grDevices segfault when building R4.4.0 on RHEL 9.1. - R-help

Tue, Jul 16, 2024 7:35 PM #

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.

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 esteva.m at wehi.edu.au

Web http://www.wehi.edu.au<http://www.wehi.edu.au/>