Hi Stephen, Thanks, I’m now trying to use R 3.6.3 on the HPC, I was able to run a few tests remote and get reproducible results. The batches have not yet run, but I’m hoping will give reproducible results when they do.
Thanks, Kevin On Sun, Aug 9, 2020 at 08:42 stephen sefick <ssef...@gmail.com> wrote: > Hi Kevin, > > I think Abby has suggested something similar to what I think the problem > is related to - environment setup. > > Some possible solutions: > The renv and packrat packages are a way to version your packages to help > with reproducability. Anaconda might be a solution for the R version and > package version problem, if installed on your hpc. Docker could work as > well (maybe the best option if installed). There are other workarounds, but > I would have to know how your particular hpc/compute environment is set up > to comment further. > > Brass tacks: > I think you need to ensure all your package versions (R and add-on > packages) are the same. > > Fwiw, > > Stephen > > On Sun, Aug 9, 2020, 08:26 Kevin Egan <kevinega...@gmail.com> wrote: > >> Hi Stephen, >> >> I believe I am using Renv, but on my remote computer I am running batch >> files. >> >> Thanks, >> >> Kevin >> >> On 8 Aug 2020, at 18:18, stephen sefick <ssef...@gmail.com> wrote: >> >> Caveat, I have only skimmed this email thread, so please forgive me if I >> have missed something. >> >> Are you able to use Renv, packrat, docker, or anaconda? Your compute >> environments are very different. >> Kindest regards, >> >> Stephen Sefick >> >> On Sat, Aug 8, 2020, 19:05 Abby Spurdle <spurdl...@gmail.com> wrote: >> >>> Hi Kevin, >>> >>> Intuitively, the first step would be to ensure that all versions of R, >>> and all the R packages, are the same. >>> >>> However, you mention HPC. >>> And the glmnet package imports the foreach package, which appears >>> (after a quick glance) to support multi-core and parallel computing. >>> >>> If your code uses parallel computing (?), you may need to look at how >>> random numbers, and related results, are handled... >>> >>> >>> On Sun, Aug 9, 2020 at 1:14 AM Kevin Egan <kevinega...@gmail.com> wrote: >>> > >>> > I posted this question: >>> > >>> > I am currently using R , RStudio , and a remote computer (using an R >>> script) to run the same code. I start by using set.seed(123) in all three >>> versions of the code, then using glmnet to assess a matrix. Ultimately, I >>> am having trouble reproducing the results between my local and the remote >>> computer's results. I am using R version 4.0.2 locally, and R version 3.6.0 >>> remote. >>> > >>> > After running several tests, I'm wondering if there is a difference >>> between the two versions in R which may lead to slightly different >>> coefficients. If anyone has any insight I would appreciate it. >>> > >>> > Thanks. >>> > >>> > and found that there were slight differences between using rnorm with >>> R-4.0.2 and R-3.6.0 but did not find any differences for runif between both >>> systems. In my original code, I am using rnorm and was wondering if this >>> may be the reason I am finding slight differences in coefficients for >>> glmnet and lars testing between using my local computer (R-4.0.2) and my >>> remote computer (R-3.6.0). I am running my code locally on a MacOSX and >>> remote on what I believe is an HPC. >>> > >>> > Thanks. >>> > [[alternative HTML version deleted]] >>> > >>> > ______________________________________________ >>> > 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 >>> <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 >>> <http://www.r-project.org/posting-guide.html> >>> and provide commented, minimal, self-contained, reproducible code. >>> >> >> [[alternative HTML version deleted]] ______________________________________________ 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.
