Hi Ivan, An apology, I was away for quite a bit.
To reproduce the setup: I have been using the default GCC in RHEL 9.1. gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/11/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-redhat-linux Configured with: ../configure --enable-bootstrap --enable-host-pie --enable-host-bind-now --enable-languages=c,c++,fortran,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --enable-plugin --enable-initfini-array --without-isl --enable-multilib --with-linker-hash-style=gnu --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --enable-cet --with-tune=generic --with-arch_64=x86-64-v2 --with-arch_32=x86-64 --build=x86_64-redhat-linux --with-build-config=bootstrap-lto --enable-link-serialization=1 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 11.4.1 20230605 (Red Hat 11.4.1-2) (GCC) I have been building R 4.4.0 and 4.4.1 with Flexiblas and with the built in R BLAS/LAPACK. R BLAS: ./configure --prefix=/tools/R/$RVER --enable-R-shlib --enable-memory-profiling --with-pcre2=/tools/pcre2/10.42 Flexiblas: PKG_CONFIG_PATH=/tools/flexiblas/3.4.2/lib64/pkgconfig ./configure --prefix=/tools/R/flexiblas/4.4.1 --enable-R-shlib --enable-memory-profiling --with-pcre2=/tools/pcre2/10.42 --with-blas="-lflexiblas -L/tools/flexiblas/3.4.2/lib64" --with-lapack I realised the build fails when "--with-lapack" is left unspecified, even though the configure output shows this: Source directory: . Installation directory: /tools/R/flexiblas C compiler: gcc -g -O2 Fortran fixed-form compiler: gfortran -g -O2 Default C++ compiler: g++ -std=gnu++17 -g -O2 C++11 compiler: g++ -std=gnu++11 -g -O2 C++14 compiler: g++ -std=gnu++14 -g -O2 C++17 compiler: g++ -std=gnu++17 -g -O2 C++20 compiler: g++ -std=gnu++20 -g -O2 C++23 compiler: g++ -std=gnu++23 -g -O2 Fortran free-form compiler: gfortran -g -O2 Obj-C compiler: Interfaces supported: X11, tcltk External libraries: pcre2, readline, BLAS(FlexiBlas), LAPACK(in blas), curl, libdeflate Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU Options enabled: shared R library, R profiling, memory profiling, libdeflate for lazyload Capabilities skipped: Options not enabled: shared BLAS Recommended packages: yes I replaced the "--with-lapack" flag with "--with-lapack='-lflexiblas -L/tools/flexiblas/3.4.2/lib64'" and everything built ok. >From a quick check in my emails, seems the RHEL9 system lapack packages are >broken. Will test a bit more. If you need a singularity container in the future, I can provide one with the R-dependencies installed. We setup dependencies similar to: https://github.com/rstudio/r-builds/blob/main/builder/Dockerfile.rhel-9 or subscription-manager repos --enable codeready-builder-for-rhel-9-$(arch)-rpms dnf install -y yum-utils dnf install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-9.noarch.rpm yum-builddep -y R Just bringing this to your attention as the issue is not with R by the looks, as I was unable to reproduce on Rocky Linux 9.1. Kind regards and thanks! Miguel Esteva Senior ITS Research Systems Engineer The Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville VIC 3052 Australia Phone (03) 9345 2909<callto:(03)%209345%202909> Email estev...@wehi.edu.au Web http://www.wehi.edu.au<http://www.wehi.edu.au/> ________________________________ From: Ivan Krylov <ikry...@disroot.org> Sent: Friday, 3 May 2024 9:40 PM To: Miguel Esteva via R-help <r-help@r-project.org> Cc: Miguel Esteva <estev...@wehi.edu.au> Subject: Re: [R] grDevices segfault when building R4.4.0 on RHEL 9.1. Dear Miguel Esteva, I couldn't get a Red Hat "ubi9" container to install enough dependencies to build R. Is there a way to reproduce your setup on a virtual machine somewhere? On Fri, 3 May 2024 00:42:43 +0000 Miguel Esteva via R-help <r-help@r-project.org> wrote: > *** caught segfault *** > > address 0x1801fa8f70, cause 'memory not mapped' > > > Traceback: > > 1: solve.default(rgb) This seems to crash inside the BLAS. Which BLAS are you using? Any custom ./configure arguments? Which compilers are you running? To find out more information about the crash, try to follow it with a debugger. Change directory to src/library/grDevices and run: _R_COMPILE_PKGS_=1 R_COMPILER_SUPPRESS_ALL=1 \ R_DEFAULT_PACKAGES=NULL LC_ALL=C \ ../../../bin/R -d gdb --vanilla --no-echo -e \ 'tools:::makeLazyLoading("grDevices")' (This assumes building straight from the source directory. Adjust the paths if you're using a separate build directory.) Use the "run" command to start the process. One you see a crash, use "backtrace" to see the state of the call stack at the place of the crash, or "backtrace full" to include the contents of local variables. The first few entries are probably the most important ones. Not sure what to do with this information yet, but it might provide more clues. -- Best regards, Ivan [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
