Dear Simon You state that “R itself doesn't load OpenMP”. So why is libomp.dylib loaded in core libraries of R-4.4.2 for Mac?
Please see the contents of the core R libaries for R-4.2 and R-4.4.2 in my MacOS. In both cases, these are downloads straight from CRAN. Why has libomp.dylib been included in the R core libraries? Best regards Gilberto R 4.2 ❯ ls -lha /Library/Frameworks/R.framework/Versions/4.2/Resources/lib total 19976 drwxrwxr-x 15 root admin 480B 22 Nov 15:28 . drwxrwxr-x 18 root admin 576B 22 Nov 15:28 .. -rwxrwxr-x 1 root admin 4,0M 17 Mar 2023 libR.dylib drwxrwxr-x 3 root admin 96B 17 Mar 2023 libR.dylib.dSYM -rwxrwxr-x 1 root admin 221K 17 Mar 2023 libRblas.0.dylib drwxrwxr-x 3 root admin 96B 17 Mar 2023 libRblas.0.dylib.dSYM lrwxrwxr-x 1 root admin 16B 22 Nov 15:28 libRblas.dylib -> libRblas.0.dylib drwxrwxr-x 3 root admin 96B 17 Mar 2023 libRblas.dylib.dSYM -rwxrwxr-x 1 root admin 151K 17 Mar 2023 libRblas.vecLib.dylib drwxrwxr-x 3 root admin 96B 17 Mar 2023 libRblas.vecLib.dylib.dSYM -rwxrwxr-x 1 root admin 2,2M 17 Mar 2023 libRlapack.dylib drwxrwxr-x 3 root admin 96B 17 Mar 2023 libRlapack.dylib.dSYM -rw-rw-r-- 1 root admin 157K 17 Mar 2023 libgcc_s.1.dylib -rwxrwxr-x 1 root admin 2,7M 17 Mar 2023 libgfortran.5.dylib -rwxrwxr-x 1 root admin 302K 17 Mar 2023 libquadmath.0.dylib R 4.4.2 ❯ ls -lha /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib total 27320 drwxrwxr-x 17 root admin 544B 22 Nov 15:03 . drwxrwxr-x 17 root admin 544B 22 Nov 15:03 .. -rwxrwxr-x 1 root admin 5,3M 31 Out 22:15 libR.dylib drwxrwxr-x 3 root admin 96B 31 Out 22:14 libR.dylib.dSYM -rwxrwxr-x 1 root admin 238K 31 Out 22:15 libRblas.0.dylib drwxrwxr-x 3 root admin 96B 31 Out 22:14 libRblas.0.dylib.dSYM lrwxrwxr-x 1 root admin 16B 22 Nov 15:03 libRblas.dylib -> libRblas.0.dylib drwxrwxr-x 3 root admin 96B 31 Out 22:14 libRblas.dylib.dSYM -rwxrwxr-x 1 root admin 151K 31 Out 22:15 libRblas.vecLib.dylib drwxrwxr-x 3 root admin 96B 31 Out 22:14 libRblas.vecLib.dylib.dSYM -rwxrwxr-x 1 root admin 2,3M 31 Out 22:15 libRlapack.dylib drwxrwxr-x 3 root admin 96B 31 Out 22:14 libRlapack.dylib.dSYM -rw-rw-r-- 1 root admin 183K 31 Out 22:15 libgcc_s.1.1.dylib -rwxrwxr-x 1 root admin 3,3M 31 Out 22:15 libgfortran.5.dylib -rwxrwxr-x 1 root admin 1,5M 31 Out 22:15 libomp.dylib -rwxrwxr-x 1 root admin 376K 31 Out 22:15 libquadmath.0.dylib drwxrwxr-x 3 root admin 96B 31 Out 22:11 pkgconfig ============================ 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 19:48, Simon Urbanek <simon.urba...@r-project.org> wrote: > > 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
