[R-SIG-Mac] Problems with R-4.4.2 in MacOS Sequoia with Intel chip

Fri Nov 22 19:30:38 CET 2024

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.camara using 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 <pdalgd using 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.camara using 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.urbanek using 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.camara using 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/
>>>>> =============================
>>>>> 
>>>>> _______________________________________________
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>>>>> R-SIG-Mac using r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>> 
>>>> 
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>> 
>> -- 
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Office: A 4.23
>> Email: pd.mes using cbs.dk  Priv: PDalgd using gmail.com
>> 
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