[R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

[Duncan Murdoch]

On 2024-05-22 10:18 a.m., Dirk Eddelbuettel wrote:
> 
> On 22 May 2024 at 13:54, Nixon, Michelle Pistner wrote:
> | Thank you both for your responses and help! Kurt-- your message makes a lot of
> | sense. I'll try to debug soon and will reach out if I have more questions.
> 
> Interesting.
> 
> Kurt, is there a recommended way to test for this (rare, I may add) case of
> 'OpenMP present but usage verboten by R' ?  I do not see an option for 'R CMD
> config' jumping out, and there is no pkg-config file either.
> 
> Testing via 'nm' as you show is possible but not exactly 'portable'.  So any
> suggestions as to what to condition on here?  Michelle did AFAICT the Right
> Thing (TM) by 'borrowing' from the fairly mature check in RcppArmadillo.

Not that I know much about writing configure tests, but won't 
src/include/config.h in the R build dir have "HAVE_OPENMP" defined if 
OpenMP is supported?

Duncan

> 
> Dirk
> 
> |
> | Thanks,
> | Michelle
> | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
> | From: Kurt Hornik <Kurt.Hornik using wu.ac.at>
> | Sent: Wednesday, May 22, 2024 3:57 AM
> | To: Dirk Eddelbuettel <edd using debian.org>
> | Cc: Nixon, Michelle Pistner <map5672 using psu.edu>; r-package-devel using r-project.org
> | <r-package-devel using r-project.org>; Kurt Hornik <Kurt.Hornik using wu.ac.at>
> | Subject: Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang
> | with OpenMP
> |
> | [You don't often get email from kurt.hornik using wu.ac.at. Learn why this is
> | important at https://aka.ms/LearnAboutSenderIdentification ]
> |
> | >>>>> Dirk Eddelbuettel writes:
> |
> | Friends, the Debian pretest check system uses LLVM 18 and has the
> | corresponding OpenMP headers and libraries installed, but R is
> | configured not to use these.  However, the configure test in fido does
> |
> | cat <<EOF > test-omp.cpp
> | #include <omp.h>
> | int main() {
> |   return omp_get_num_threads();
> | }
> | EOF
> |
> | ## Execute R CMD SHLIB.
> | "${R_HOME}/bin/R" CMD SHLIB test-omp.cpp >/dev/null 2>&1
> | if test x"$?" = x"0"; then
> |     AC_MSG_RESULT([yes])
> |     openmp_already_works="yes"
> | else
> |     AC_MSG_RESULT([no])
> | fi
> |
> | which does not work as intended: R CMD SHLIB will happily link but the
> | .so will end up with an unresolved symbol:
> |
> | $ nm test-omp.so | grep omp_
> |                  U omp_get_num_threads
> |
> | Hth
> | -k
> |
> | > Hi Michelle,
> |
> | > On 21 May 2024 at 13:46, Nixon, Michelle Pistner wrote:
> | > | Hi all,
> | > |
> | > | I'm running into build issues for my package (fido: https://
> | nam10.safelinks.protection.outlook.com/?url=
> | https%3A%2F%2Fgithub.com%2Fjsilve24%2Ffido&data=
> | 05%7C02%7Cmap5672%40psu.edu%7C7993944f52ae4a017d3d08dc7a34d1d6%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638519614500263726%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C
> | &sdata=C4BI6%2FUgTjd%2FCRPzBF8NuUkPvlQkIxb2r1%2BzIqKNPpE%3D&reserved=0) on the
> | r-devel-linux-x86_64-debian-clang system on CRAN (full check log here: https://
> | nam10.safelinks.protection.outlook.com/?url=
> | https%3A%2F%2Fwin-builder.r-project.org%2Fincoming_pretest%2Ffido_1.1.0_20240515_211644%2FDebian%2F00install.out
> | &data=
> | 05%7C02%7Cmap5672%40psu.edu%7C7993944f52ae4a017d3d08dc7a34d1d6%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638519614500272862%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C
> | &sdata=TKpQrkImemwz%2FuK7yYqCLEECU6WCCvgYwcrAId%2Bpmb0%3D&reserved=0). fido
> | relies on several of the Rcpp packages, and I think the error is due to how
> | OpenMP is set up in our package. The error in question states:
> | > |
> | > | "Error: package or namespace load failed for �fido� in dyn.load(file,
> | DLLpath = DLLpath, ...):
> | > |  unable to load shared object '/home/hornik/tmp/R.check/r-devel-clang/Work/
> | build/Packages/00LOCK-fido/00new/fido/libs/fido.so':
> | > |   /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-fido/
> | 00new/fido/libs/fido.so: undefined symbol: omp_get_thread_num"
> | > |
> | > | I've had a hard time recreating the error, as I can successfully get the
> | package to build on other systems (GitHub action results here: https://
> | nam10.safelinks.protection.outlook.com/?url=
> | https%3A%2F%2Fgithub.com%2Fjsilve24%2Ffido%2Factions&data=
> | 05%7C02%7Cmap5672%40psu.edu%7C7993944f52ae4a017d3d08dc7a34d1d6%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638519614500275695%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C
> | &sdata=zXCul23gWAevfEhCsfyJg8KewU8fjSuy1qZgZemNy7M%3D&reserved=0) including a
> | system using the same version of R/clang as the failing CRAN check. Looking at
> | the logs between the two, the major difference is the lack of -fopenmp in the
> | compiling function on the CRAN version (which is there on the r-hub check
> | version with the same specifications):
> | > |
> | > | (From the CRAN version) clang++-18 -std=gnu++17 -shared -L/home/hornik/tmp/
> | R-d-clang-18/lib -Wl,-O1 -o fido.so ConjugateLinearModel.o
> | MaltipooCollapsed_LGH.o MaltipooCollapsed_Optim.o MatrixAlgebra.o
> | PibbleCollapsed_LGH.o PibbleCollapsed_Optim.o PibbleCollapsed_Uncollapse.o
> | PibbleCollapsed_Uncollapse_sigmaKnown.o RcppExports.o SpecialFunctions.o
> | test_LaplaceApproximation.o test_MultDirichletBoot.o test_utils.o -L/home/
> | hornik/tmp/R-d-clang-18/lib -lR
> | > |
> | > | My initial thought was an issue in the configure scripts (which we borrowed
> | heavily from RcppArmadillo but made slight changes to (which is the most likely
> | cause if there is issue here)) or that there is some mismatch somewhere as to
> | whether or not OpenMP is available, but there isn't an obvious bug to me.
> | > |
> | > | Any guidance on how to debug would be greatly appreciated!
> |
> | > I seem to recall that that machine is 'known-bad' for OpenMP due to the
> | > reliance on clang-18 which cannot (?) build with it.  Might be best to
> | > contact Kurt Hornik (CC'ed) and/or CRAN.
> |
> | > Best, Dirk
> |
> |
> | > | Thanks,
> | > | Michelle
> | > |
> | > | Michelle Nixon, PhD
> | > |
> | > | Assistant Research Professor
> | > | College of Information Sciences and Technology
> | > | The Pennsylvania State University
> | > |
> | > |     [[alternative HTML version deleted]]
> | > |
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> | > --
> | > dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
>