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.
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.
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.
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 at R-project.org>
Date: Friday, June 28, 2024 at 12:31?AM
To: Balamuta, James <balamut2 at illinois.edu>
Cc: Timothy Bates <tim.bates at ed.ac.uk>, Kasper Daniel Hansen <kasperdanielhansen at gmail.com>, Sparapani, Rodney <rsparapa at mcw.edu>, R list <R-SIG-Mac at 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 at 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 at R-project.org>
Date: Thursday, June 27, 2024 at 10:25?AM
To: Balamuta, James <balamut2 at illinois.edu>
Cc: Timothy Bates <tim.bates at ed.ac.uk>, Kasper Daniel Hansen <kasperdanielhansen at gmail.com>, Sparapani, Rodney <rsparapa at mcw.edu>, R list <R-SIG-Mac at 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 at 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 at r-project.org> on behalf of Timothy Bates <tim.bates at ed.ac.uk> Sent: Tuesday, June 25, 2024 10:00 PM To: Kasper Daniel Hansen <kasperdanielhansen at gmail.com>; Sparapani, Rodney <rsparapa at mcw.edu> Cc: R list <R-SIG-Mac at 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 at gmail.com> Sent: Tuesday, June 25, 2024 11:34:42 AM To: Sparapani, Rodney <rsparapa at mcw.edu> Cc: Timothy Bates <tim.bates at ed.ac.uk>; R list <R-SIG-Mac at 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 at r-project.org<mailto:r-sig-mac at 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 at r-project.org<mailto:r-sig-mac-bounces at r-project.org>> on behalf of Timothy Bates <tim.bates at ed.ac.uk<mailto:tim.bates at ed.ac.uk>> Date: Monday, June 24, 2024 at 4:00?PM To: R list <R-SIG-Mac at r-project.org<mailto:R-SIG-Mac at 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 Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336. _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org<mailto:R-SIG-Mac at r-project.org> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!H8mHWRdzp34!4HZ0uFxJQ121gF_TnX99OuMlgIXM600pq8wCbWruoLsdLTtaFgRB5_gMopCtxD0N9M4tUOO-7hBGdICDldE$<https://urldefense.com/v3/__https:/stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!H8mHWRdzp34!4HZ0uFxJQ121gF_TnX99OuMlgIXM600pq8wCbWruoLsdLTtaFgRB5_gMopCtxD0N9M4tUOO-7hBGdICDldE$><https://urldefense.com/v3/__https:/stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!H8mHWRdzp34!4HZ0uFxJQ121gF_TnX99OuMlgIXM600pq8wCbWruoLsdLTtaFgRB5_gMopCtxD0N9M4tUOO-7hBGdICDldE$%3chttps:/urldefense.com/v3/__https:/stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!H8mHWRdzp34!4HZ0uFxJQ121gF_TnX99OuMlgIXM600pq8wCbWruoLsdLTtaFgRB5_gMopCtxD0N9M4tUOO-7hBGdICDldE$%3e> [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org<mailto:R-SIG-Mac at r-project.org> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!DZ3fjg!_OUXHENJ_6aGlU-humThmTaUR5okhDKW2EGEY49AjJ4AN8eXBWtZCWE3O01pnyxbRpGQDhCl8MMLThVBbYOwLI1d$<https://urldefense.com/v3/__https:/stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!DZ3fjg!_OUXHENJ_6aGlU-humThmTaUR5okhDKW2EGEY49AjJ4AN8eXBWtZCWE3O01pnyxbRpGQDhCl8MMLThVBbYOwLI1d$> -- Best, Kasper [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!DZ3fjg!_OUXHENJ_6aGlU-humThmTaUR5okhDKW2EGEY49AjJ4AN8eXBWtZCWE3O01pnyxbRpGQDhCl8MMLThVBbYOwLI1d$<https://urldefense.com/v3/__https:/stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!DZ3fjg!_OUXHENJ_6aGlU-humThmTaUR5okhDKW2EGEY49AjJ4AN8eXBWtZCWE3O01pnyxbRpGQDhCl8MMLThVBbYOwLI1d$> [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!DZ3fjg!9XPrFiayt1-V0BmNqWv4wn0V_G6ZIC6DgkviDYpRV4s-dmAnj9Qp_QFEHPG5dbO-Sk0IhdfC3lB0qeeJBDE2ann7kz0eS7A$<https://urldefense.com/v3/__https:/stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!DZ3fjg!9XPrFiayt1-V0BmNqWv4wn0V_G6ZIC6DgkviDYpRV4s-dmAnj9Qp_QFEHPG5dbO-Sk0IhdfC3lB0qeeJBDE2ann7kz0eS7A$>