Gilberto, you still didn't provide any useful examples, and all you have are baseless speculations. R itself doesn't load OpenMP, so the problem could very well be in the other software or libraries you use - it may have nothing to do with R, but without an example we can neither tell nor help. Based on this there is nothing to solve "at the highest level of R core developers for Mac" - it has to start with you providing a working example as no one else has that problem.
Cheers, Simon > On Nov 23, 2024, at 7:30 AM, Gilberto Camara <gilberto.cam...@inpe.br> wrote: > > Dear Peter and Simon > > I may have found the cause of the crashes in R-4.4.2 in the Intel MacOs > environment. In R-4.4.2 for MacOS, the “libomp.dylib” is loaded from the CRAN > version. Comparing with earlier version, this is a new addition to the core R > libraries. The OpenMP library is not provided in R-4.2. > > It so happens that the “torch” package is also including the an OpenMP > library (“libiomp5.dylib”) which is causing the crash. In previous R > versions, this behavoir did not cause problems, since R did not provide the > OpenMP library by default. > > Thus, the problem needs to be solved at the highest level of R core > developers for Mac. Please bear in mind that the “torch” package is essential > for running deep learning algorithms in R. I hope you can find a solution > that preserves the use of “torch” in R. I am copying the message to Daniel > Falbel, who is the maintainer of the “torch” package. > > Your support in solving this problem is highly appreciated. > > Best regards > Gilberto > ============================ > Prof Dr Gilberto Camara > Senior Researcher > Getulio Vargas Foundation (FGV) > National Institute for Space Research (INPE), Brazil > https://gilbertocamara.org/ > ============================= > > > > > >> On 22 Nov 2024, at 14:18, Gilberto Camara <gilberto.cam...@inpe.br> wrote: >> >> Dear Peter >> >> Many thanks for your help. I ran R in a terminal, something I admit I had >> not done before. >> >> It crashed and produced the following message: >> >> === >> OMP: Error #15: Initializing libiomp5.dylib, but found libomp.dylib already >> initialized. >> OMP: Hint This means that multiple copies of the OpenMP runtime have been >> linked into the program. That is dangerous, since it can degrade performance >> or cause incorrect results. The best thing to do is to ensure that only a >> single OpenMP runtime is linked into the process, e.g. by avoiding static >> linking of the OpenMP runtime in any library. As an unsafe, unsupported, >> undocumented workaround you can set the environment variable >> KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but >> that may cause crashes or silently produce incorrect results. For more >> information, please see http://www.intel.com/software/products/support/. >> === >> >> I am using Rcpp Armadillo, and I am following its guidelines for C++ >> compilation. The “Makevars” file is produced by running >> >>> usethis::use_rcpp_armadillo() >> >> which produces the following Makevars file: >> >> PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) >> PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) >> >> I removed the Makevars file, compiled my package from scratch but the error >> continues. Any help on how to solve this problem would be most appreciated. >> >> Best regards >> Gilberto >> >> ============================ >> Prof Dr Gilberto Camara >> Senior Researcher >> Getulio Vargas Foundation (FGV) >> National Institute for Space Research (INPE), Brazil >> https://gilbertocamara.org/ >> ============================= >> >> >> >> >> >>> On 22 Nov 2024, at 12:08, peter dalgaard <pda...@gmail.com> wrote: >>> >>> A couple of questions: >>> >>> - Is it the GUI or R itself that crashes? (i.e, can you run R in Terminal >>> an still crash it? or even RStudio?) >>> - Is it a Sequoia issue as such? I'm not seeing issues on Monterey/4.4.1 >>> (I'm a little superstitious about upgrading production machines >>> mid-semester and some of my machines are too old for Sequoia.) The source >>> tarballs 4.4.2 were built and tested on Intel/Monterey. >>> >>> - pd >>> >>>> On 21 Nov 2024, at 16:07 , Gilberto Camara <gilberto.cam...@inpe.br> wrote: >>>> >>>> Dear Simon >>>> >>>> Since your message last week, I have been trying to reproduce the errors I >>>> am finding with R-4.4.2 in an Intel MacMini to build a minimum testable >>>> example. I am not succeeding in doing so. >>>> >>>> The error is a total collapse of R and occurs in a random fashion. >>>> Sometimes calling another package (e.g. “xgboost”) produces the error. >>>> Sometimes making a simple operation in a data table leads to error. >>>> >>>> The problem affects only Intel-based MacMinis with R-4.4.2. Running >>>> MacMinis with R-4.2.3 work will. All is also well with R-4.4.2 in Macs >>>> with ARM, in Windows and in Lunix/Ubuntu and Linux/Fedora. >>>> >>>> One issue I noticed is that the default C++ compiler in MacOS Sequoia is >>>> compatible with c++-17, while the one used by CRAN is version c++-14.00. >>>> >>>> Do you have any ideas on how to proceed? Any test data set I could use? >>>> >>>> Many thanks >>>> Gilberto >>>> ============================ >>>> Prof Dr Gilberto Camara >>>> Senior Researcher >>>> Getulio Vargas Foundation (FGV) >>>> National Institute for Space Research (INPE), Brazil >>>> https://gilbertocamara.org/ >>>> ============================= >>>> >>>> >>>> >>>> >>>> >>>>> On 12 Nov 2024, at 18:53, Simon Urbanek <simon.urba...@r-project.org> >>>>> wrote: >>>>> >>>>> Gilberto, >>>>> >>>>> please read https://www.r-project.org/bugs.html first, in particular >>>>> about how to report a problem. Just saying "cannot execute my scripts" is >>>>> not helpful at all - please provide exact output, how it differs between >>>>> the versions etc. For example, the problem may be in your code or >>>>> packages used - we have no way of knowing without the necessary >>>>> additional information. >>>>> >>>>> Thanks, >>>>> Simon >>>>> >>>>> >>>>>> On Nov 13, 2024, at 9:44 AM, Gilberto Camara <gilberto.cam...@inpe.br> >>>>>> wrote: >>>>>> >>>>>> Dear R-SIG-MAC >>>>>> >>>>>> I have problems with R-4.4.2 in the latest Mac OS Sequoia (15.1) version >>>>>> in a Mac mini with an Intel chip. R-4.4.2 cannot execute my scripts. No >>>>>> such problems occur with R-4.4.2 in MacBook with ARM chip. >>>>>> >>>>>> I went back to R-4.2.3 and all is well in my environment (MacMini, >>>>>> Intel, MacOS X 15.1). >>>>>> >>>>>> >>>>>> I will try to provide an MWE to help those of you who know a lot about >>>>>> Mac OS X. >>>>>> >>>>>> Best >>>>>> 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 >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >>> -- >>> Peter Dalgaard, Professor, >>> Center for Statistics, Copenhagen Business School >>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark >>> Phone: (+45)38153501 >>> Office: A 4.23 >>> Email: pd....@cbs.dk Priv: pda...@gmail.com >>> >>> _______________________________________________ >>> 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 > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
