.ch/mailman/listinfo/r-help> PLEASE do read the > >> posting guide http://www.R-project.org/posting-guide.html > >> <http://www.r-project.org/posting-guide.html> and provide > >> commented, minimal, self-contained, reproducible code. > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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.-- Olivier Crouzet, PhD /Ma?tre de Conf?rences/ @LLING - Laboratoire de Linguistique de Nantes UMR6310 CNRS / Universit? de Nantes /Guest Researcher/ @UMCG (University Medical Center Groningen) ENT department Rijksuniversiteit Groningen
To check whether the data are being read in appropriately, what happens when you plot the distribution of each of the independent variables on the respective systems? -A On Wed, 5 Jun 2019 12:32:28 +0200 Olivier Crouzet <olivier.crouzet at univ-nantes.fr> wrote:> Hi, > > 32bit vs. 64bit systems? > > Another thing I would look at would be how the windows machine will > read the data file. Though issues should probably only arise with > respect to text data, I've often experienced problems with reading > unicode csv files on windows computers compared with unix-based > computers. No guarantee though, just suggestions... > > Olivier. > > On Wed, 5 Jun 2019 12:15:53 +0200 > Nicolas Schuck <nico.schuck at gmail.com> wrote: > > > bert: you are right, sorry for not cc-ing the list. thanks also for > > the hint. > > > > I wanted to bring this up here again, emphasising that we do find in > > at least one case *a very large difference* in the p value, using > > the same scripts and data on a windows versus mac machine (see > > reproducible example in the gitlab link posted below). I have now > > come across several instances in which results of (g)lmer models > > don?t agree on windows vs unix-based machines, which I find a bit > > disturbing. any ideas where non-negligible differences could come > > from? > > > > thanks, > > nico > > > > > > > On 30. May 2019, at 16:58, Bert Gunter <bgunter.4567 at gmail.com> > > > wrote: > > > > > > > > > Unless there us good reason not to, always cc the list. I have > > > done so here. > > > > > > The R Installation manual has some info on how to use different > > > BLASes I believe, but someone with expertise (I have none) needs > > > to respond to your queries. > > > > > > On Thu, May 30, 2019 at 7:50 AM Nicolas Schuck > > > <nico.schuck at gmail.com <mailto:nico.schuck at gmail.com>> wrote: I > > > know that it is in use on the Mac, see sessionInfo below. I have > > > to check on the Win system. Why would that make such a difference > > > and how could I make the Win get the same results as the Unix > > > Systems? > > > > > > R version 3.6.0 (2019-04-26) > > > Platform: x86_64-apple-darwin15.6.0 (64-bit) > > > Running under: macOS Mojave 10.14.5 > > > Matrix products: default > > > BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib > > > LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib > > > Random number generation: > > > RNG: Mersenne-Twister > > > Normal: Inversion Sample: Rounding > > > locale: [1] > > > en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > attached base packages: [1] stats graphics grDevices utils > > > datasets methods base Thanks, Nico On 30. May 2019, at 16:34, > > > Bert Gunter <bgunter.4567 at gmail.com > > > <mailto:bgunter.4567 at gmail.com>> wrote: > > > > > >> The BLAS in use on each? > > >> > > >> Bert Gunter > > >> > > >> "The trouble with having an open mind is that people keep coming > > >> along and sticking things into it." > > >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip > > >> ) > > >> > > >> > > >> On Thu, May 30, 2019 at 5:27 AM Nicolas Schuck > > >> <nico.schuck at gmail.com <mailto:nico.schuck at gmail.com>> wrote: > > >> Dear fellow R coders, > > >> > > >> I am observing differences in results obtained using glmer when > > >> using a Mac or Linux computer versus a PC. Specifically, I am > > >> talking about a relatively complex glmer model with a nested > > >> random effects structure. The model is set up in the following > > >> way: gcctrl = glmerControl(optimizer=c('nloptwrap'), optCtrl > > >> list (maxfun = 500000), calc.derivs = FALSE) > > >> > > >> glmer_pre_instr1 = glmer( > > >> formula = cbind(FREQ, NSAMP-FREQ) ~ FDIST_minz + poly > > >> (RFREQ,2) + ROI + (1 + FDIST_minz + RFREQ + ROI|ID/COL), data > > >> cdf_pre_instr, family = binomial, > > >> control = gcctrl) > > >> > > >> Code and data of an example for which I find reproducible, > > >> non-negligible differences between Mac/Win can be found here: > > >> https://gitlab.com/nschuck/glmer_sandbox/tree/master > > >> <https://gitlab.com/nschuck/glmer_sandbox/tree/master> > > >> <https://gitlab.com/nschuck/glmer_sandbox/tree/master > > >> <https://gitlab.com/nschuck/glmer_sandbox/tree/master>> The > > >> differences between the fitted models seem to be most pronounced > > >> regarding the estimated correlation structure of the random > > >> effects terms. Mac and Linux yield very similar results, but > > >> Windows deviates quite a bit in some cases. This has a large > > >> impact on p values obtained when performing model comparisons. I > > >> have tried this on Mac OS 10.14, Windows 10 and Ubuntu and > > >> Debian. All systems I have tried are using lme 1.1.21 and R > > >> 3.5+. > > >> > > >> Does anyone have an idea what the underlying cause might be? > > >> > > >> Thanks, > > >> Nico > > >> > > >> > > >> > > >> > > >> [[alternative HTML version deleted]] > > >> > > >> ______________________________________________ > > >> R-help at r-project.org <mailto:R-help at r-project.org> mailing list > > >> -- To UNSUBSCRIBE and more, see > > >> https://stat.ethz.ch/mailman/listinfo/r-help > > >> <https://stat.ethz.ch/mailman/listinfo/r-help> PLEASE do read the > > >> posting guide http://www.R-project.org/posting-guide.html > > >> <http://www.r-project.org/posting-guide.html> and provide > > >> commented, minimal, self-contained, reproducible code. > > > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help at 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. > >