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
