Simon, Excellent! Many thanks! I used your command to fix the problem for the time being and also opened an issue for “torch” package maintainers:
https://github.com/mlverse/torch/issues/1213 Your support is much appreciated. Best Gilberto ============================ Prof Dr Gilberto Camara Senior Researcher Getulio Vargas Foundation (FGV) National Institute for Space Research (INPE), Brazil https://gilbertocamara.org/ ============================= > On 23 Nov 2024, at 04:44, Simon Urbanek <simon.urba...@r-project.org> wrote: > > Gilberto, > > thanks! TLDR; its a bug in the torch package - fix below. > > It took a while to sort out your example as it was very incomplete, here are > the full required steps: > > --- > ## sits doesn't install tests, so have the get them from sources: > download.packages("sits", type='source') > untar(Sys.glob("sits_*.tar.gz")) > ## there are many other packages required for the tests > install.packages(c("sits","torch","lwgeom","randomForest","gdalcubes","xgboost","devtools")) > > ## also torch installation is incomplete so it requires additional downloads > on first load > # (NB: this looks like a serious problem - does it mean torch bypasses CRAN > checks?) > #> library(torch) > # - Additional software needs to be downloaded and installed for torch to > work correctly. > #Do you want to continue? (Yes/no/cancel) yes > > devtools::test(“sits”) > --- > > But all of it is not necessary since the key is that the tests load both > data.table and torch so this is a more minimal example (based on one of the > sits tests): > > library(data.table) > library(sits) > sits_tuning(samples_modis_ndvi, > ml_method = sits_tempcnn(), > params = sits_tuning_hparams(epochs = 10, optimizer = > torch::optim_adam, > opt_hparams = list(lr = choice(0.01, 0.05, 0.001, 0.0005))), > trials = 2,multicores = 1, progress = FALSE > ) > > The use of data.table is just an example, any OpenMP-enabled package will > trigger the bug. As the error you sent indicated the problem is the > incompatibility of the run-time used by torch. If you use any R package with > OpenMP support (which loads the official OpenMP run-time - in above example > it is data.table) and then run torch afterwards, torch will fail, because it > loads its private OpenMP run-time which is incompatible. This is precisely > why we provide a common run-time and torch fails to use it so I would > recommend filing a bug report with the torch package. It is easily fixed with > something like > > system( > paste("ln","-sfn",shQuote(file.path(R.home(),"lib","libomp.dylib")), > shQuote(system.file("lib","libiomp5.dylib",package="torch")))) > > to point torch to the common run-time which guarantees compatibility between > packages. After that fix torch and the above example works again. > > The current torch setup is really bad by design, because it essentially means > that no one may use OpenMP as it will always clash with its private library > (since no one else can use it). Even though it may not bite many people now > given the sequence of packages involved, if we decided to enable OpenMP in > CRAN build of R then torch won't work at all until this is fixed. > > Cheers, > Simon > > >> On Nov 23, 2024, at 5:36 PM, Gilberto Camara <gilberto.cam...@inpe.br> wrote: >> >> Dear Simon >> >> I understand your responses and your point. I hope you'll be able to >> understand my problem. It is hard to provide a simple working example, since >> we need to find a case where a package loads an OpenMP library that >> conflicts with the OpenMP library loaded by R. >> >> Replicating the problems I'm facing can be done by following the same >> actions I did. Please run the following commands on an R terminal to get the >> same error as we have using version R-4.4.2 >> >> == r code >> % install.packages(“sits”) >> % devtools::test(“sits”) >> === >> >> You should get the same error as I do. >> >> As I stated earlier, there is a conflict between “libomp.dylib" loaded in >> the R core libraries and the "libiomp5.dylib" loaded by the “torch” package. >> Since our package (“sits”) uses the torch package, I did the following >> experiment: (a) removed “libomp.dylib” from the R core libraries; and (b) >> ran the same two lines above. Everything works. >> >> Meanwhile, I will try to produce an MWE that does not need to use the “sits” >> package. >> >> Best regards >> Gilberto >> >> ============================ >> Prof Dr Gilberto Camara >> Senior Researcher >> Getulio Vargas Foundation (FGV) >> National Institute for Space Research (INPE), Brazil >> https://gilbertocamara.org/ >> ============================= >> >> > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
