symbol not found in flat namespace '___kmpc_critical' - R-SIG-Mac

Sun, Apr 30, 2023 7:59 PM #

Given some of the misinformation in this thread I have to clarify a few things for posterity.

Firstly, the issue was very simple one - the package failed to link the omp library which is required and documented at https://mac.r-project.org/openmp/ -- the required flags are:

PKG_CPPFLAGS='-Xclang -fopenmp'
PKG_LIBS=-lomp

and the latter was missing in the package.

Any code using OpenMP must link to the OpenMP run-time library which provides the actual implementation, otherwise it doesn't work.

Second, there are no special compilers required, but the Apple driver don't accept the -fopenmp flag so it has to be specified as above, essentially working around the driver removing it - which is why this is considered experimental.

Finally, the only officially supported way is to use OpenMP flags provided by R. However, the macOS R releases are not built with OpenMP support, because the run-time is not part of macOS and current R doesn't know about the work-arounds. That said, in order to prepare for a possible OpenMP support on macOS, the R 4.3.0 release includes the LLVM OpenMP run-time compatible with Xcode 14.2. This is intended as a stepping stone where the possibly of OpenMP support using Apple compilers is can be tested. R itself currently does not have a provision to leverage this "non-standard" support, but it could be added in the future.

Cheers,
Simon

On 1/05/2023, at 1:34 PM, Kasper Daniel Hansen <kasperdanielhansen at gmail.com> wrote:

Rodney,

I don't know much about OpenMP and macOS, but note that these days
 https://mac.r-project.org/tools/
says
 "Additional information on the OpenMP page is available for those
interested in OpenMP support which is not supported by Apple, but still
possible with additional libraries."
and links to
 https://mac.r-project.org/openmp/

I _believe_ that this requires the _user_ (or the check/build system) of
the package on macOS to install one of the custom clang compilers listed on
the page. For this reason, I don't think it is trivial to get the
package through CRAN or distribute the package if it links / uses OpenMP. I
could be wrong of course, since it is not something I follow. I am guessing
the best solution (which could be complicated) is to have a configure
script which checks at build time whether the system supports OpenMP. This
feels like something someone has thought about.

Best,
Kasper




On Sat, Apr 29, 2023 at 6:32?PM Sparapani, Rodney via R-SIG-Mac <
r-sig-mac at r-project.org> wrote:

Oh, that was totally self-inflicted.
I had commented out PKG_LIBS in Makevars.in
That does work on Linux with OpenMP somehow.
However, it does NOT with macOS.  Thanks

--
Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
Director, Wisconsin Chapter of the American Statistical Association
Institute for Health and Equity, Division of Biostatistics
Medical College of Wisconsin, Milwaukee Campus


From: R-SIG-Mac <r-sig-mac-bounces at r-project.org> on behalf of Sparapani,
Rodney via R-SIG-Mac <r-sig-mac at r-project.org>
Date: Saturday, April 29, 2023 at 4:18 PM
To: r-sig-mac at r-project.org <r-sig-mac at r-project.org>
Subject: [R-SIG-Mac] symbol not found in flat namespace '___kmpc_critical'
ATTENTION: This email originated from a sender outside of MCW. Use caution
when clicking on links or opening attachments.

________________________________

Hi Gang:

After hours of debugging, I?m stuck and hoping that someone has an
idea of what the issue is here.  Any hints/tips/etc. are greatly
appreciated!

I?m getting this error from my CRAN package, nftbart.  Right now, I?m
preparing for a new release: v1.6.  However, I?m stumped by this error
message that I get when installing with OpenMP.  Without OpenMP,
everything is fine; however, the package benefits greatly from OpenMP.

I am getting the same results for R 4.2.3 and 4.3.0 RC.  The source code is
on github at
https://urldefense.com/v3/__https://github.com/rsparapa/bnptools.git__;!!H8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$
<
https://urldefense.com/v3/__https:/github.com/rsparapa/bnptools.git__;!!H8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$


So, to demonstrate, you just need to do something like this?


$ git clone
https://urldefense.com/v3/__https://github.com/rsparapa/bnptools.git__;!!H8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$
<
https://urldefense.com/v3/__https:/github.com/rsparapa/bnptools.git__;!!H8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$>
DIR

$ cd DIR

$ R CMD build nftbart

$ R CMD INSTALL nftbart_1.6.tar.gz

* installing to library
?/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library?

* installing *source* package ?nftbart? ...

** using staged installation

checking whether the C++ compiler works... yes

checking for C++ compiler default output file name... a.out

checking for suffix of executables...

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C++ compiler... yes

checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... yes

checking for clang++ -arch x86_64 -std=gnu++17 option to support OpenMP...
-lomp -Xclang -fopenmp

configure: creating ./config.status

config.status: creating src/Makevars

** libs

using C compiler: ?Apple clang version 14.0.3 (clang-1403.0.22.14.1)?

using C++ compiler: ?Apple clang version 14.0.3 (clang-1403.0.22.14.1)?

using SDK: ??

clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include"
-DNDEBUG -lomp -Xclang -fopenmp
-I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include'
-I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c
init.c -o init.o

clang++ -arch x86_64 -std=gnu++17
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -lomp
-Xclang -fopenmp
-I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include'
-I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c
nftbart.cpp -o nftbart.o

clang++ -arch x86_64 -std=gnu++17 -dynamiclib
-Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
-multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib
-L/opt/R/x86_64/lib -o nftbart.so init.o nftbart.o
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation

installing to
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-nftbart/00new/nftbart/libs

** R

** data

** demo

** byte-compile and prepare package for lazy loading

** help

*** installing help indices

** building package indices

** testing if installed package can be loaded from temporary location

Error: package or namespace load failed for ?nftbart? in dyn.load(file,
DLLpath = DLLpath, ...):

unable to load shared object
'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-nftbart/00new/nftbart/libs/nftbart.so':


dlopen(/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-nftbart/00new/nftbart/libs/nftbart.so,
0x0006): symbol not found in flat namespace '___kmpc_critical'

Error: loading failed

Execution halted

ERROR: loading failed

* removing
?/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nftbart?

* restoring previous
?/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nftbart?

sessionInfo()
R version 4.3.0 Patched (2023-04-27 r84338)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.2.1

Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;
LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.3.0


OpenMP Build: LLVM 14.0.6

$ codesign -d -vv /usr/local/lib/libomp.dylib

Executable=/usr/local/lib/libomp.dylib

Identifier=libomp

Format=Mach-O universal (x86_64 arm64)

CodeDirectory v=20400 size=6506 flags=0x0(none) hashes=198+2
location=embedded

Signature size=8977

Authority=Developer ID Application: Simon Urbanek (VZLD955F6P)

Authority=Developer ID Certification Authority

Authority=Apple Root CA

Timestamp=Feb 5, 2023 at 4:26:54 PM

Info.plist=not bound

TeamIdentifier=VZLD955F6P

Sealed Resources=none

Internal requirements count=1 size=168

--
Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
Director, Wisconsin Chapter of the American Statistical Association
Institute for Health and Equity, Division of Biostatistics
Medical College of Wisconsin, Milwaukee Campus

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