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Today's Topics:
1. Re: procedure to ship libomp.dylib run-time with package
(Bram Boeckx)
2. Re: procedure to ship libomp.dylib run-time with package
(Bram Boeckx)
----------------------------------------------------------------------
Message: 1
Date: Wed, 26 Jun 2024 07:36:39 +0000
From: Bram Boeckx <bram.boeckx at kuleuven.be>
To: "Sparapani, Rodney via R-SIG-Mac" <R-SIG-Mac at r-project.org>
Subject: Re: [R-SIG-Mac] procedure to ship libomp.dylib run-time with
package
Message-ID: <72B3DAB6-6B6F-46BF-921E-6B4DE21307C3 at kuleuven.be>
Content-Type: text/plain; charset="utf-8"
Dear,
Thanks for your message,
I'm currently on paternity leave until 23th of July and cannot respond to your email. Please contact my colleagues if you have questions or need assistance.
Best Wishes,
Bram
On 25 Jun 2024, at 14:20, Sparapani, Rodney via R-SIG-Mac <R-SIG-Mac at r-project.org> wrote:
Hi Tim:
/usr/local/lib it seems. See the following page
https://mac.r-project.org/openmp/
--
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> on behalf of Timothy Bates <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>
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$<https://urldefense.com/v3/__https:/mac.r-project.org/openmp/__;!!H8mHWRdzp34!4HZ0uFxJQ121gF_TnX99OuMlgIXM600pq8wCbWruoLsdLTtaFgRB5_gMopCtxD0N9M4tUOO-7hBGADHx1sk$> 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
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Message: 2
Date: Wed, 26 Jun 2024 10:18:20 +0000
From: Bram Boeckx <bram.boeckx at kuleuven.be>
To: Prof Brian Ripley via R-SIG-Mac <R-SIG-Mac at r-project.org>
Subject: Re: [R-SIG-Mac] procedure to ship libomp.dylib run-time with
package
Message-ID: <9B5F82F3-B07B-4A05-9ED1-419CD6924D02 at kuleuven.be>
Content-Type: text/plain; charset="utf-8"
Dear,
Thanks for your message,
I'm currently on paternity leave until 23th of July and cannot respond to your email. Please contact my colleagues if you have questions or need assistance.
Best Wishes,
Bram
On 26 Jun 2024, at 11:57, Prof Brian Ripley via R-SIG-Mac <R-SIG-Mac at r-project.org> wrote:
On 26/06/2024 06:41, Balamuta, James 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.
Package installation also requires the libomp.dylib, and to know where to find it both when linking and loading.
Unfortunately, there isn't going to be an easier way as OpenMP on macOS with R is experimental by nature.
Rather, macOS makes it deliberately hard, but those instructions are not current.
- The standard way for the macOS linker to record paths to a dependent dylib is as an absolute path. E.g. (arm64)
% otool -L library/stats/libs/stats.so
library/stats/libs/stats.so:
stats.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.1)
...
That is a location that is not writeable to an end user. However, it appears that R 4.4.1 for arm64 ships with a bi-arch libomp.dylib there.
auk2% file `R RHOME`/lib/libomp.dylib
/Library/Frameworks/R.framework/Resources/lib/libomp.dylib: Mach-O universal binary with 2 architectures: [x86_64:Mach-O 64-bit dynamically linked shared library x86_64] [arm64:Mach-O 64-bit dynamically linked shared library arm64]
/Library/Frameworks/R.framework/Resources/lib/libomp.dylib (for architecture x86_64): Mach-O 64-bit dynamically linked shared library x86_64
/Library/Frameworks/R.framework/Resources/lib/libomp.dylib (for architecture arm64): Mach-O 64-bit dynamically linked shared library arm64
So it is likely that libomp.dylib is already available somewhere that will be searched at both link and load times. (omp.h needs to be put in a suitable place, e.g. /usr/local/include for Intel, but that needs admin privileges. That is only needed at compilation, so could be put anywhere and -I specified.)
- Another issue: That page provides multiple copies on libomp.dylib: how could package installation know which is appropriate? I do not know which one was shipped with R, nor how find out. But it suggests shipping one with a package would be unsafe.
It seems the OP asked the wrong question: apparently he distributed a package built with R 4.3.x, and someone tried to use it on 4.4.x. R binary packages are tied to an R x.y series (as the manual would have told you).
I was able to build OpenMx with OpenMP on arch64 by using
PKG_CPPFLAGS = -Xclang -fopenmp -I/path/to/omp.h
PKG_LIBS= -lomp \
...
(Caveat: for OpenMx, <omp.h> is used so the -I adds to the system include path and there is danger of conflicts. Best to use a separate directory for the OpenMP headers.)
And please comply with the posting guide, not send HTML and not mangle URLs.
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$
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_$
--
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$<https://urldefense.com/v3/__https:/mac.r-project.org/openmp/__;!!H8mHWRdzp34!4HZ0uFxJQ121gF_TnX99OuMlgIXM600pq8wCbWruoLsdLTtaFgRB5_gMopCtxD0N9M4tUOO-7hBGADHx1sk$> 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
There is a version mismatch here ....
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
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