[R-SIG-Mac] procedure to ship libomp.dylib run-time with package

Mikael Jagan j@g@nmn2 @end|ng |rom gm@||@com
Sat Jul 6 01:40:30 CEST 2024 

Typo below ... not *_CPPFLAGS, but rather *_CFLAGS or *_CXXFLAGS: -fopenmp
is not a preprocessor option ...

Mikael

On 2024-07-05 4:53 pm, Mikael Jagan wrote:
> Some thoughts in line below, not "certified" but maybe helpful.  Corrections
> welcome ...
> 
> Mikael
> 
>> From: "Balamuta, James" <balamut2 using illinois.edu>
>> To: Simon Urbanek <simon.urbanek using R-project.org>
>> Cc: Timothy Bates <tim.bates using ed.ac.uk>, Kasper Daniel Hansen
>> 	<kasperdanielhansen using gmail.com>, "Sparapani, Rodney"
>> 	<rsparapa using mcw.edu>, R list <R-SIG-Mac using r-project.org>
>> Subject: Re: [R-SIG-Mac]  procedure to ship libomp.dylib run-time with
>> 	package
>> Message-ID:
>> 	<IA0PR11MB781323FB004CD73F96E34E86EBDE2 using IA0PR11MB7813.namprd11.prod.outlook.com>
>> 	
>> Content-Type: text/plain; charset="utf-8"
>>
>> Simon,
>>
>> Thanks for the update. I’m aware of the linking instructions [1,2,3,4] and the purpose of configure{.ac} [5]. What I was not aware of was the CRAN macOS build machine were outfitted with the appropriate OpenMP setup [6, 7] in a post R 4.0.0 world. Thus, more than just local configurations that adopted [8] could benefit from OpenMP especially since the top of [8] contains:
>>
>>> Warning! Everything described on this page is strictly experimental and not officially supported by CRAN, R-core or R Foundation. In may break at any time. The information is provided in the hope of being useful to some tech-savvy people. It is not intended for the regular R user.
>>
>> Changing focus, I’m interested in re-enabling OpenMP with respect to RcppArmadillo, my questions here are:
>>
>>
>>     1.  When did libomp.dylib start shipping with the CRAN build? R 4.1, 4.2, 4.3, or 4.4?
>>        *   This will allow me to petition to have an R version dependency change.
> 
> The binaries are archived, so one can just look "there" ...
> 
>       https://cran.r-project.org/bin/macosx/base/
>       https://cran.r-project.org/bin/macosx/big-sur-x86_64/base/
>       https://cran.r-project.org/bin/macosx/big-sur-arm64/base/
> 
> I see libomp.dylib in R 4.3.0, but not in R 4.2.3, just inspecting the arm64
> ones ...
> 
>       $ lsbom -p f `pkgutil --bom R-4.4.1-arm64.pkg` | grep libomp[.]dylib
>       ./R.framework/Versions/4.4-arm64/Resources/lib/libomp.dylib
> 
> But I don't see how that would motivate a dependency on R >= 4.3.  Not everyone
> running R under macOS obtains R from CRAN, and not everyone running CRAN R has
> omp.h in the search path ...
> 
>>     2.  If a package only needs to compile code only once, then it’s sufficient to use the usual ` $(SHLIB_OPENMP_CXXFLAGS)` in src/Makevars with the appropriate ifdef pre-processor on including #include <omp.h>?
>>        *   This provides improved guidance related to best package development practices.
> 
> CRAN configures R with empty SHLIB_OPENMP_*FLAGS, which you can verify by
> looking at any CRAN R installation's etc/Makeconf.
> 
>       $ grep SHLIB_OPENMP `R RHOME`/etc/Makeconf
>       SHLIB_OPENMP_CFLAGS =
>       SHLIB_OPENMP_CXXFLAGS =
>       SHLIB_OPENMP_FFLAGS =
> 
> So, AFAICT, _automatic_ OpenMP support [1] still requires _regular_ users [2]
> to install OpenMP-using packages from sources and still requires OpenMP-using
> packages to have a src/Makevars containing
> 
>       PKG_CPPFLAGS = @THISPACKAGE_CPPFLAGS@
>       PKG_LIBS = @THISPACKAGE_LIBS@
> 
> and a configure.ac arranging for those macros to be substituted with
> 
>       THISPACKAGE_CPPFLAGS=[-Xclang ]-fopenmp
>       THISPACKAGE_LIBS=-lomp
> 
> conditional on a proper configure test (one that attempts to compile a program
> including omp.h and calling (say) omp_get_num_threads()).  On macOS, you'd try
> compiling twice, first with -fopenmp and again with -Xclang -fopenmp if -fopenmp
> alone was not enough.  Simon has said this already ...
> 
> Even if CRAN did configure R with nonempty SHLIB_OPENMP_*FLAGS, it does not
> (yet) bundle omp.h with R.
> 
>       $ lsbom -p f `pkgutil --bom R-4.4.1-arm64.pkg` | grep omp[.]h
> 
> The user would in many cases still need to arrange for omp.h to be found on the
> search path, notably as R-exts says:
> 
>       For portability, any C/C++ code using the omp_* functions should
>       include the omp.h header: some compilers (but not all) include it
>       when OpenMP mode is switched on (e.g. via flag -fopenmp).
> 
> But maybe CRAN would consider shipping omp.h in addition to libomp.dylib
> in the future ... ?
> 
> ----
> 
>       [1] "automatic" in the sense of _not_ requiring the user to pass flags to
>           R CMD INSTALL on the command line or through their personal Makevars
>       [2] "regular" meaning that they obtained R from CRAN rather than, say,
>           configuring R themselves with SHLIB_OPENMP_*FLAGS set
> 
>>     3.  For packages that compile code first on CRAN and, then, dynamically on a user’s computer, what is the best approach to ensuring that instructions in [8] are set?
>>        *   This would ensure armadillo-oriented code could take full use of the cores on macOS.
>>
> 
> As Simon has emphasized already, the only robust test for OpenMP support is
> to attempt to compile a program with suitable flags.  Testing for a specific
> user configuration (such as that described in mac.r-project.org/openmp/) is
> fragile and restrictive for no reason.
> 
> If your package has an R function that invokes R CMD SHLIB, then that function
> could perform a configure step, adjusting flags depending on the test result.
> 
>> Best regards,
>>
>> James
>>
>> [1]: https://stat.ethz.ch/pipermail/r-sig-mac/2020-April/013346.html
>> [2]: https://stat.ethz.ch/pipermail/r-sig-mac/2019-May/012987.html
>> [3]: https://stat.ethz.ch/pipermail/r-sig-mac/2019-June/012996.html
>> [4]: https://stat.ethz.ch/pipermail/r-sig-mac/2020-May/013451.html
>> [5]: https://stackoverflow.com/a/42281495/1345455
>> [6]: https://github.com/RcppCore/RcppArmadillo/pull/219#issuecomment-383100722
>> [7]: https://stat.ethz.ch/pipermail/r-sig-mac/2020-April/013289.html
>> [8]: https://mac.r-project.org/openmp/
>>
>>
>>
>> From: Simon Urbanek <simon.urbanek using R-project.org>
>> Date: Friday, June 28, 2024 at 12:31 AM
>> To: Balamuta, James <balamut2 using illinois.edu>
>> Cc: Timothy Bates <tim.bates using ed.ac.uk>, Kasper Daniel Hansen <kasperdanielhansen using gmail.com>, Sparapani, Rodney <rsparapa using mcw.edu>, R list <R-SIG-Mac using r-project.org>
>> Subject: Re: [R-SIG-Mac] procedure to ship libomp.dylib run-time with package
>>
>>
>>> On 27 Jun 2024, at 23:57, Balamuta, James <balamut2 using illinois.edu> wrote:
>>>
>>> Simon,
>>>    I think there is a communication issue regarding OpenMP for the macOS R community. That said, I’m both thrilled and delighted that I’m wrong in this case! To my knowledge, there was never a public facing note regarding `libomp`  shipping with CRAN’s official R binary for mac, [1]. In fact, the last tracking I have with respect to OpenMP and R on macOS was its abrupt and painful removal that led to the instructions for experimental inclusion of OpenMP on mac within the developer website [2] (gently acknowledge by Prof. Ripley as being not current). This has led to a lot of lobotomization in compiled code regarding macOS that can now hopefully be adjusted for the multi-core world, [3].
>>>    With this in mind, I suppose this means that we would need to revisit the `configure.ac` [3]. Potentially, as Prof. Ripley mentioned, we’re looking at including on path/detecting:
>>>    `R RHOME`/lib/libomp.dylib/Library/Frameworks/R.framework/Resources/lib/libomp.dylib
>>
>>
>> That's entirely unnecessary - you should not be requiring specific file paths - that's not how linking tests work. All the instructions are on the OpenMP page for years - it is as simple as -lomp (which is standard almost everywhere). The only non-standard requirement compared to other platforms is that instead of -fopemp in C flags the package should also check for -Xclang -fopenmp.
>>
>> If a package explicitly disables OpenMP for Apple compilers, it is its deliberate choice - it was never necessary. The whole point of configure scripts is to detect functionality by testing it and use it if available.
>>
>> Cheers,
>> Simon
>>
>>
>>>    Thus, the package binary downloaded from CRAN would correctly set and detect cores per:
>>>    # install.packages("RcppArmadillo")
>>>    # Determine the number of active threads
>>> RcppArmadillo::armadillo_get_number_of_omp_threads()
>>> [1] 1
>>>    # Set number of threads
>>> RcppArmadillo::armadillo_set_number_of_omp_threads(3)
>>>    # Retrieve OpenMP threads after setting
>>> RcppArmadillo::armadillo_get_number_of_omp_threads()
>>> [1] 1
>>> # This should be 3.
>>>    I’m happy to talk more on the list or off the list.  Best,
>>>    James
>>>    [1]: https://urldefense.com/v3/__https://cran.r-project.org/doc/manuals/r-release/NEWS.html__;!!DZ3fjg!57krJgj2EE5sq_qaDsKls4jb5f99c2iyQaXHoJ_7OBQAbpapE-x_fRkzBh-Fy_cnsu-sUJpdhelgLqI006PhaLiBVYB5MDA$<https://urldefense.com/v3/__https:/cran.r-project.org/doc/manuals/r-release/NEWS.html__;!!DZ3fjg!57krJgj2EE5sq_qaDsKls4jb5f99c2iyQaXHoJ_7OBQAbpapE-x_fRkzBh-Fy_cnsu-sUJpdhelgLqI006PhaLiBVYB5MDA$>
>>> [2]: https://urldefense.com/v3/__https://mac.r-project.org/openmp/__;!!DZ3fjg!57krJgj2EE5sq_qaDsKls4jb5f99c2iyQaXHoJ_7OBQAbpapE-x_fRkzBh-Fy_cnsu-sUJpdhelgLqI006PhaLiBmw9UV3o$<https://urldefense.com/v3/__https:/mac.r-project.org/openmp/__;!!DZ3fjg!57krJgj2EE5sq_qaDsKls4jb5f99c2iyQaXHoJ_7OBQAbpapE-x_fRkzBh-Fy_cnsu-sUJpdhelgLqI006PhaLiBmw9UV3o$>
>>> [3]: https://urldefense.com/v3/__https://github.com/RcppCore/RcppArmadillo/blob/37461ba36472305c699263afc229919d37daa5e3/configure.ac*L109__;Iw!!DZ3fjg!57krJgj2EE5sq_qaDsKls4jb5f99c2iyQaXHoJ_7OBQAbpapE-x_fRkzBh-Fy_cnsu-sUJpdhelgLqI006PhaLiB8rnPPRw$<https://urldefense.com/v3/__https:/github.com/RcppCore/RcppArmadillo/blob/37461ba36472305c699263afc229919d37daa5e3/configure.ac*L109__;Iw!!DZ3fjg!57krJgj2EE5sq_qaDsKls4jb5f99c2iyQaXHoJ_7OBQAbpapE-x_fRkzBh-Fy_cnsu-sUJpdhelgLqI006PhaLiB8rnPPRw$>
>>>     From: Simon Urbanek <simon.urbanek using R-project.org>
>>> Date: Thursday, June 27, 2024 at 10:25 AM
>>> To: Balamuta, James <balamut2 using illinois.edu>
>>> Cc: Timothy Bates <tim.bates using ed.ac.uk>, Kasper Daniel Hansen <kasperdanielhansen using gmail.com>, Sparapani, Rodney <rsparapa using mcw.edu>, R list <R-SIG-Mac using r-project.org>
>>> Subject: Re: [R-SIG-Mac] procedure to ship libomp.dylib run-time with package
>>> Most of the claims below are false - libomp is shipped with CRAN R for quite some time specifically so that packages which benefit from it significantly can enable OpenMP reasonably easily - they only need to add the flags as noted on the cited page and CRAN takes care of the rest. If there are any problems, please feel free to contact me.
>>>
>>> Cheers,
>>> Simon
>>>
>>>
>>>> On 26 Jun 2024, at 07:41, Balamuta, James <balamut2 using illinois.edu> wrote:
>>>>
>>>> Tim,
>>>>
>>>> Unfortunately, there isn't a nice way of including OpenMP for macOS within a package.  One potential avenue would be to use a `configure.ac` file to check for whether OpenMP headers are present on the macOS computer and, then, allow the correct OpenMP compilation flags to be set. However, this requires the user to compile from source instead of using a CRAN binary.
>>>>
>>>> Unfortunately, there isn't going to be an easier way as OpenMP on macOS with R is experimental by nature.
>>>>
>>>> Best regards,
>>>>
>>>> James
>>>> ________________________________
>>>> From: R-SIG-Mac <r-sig-mac-bounces using r-project.org> on behalf of Timothy Bates <tim.bates using ed.ac.uk>
>>>> Sent: Tuesday, June 25, 2024 10:00 PM
>>>> To: Kasper Daniel Hansen <kasperdanielhansen using gmail.com>; Sparapani, Rodney <rsparapa using mcw.edu>
>>>> Cc: R list <R-SIG-Mac using r-project.org>
>>>> Subject: Re: [R-SIG-Mac] procedure to ship libomp.dylib run-time with package
>>>>
>>>> Thanks Kasper,
>>>> I read those lines and had installed the openmp software as instructed. It all works fine for me. But users don’t have my usr/ folder, not can a package write to their usr/ folder.
>>>>
>>>> so what is confusing is how the user will get this lib. Where should make place libraries like libomp within the package so that if a user merely install.packages() it, the library will be found and loaded?
>>>> Best, tim
>>>>
>>>>
>>>> Sent from Outlook for iOS<https://urldefense.com/v3/__https://aka.ms/o0ukef__;!!DZ3fjg!_OUXHENJ_6aGlU-humThmTaUR5okhDKW2EGEY49AjJ4AN8eXBWtZCWE3O01pnyxbRpGQDhCl8MMLThVBbUXDuipI$ >
>>>> ________________________________
>>>> From: Kasper Daniel Hansen <kasperdanielhansen using gmail.com>
>>>> Sent: Tuesday, June 25, 2024 11:34:42 AM
>>>> To: Sparapani, Rodney <rsparapa using mcw.edu>
>>>> Cc: Timothy Bates <tim.bates using ed.ac.uk>; R list <R-SIG-Mac using r-project.org>
>>>> Subject: Re: [R-SIG-Mac] procedure to ship libomp.dylib run-time with package
>>>>
>>>> This email was sent to you by someone outside the University.
>>>> You should only click on links or attachments if you are certain that the email is genuine and the content is safe.
>>>> If you read the next couple of sentences on that page, it says
>>>>
>>>> The following are links to libomp OpenMP run-time built from official LLVM release sources using Xcode compilers. They are signed and support macOS 10.13 (High Sierra) and higher. All tar-balls contain the system tree usr/local/lib and usr/local/include so the recommended installation is to type in Terminal:
>>>>
>>>>      curl -O https://urldefense.com/v3/__https://mac.r-project.org/openmp/openmp-14.0.6-darwin20-Release.tar.gz__;!!DZ3fjg!_OUXHENJ_6aGlU-humThmTaUR5okhDKW2EGEY49AjJ4AN8eXBWtZCWE3O01pnyxbRpGQDhCl8MMLThVBbWfUKf7B$<https://urldefense.com/v3/__https:/mac.r-project.org/openmp/openmp-14.0.6-darwin20-Release.tar.gz__;!!DZ3fjg!_OUXHENJ_6aGlU-humThmTaUR5okhDKW2EGEY49AjJ4AN8eXBWtZCWE3O01pnyxbRpGQDhCl8MMLThVBbWfUKf7B$>
>>>>      sudo tar fvxz openmp-14.0.6-darwin20-Release.tar.gz -C /
>>>>
>>>>
>>>> I think that is pretty clear? Note the -C / as part of the last line, that tells tar where to put it on the system.
>>>>
>>>> On Tue, Jun 25, 2024 at 8:20 AM Sparapani, Rodney via R-SIG-Mac <r-sig-mac using r-project.org<mailto:r-sig-mac using r-project.org>> wrote:
>>>> Hi Tim:
>>>>
>>>> /usr/local/lib it seems.  See the following page
>>>> https://urldefense.com/v3/__https://mac.r-project.org/openmp/__;!!DZ3fjg!_OUXHENJ_6aGlU-humThmTaUR5okhDKW2EGEY49AjJ4AN8eXBWtZCWE3O01pnyxbRpGQDhCl8MMLThVBbaQGheD_$<https://urldefense.com/v3/__https:/mac.r-project.org/openmp/__;!!DZ3fjg!_OUXHENJ_6aGlU-humThmTaUR5okhDKW2EGEY49AjJ4AN8eXBWtZCWE3O01pnyxbRpGQDhCl8MMLThVBbaQGheD_$>
>>>>
>>>> --
>>>> Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
>>>> Vice President, Wisconsin Chapter of the American Statistical Association
>>>> Institute for Health and Equity, Division of Biostatistics
>>>> Medical College of Wisconsin, Milwaukee Campus
>>>>
>>>> If this is outside of working hours, then please respond when convenient.
>>>>
>>>> From: R-SIG-Mac <r-sig-mac-bounces using r-project.org<mailto:r-sig-mac-bounces using r-project.org>> on behalf of Timothy Bates <tim.bates using ed.ac.uk<mailto:tim.bates using ed.ac.uk>>
>>>> Date: Monday, June 24, 2024 at 4:00 PM
>>>> To: R list <R-SIG-Mac using r-project.org<mailto:R-SIG-Mac using r-project.org>>
>>>> Subject: [R-SIG-Mac] procedure to ship libomp.dylib run-time with package
>>>> ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
>>>> ________________________________
>>>>
>>>> At https://urldefense.com/v3/__https://mac.r-project.org/openmp/__;!!H8mHWRdzp34!4HZ0uFxJQ121gF_TnX99OuMlgIXM600pq8wCbWruoLsdLTtaFgRB5_gMopCtxD0N9M4tUOO-7hBGADHx1sk$<https://urldefense.com/v3/__https:/mac.r-project.org/openmp/__;!!H8mHWRdzp34!4HZ0uFxJQ121gF_TnX99OuMlgIXM600pq8wCbWruoLsdLTtaFgRB5_gMopCtxD0N9M4tUOO-7hBGADHx1sk$><https://urldefense.com/v3/__https:/mac.r-project.org/openmp/__;!!H8mHWRdzp34!4HZ0uFxJQ121gF_TnX99OuMlgIXM600pq8wCbWruoLsdLTtaFgRB5_gMopCtxD0N9M4tUOO-7hBGADHx1sk$%3chttps:/urldefense.com/v3/__https:/mac.r-project.org/openmp/__;!!H8mHWRdzp34!4HZ0uFxJQ121gF_TnX99OuMlgIXM600pq8wCbWruoLsdLTtaFgRB5_gMopCtxD0N9M4tUOO-7hBGADHx1sk$%3e>  it  says
>>>> "any package you compile against libomp.dylib will need that run-time so you have to ship it with your package or have users install it”
>>>>
>>>> Are there  any  instructions on what to do/where to put libomp.dylib so it will be found?
>>>>
>>>> I’ve compiled a package (OpenMx) in which OpenMP is working locally but other users get the error:
>>>>
>>>> require(OpenMx)
>>>> Error: package or namespace load failed for ‘OpenMx’ in dyn.load(file, DLLpath = DLLpath, ...):
>>>> unable to load shared object '/Users/***/Library/R/x86_64/4.4/library/OpenMx/libs/OpenMx.so':
>>>>
>>>> dlopen(/Users/***/Library/R/x86_64/4.4/library/OpenMx/libs/OpenMx.so, 0x0006): Library not loaded: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libomp.dylib
>>>>
>>>>
>>>> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
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>>>>
>>>>          [[alternative HTML version deleted]]
>>>>
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>>>>
>>>>
>>>> --
>>>> Best,
>>>> Kasper
>>>>
>>>>          [[alternative HTML version deleted]]
>>>>
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