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-boun...@r-project.org> on behalf of Timothy Bates
<tim.ba...@ed.ac.uk>
Sent: Tuesday, June 25, 2024 10:00 PM
To: Kasper Daniel Hansen <kasperdanielhan...@gmail.com>; Sparapani, Rodney
<rspar...@mcw.edu>
Cc: R list <R-SIG-Mac@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
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>
________________________________
From: Kasper Daniel Hansen <kasperdanielhan...@gmail.com>
Sent: Tuesday, June 25, 2024 11:34:42 AM
To: Sparapani, Rodney <rspar...@mcw.edu>
Cc: Timothy Bates <tim.ba...@ed.ac.uk>; R list <R-SIG-Mac@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@r-project.org<mailto:r-sig-mac@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-boun...@r-project.org<mailto:r-sig-mac-boun...@r-project.org>>
on behalf of Timothy Bates <tim.ba...@ed.ac.uk<mailto:tim.ba...@ed.ac.uk>>
Date: Monday, June 24, 2024 at 4:00 PM
To: R list <R-SIG-Mac@r-project.org<mailto:R-SIG-Mac@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, rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
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