R/4.4.1-cpeGNU-24.03-OpenMP-raw (R-4.4.1-cpeGNU-24.03-OpenMP-raw.eb)
Install with the EasyBuild-user module:
To access module help after installation and get reminded for which stacks and partitions the module is installed, usemodule spider R/4.4.1-cpeGNU-24.03-OpenMP-raw.
EasyConfig:
#DOC This EasyConfig offers R with only the base R packages and - because it is hard to install properly
#DOC with Rcmd - Rmpi already pre-installed.
name = 'R'
version = '4.4.1'
versionsuffix = '-OpenMP-raw'
local_bzip2_version = '1.0.8' # http://www.bzip.org/downloads.html
local_cairo_version = '1.18.0' # https://www.cairographics.org/
local_cURL_version = '8.3.0' # https://curl.haxx.se/download/
local_gzip_version = '1.13' # https://ftp.gnu.org/gnu/gzip/
local_libjpegturbo_version = '3.0.1' # https://github.com/libjpeg-turbo/libjpeg-turbo/releases
local_libpng_version = '1.6.40' # http://www.libpng.org/pub/png/libpng.html
local_libreadline_version = '8.2' # https://ftp.gnu.org/pub/gnu/readline/
local_libtiff_version = '4.6.0' # https://download.osgeo.org/libtiff/
local_ncurses_version = '6.4' # https://ftp.gnu.org/pub/gnu/ncurses/
local_Pango_version = '1.51.0' # http://ftp.gnome.org/pub/GNOME/sources/pango/
local_PCRE2_version = '10.42' # https://ftp.pcre.org/pub/pcre/
local_Tk_version = '8.6.13' # https://tcl.tk/
local_XZ_version = '5.4.4' # https://tukaani.org/xz/
local_zlib_version = '1.3.1' # https://zlib.net/
local_Zip_version = '3.0'
local_UnZip_version = '6.0'
homepage = 'https://www.r-project.org/'
whatis = [
"Description: R is a free software environment for statistical computing and graphics."
]
description = """
This module provides a base R package, without many bells and whistles.
A fully-featured R has many dependencies that do not all make sense on
the compute nodes of LUMI, in particular when it comes to graphics.
Similarly, the build process as-is will not find a web browser nor
PDF viewer as these are not currently available on regular compute
nodes of LUMI.
This version of R links with the multithreaded version of
Cray LibSci, so its linear algebra routines support multithreading
by setting OMP_NUM_THREADS.
We have observed crashes in the linear algebra libraries when running
multithreaded. It appears that setting OMP_STACKSIZE=256M,
which is now done in the module, reduces those crashes.
Using ulimit -s 300000 may also help. The problem has been discussed with
HPE Cray, but a solution will come at the earliest with 25.03.
"""
toolchain = {'name': 'cpeGNU', 'version': '24.03'}
toolchainopts = {'openmp': True}
source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s']
sources = [SOURCE_TAR_GZ]
checksums = [
'b4cb675deaaeb7299d3b265d218cde43f192951ce5b89b7bb1a5148a36b2d94d', # R-4.4.1.tar.gz
]
# Note: R will not be able to tell which BLAS library was used as it is linked
# in automatically and does not appear in BLAS_LIBS so that the code in the
# configure script cannot figure out which BLAS is being used and set
# r_blas properly.
builddependencies = [
('buildtools', '%(toolchain_version)s', '', SYSTEM),
]
dependencies = [
# Base R
('ncurses', local_ncurses_version),
('libreadline', local_libreadline_version),
('zlib', local_zlib_version),
('bzip2', local_bzip2_version),
('gzip', local_gzip_version),
('XZ', local_XZ_version),
('Info-ZIP', f'{local_Zip_version}-{local_UnZip_version}'), # Not really needed as anything in this module is also in the system-installed versions.
# TODO: Add a zip/unzip command, though the system one might be OK as it only uses the commands.
('PCRE2', local_PCRE2_version),
('cURL', local_cURL_version), # for RCurl but also used by the base R package
('X11', '%(toolchain_version)s'),
('Tk', local_Tk_version), # for tcltk (base package)
('libpng', local_libpng_version), # for plotting in R
('libjpeg-turbo', local_libjpegturbo_version), # for plottting in R
('LibTIFF', local_libtiff_version),
('cairo', local_cairo_version),
('Pango', local_Pango_version),
]
# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols.
# Adding it to FLIBS makes sure it is present when needed.
preconfigopts = 'export FLIBS="$FLIBS -lm" && '
# We also need to ensure a single Cray LibSci library is used. It looks like R compiles
# some files with OpenMP if it figures out that the compiler supports OpenMP, but does
# not add the flag to the link options, resulting in problems with Cray LibSci. Hence
# we enforce OpenMP and manually add it to the linker flags as that is not done by
# the build process.
preconfigopts += 'export LDFLAGS="-fopenmp $LDFLAGS" && '
configopts = "--with-pic --enable-threads --enable-R-shlib"
# some recommended packages may fail in a parallel build (e.g. Matrix), and
# we're installing them anyway below
configopts += " --with-recommended-packages=no"
# specify that at least EasyBuild v3.5.0 is required,
# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK
easybuild_version = '3.5.0'
exts_default_options = {
'source_urls': [
'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive
'https://cran.r-project.org/src/contrib/', # current version of packages
'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages
],
'source_tmpl': '%(name)s_%(version)s.tar.gz',
}
# !! order of packages is important !!
# packages updated on 4th January 2024
exts_list = [
# include packages that are part of the base installation of R,
# both to make sure they are available (via sanity check),
# and to be able to pass the check for required dependencies when installing extensions in parallel
'base',
'compiler',
'datasets',
'graphics',
'grDevices',
'grid',
'methods',
'parallel',
'splines',
'stats',
'stats4',
'tcltk',
'tools',
'utils',
#
# Do firsts because of potential problems
#
('Rmpi', '0.7-2', {
'easyblock': 'RPackage',
'patches': ['Rmpi-%(version)s_Cray.patch'],
'installopts': '--configure-args="--with-Rmpi-type=CRAY --with-Rmpi-include=$CRAY_MPICH_DIR/include --with-Rmpi-libpath=$CRAY_MPICH_DIR/lib" ',
'checksums': ['8591fa9f50de52535a32b36e7ed142c6ca4e03fdfdbef79a1e27a63ed5322eef'],
}),
]
# Set OMP_STACKSIZE to avoid crashes in LibSci
modextravars = {
'OMP_STACKSIZE': '256M',
}
moduleclass = 'lang'