Gilberto,
> On Nov 23, 2024, at 12:40 PM, Gilberto Camara <gilberto.cam...@inpe.br> wrote: > > 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? > It is not loaded - you can check yourself: echo '' | R CMD sh -c 'DYLD_PRINT_LIBRARIES=1 $R_HOME/bin/exec/R' 2>&1 | grep libomp > 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? > We simply distribute it as a convenience, because some packages (like data.table) benefit hugely from OpenMP so by providing a fixed location it allows them to avoid shipping it separately and they all can use one shared version. See also https://mac.r-project.org/openmp/ for details But as noted, I don't think this has anything to do with your problem precisely because it is not loaded by R itself. As I said before I would appreciate is you avoided random speculations (there are many changes between R 4.2 and 4.4 especially in the packages between the two versions) as that is not productive, but instead share a reproducible example that we can look at. Any discussion is entirely pointless until you do that. Cheers, Simon > 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
