systools/25.09-2 (systools-25.09-2.eb)
To access module help and find out for which stacks and partitions the module is
installed, use module spider systools/25.09-2.
EasyConfig:
#DOC Libraries for use in LUMI/25.03 or on CrayEnv when the LUMI/25.03 stack is also on the system.
#
#LUMISTACK 25.09
#
easybuild_version = '5.0.0'
easyblock = 'Bundle'
local_LUMI_version = '25.09'
name = 'systools'
version = f'{local_LUMI_version}-2'
homepage = '(none)'
whatis = [
"Description: A number of small and popular tools that just make life easier.",
"Contains: gpp, htop, tree, lstopo, proot",
]
local_systools_GPP_version = '2.28' # https://github.com/logological/gpp/releases
local_systools_htop_version = '3.4.1' # https://github.com/htop-dev/htop/releases
local_systools_pbzip2_version = '1.1.13' # http://compression.great-site.net/pbzip2/
local_systools_libtree_version = '3.1.1' # https://github.com/haampie/libtree/releases
local_systools_tree_version = '2.2.1' # https://gitlab.com/OldManProgrammer/unix-tree/-/tags
local_systools_lstopo_version = '2.13.0' # https://www.open-mpi.org/projects/hwloc/
local_systools_PRoot_version = '5.4.0' # https://github.com/proot-me/proot/releases
description = f"""
This module provides a number of popular tools to view and manage Linux processes
or files or to process files.
Overview of included tools:
+ gpp (version {local_systools_GPP_version}: a general-purpose preprocessor with customizable syntax,
suitable for a wide range of preprocessing tasks. Its independence from any
one programming language makes it much more versatile than the C
preprocessor (cpp), while its syntax is lighter and more flexible than that
of GNU m4. There are built-in macros for use with C/C++, LaTeX, HTML, XHTML,
and Prolog files.
GPP is Free Software. It is distributed under the terms of the GNU Lesser
General Public Licence.
+ htop (version {local_systools_htop_version}): an interactive process viewer for Unix/Linux.
Note that by default, htop will not show the load of individual cores as
you may be used from many other sites. However, given that there are 256
virtual cores on most nodes, this produces visual overload for may. It is
still possible to change the settings in htop by going into the settings
screen using "SHFIT-S" and then changing the meters, e.g., adding
"CPUS (1-4/8): first half in 4 shorter columns" to the first half and
"CPUS (5-8/8): second half in 4 shorter columns" to the second.
This configuration will be stored in ~/.config/htop/htoprc, so you can also
copy settings from another user by exchanging that file.
+ pbzip2 (version {local_systools_pbzip2_version}): a parallel implementation of the bzip2
block-sorting file compressor that uses pthreads and achieves near-linear
speedup on SMP machines. The output of this version is fully compatible with
bzip2 v1.0.2 or newer (ie: anything compressed with pbzip2 can be
decompressed with bzip2).
Note that development has halted long ago, so consider this unsupported
software and problems will not get fixed. As this is old code, the amount
of memory that one can request through the -m command line argument is
also limited and the maximum value for the argument is 2000 as otherwise
unexpected behaviour can occur (and this is not properly checked in the
current version).
A small patch is applied to detect the correct number of CPUs allocated to
the job and to limit the default number of threads on the login nodes of
LUMI to not flood the login nodes with threads that would be very
ineffective anyway due to restrictions on the amount of CPU resources a
user can use.
+ libtree (version {local_systools_libtree_version}) is a tool that turns ldd into a tree, explains why
shared libraries are found and why not and optionally deploys executables
and dependencies into a single directory.
+ tree (version {local_systools_tree_version}): a recursive directory listing command that produces a
depth indented listing of files, which is colorized ala dircolors if the
LS_COLORS environment variable is set and output is to tty.
+ lstopo (version {local_systools_lstopo_version}): a command to show the structure of a node.
This version is compiled with ROCm support, which is missing in the
`lstopo-no-graphics` command on the system.
Note that when run on a node without GPU, lstopo will start with an error
message: "hwloc/rsmi: Failed to initialize with rsmi_init():
RSMI_STATUS_INIT_ERROR: An error occurred during initialization, during
monitor discovery or when when initializing internal data structures". This
message is harmless, but if you don't want it in the output, run
HWLOC_COMPONENTS=-rsmi lstopo
or set
export HWLOC_COMPONENTS=-rsmi
before running lstopo.
+ PRoot (version {local_systools_PRoot_version}) is a user-space implementation of chroot, mount --bind,
and binfmt_misc. This means that users don't need any privileges or setup
to do things like using an arbitrary directory as the new root filesystem,
making files accessible somewhere else in the filesystem hierarchy, or
executing programs built for another CPU architecture transparently through
QEMU user-mode.
It is provided in this module mainly for use with singularity.
"""
doc_urls = [
'GPP: Web-based documentation on: https://files.nothingisreal.com/software/gpp/gpp.html',
'GPP: Mal page in section 1 (man 1 gpp)',
'htop: Man page in section 1 (man 1 htop)',
'pbzip2: Man page in section 1 (man pbzip2)',
'libtree: Man page in section 1 (man 1 libtree)',
'tree: Man page in section 1 (man 1 tree)',
'lstopo: Man page `man 1 lstopo`',
'PRoot: Web-based documentation on: https://proot-me.github.io/',
]
toolchain = SYSTEM
build_deps = [
('buildtools', local_LUMI_version),
('syslibs', local_LUMI_version, '-static'), # for libreadline
]
local_systools_lstopo_version_mm = '.'.join(local_systools_lstopo_version.split('.')[:2])
default_easyblock = 'ConfigureMake'
components = [
('GPP', local_systools_GPP_version, {
'easyblock': 'ConfigureMake',
'sources': [ {
'filename': SOURCELOWER_TAR_BZ2,
'source_urls': ['https://github.com/logological/gpp/releases/download/%(version)s']
} ],
'checksums': ['343d33d562e2492ca9b51ff2cc4b06968a17a85fdc59d5d4e78eed3b1d854b70'],
'start_dir': '%(namelower)s-%(version)s',
'pre_configure_opts': 'CFLAGS="-O2 -march=znver1" CXXFLAGS="-O2 -march=znver1" ',
'install_opts': ' && mkdir -p %(installdir)s/share/licenses/%(name)s' +
' && cp COPYING COPYING.LESSER NEWS THANKS %(installdir)s/share/licenses/%(name)s'
}),
('htop', local_systools_htop_version, {
'easyblock': 'ConfigureMake',
'sources': [ { # https://github.com/htop-dev/htop/releases/download/3.3.0/htop-3.3.0.tar.xz
'filename': SOURCE_TAR_XZ,
'source_urls': [f'https://github.com/htop-dev/htop/releases/download/{local_systools_htop_version}']
} ],
'checksums': ['904f7d4580fc11cffc7e0f06895a4789e0c1c054435752c151e812fead9f6220'],
'start_dir': '%(name)s-%(version)s',
'pre_configure_opts': 'CFLAGS="-O2 -march=znver1" CXXFLAGS="-O2 -march=znver1" LDFLAGS="-L$EBROOTNCURSES/lib" ',
#'configure_opts': '--enable-static --enable-unicode --enable-affinity',
'configure_opts': '--with-curses=ncursesw --enable-unicode --enable-affinity', # A fully static build causes issues when upgrading the OS...
'install_opts': ' && mkdir -p %(installdir)s/share/licenses/%(name)s' +
' && cp COPYING %(installdir)s/share/licenses/%(name)s'
}),
('pbzip2', local_systools_pbzip2_version, {
'easyblock': 'ConfigureMake',
'sources': [ { # https://github.com/haampie/libtree/archive/refs/tags/v3.1.1.tar.gz
'filename': SOURCELOWER_TAR_GZ,
'source_urls': ['https://launchpad.net/pbzip2/1.1/1.1.13/+download']
} ],
'patches': ['%(name)s-%(version)s_LUMI.patch'],
'checksums': [
{'pbzip2-1.1.13.tar.gz': '8fd13eaaa266f7ee91f85c1ea97c86d9c9cc985969db9059cdebcb1e1b7bdbe6'},
{'pbzip2-1.1.13_LUMI.patch': 'eae828715f36d125cb6319af15c517818b20bc783c86e201df471c32e705acc3'}
],
'start_dir': '%(name)s-%(version)s',
'skip_steps': ['configure'],
'pre_build_opts': 'sed -e "s|CXXFLAGS = -O2|CXXFLAGS = -O2 -march=znver1 -std=c++98 -DLUMI_PATCH|" -i Makefile &&',
'install_opts': 'PREFIX=%(installdir)s' +
' && mkdir -p %(installdir)s/share/licenses/%(name)s' +
' && cp AUTHORS COPYING README %(installdir)s/share/licenses/%(name)s',
}),
('libtree', local_systools_libtree_version, {
'easyblock': 'MakeCp',
'sources': [ { # https://github.com/haampie/libtree/archive/refs/tags/v3.1.1.tar.gz
'download_filename': 'v%(version)s.tar.gz',
'filename': '%(name)s-%(version)s.tar.gz',
'source_urls': ['https://github.com/haampie/libtree/archive/refs/tags']
} ],
'checksums': ['6148436f54296945d22420254dd78e1829d60124bb2f5b9881320a6550f73f5c'],
'start_dir': '%(name)s-%(version)s',
'build_opts': 'CC="gcc" CFLAGS="-O2 -march=znver1" LDFLAGS="-static"',
'files_to_copy': [(['libtree'], 'bin'), (['doc/libtree.1'], 'share/man/man1'), (['LICENSE'], 'share/licenses/%(name)s')]
}),
('tree', local_systools_tree_version, {
'easyblock': 'MakeCp',
'sources': [ { # https://gitlab.com/OldManProgrammer/unix-tree/-/archive/2.1.1/unix-tree-2.1.1.tar.bz2
'filename': 'unix-tree-%(version)s.tgz',
'source_urls': ['https://gitlab.com/OldManProgrammer/unix-tree/-/archive/%(version)s']
} ],
'checksums': ['70d9c6fc7c5f4cb1f7560b43e2785194594b9b8f6855ab53376f6bd88667ee04'],
'start_dir': 'unix-tree-%(version)s',
'build_opts': 'CC="gcc" CFLAGS="-O2 -march=znver1 -ggdb -pedantic -Wall -DLINUX -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64"',
'files_to_copy': [(['tree'], 'bin'), (['doc/tree.1'], 'share/man/man1'), (['LICENSE'], 'share/licenses/%(name)s')]
}),
('lstopo', local_systools_lstopo_version, { # lstopo taken out of hwloc
'easyblock': 'ConfigureMake',
'sources': [f'hwloc-{local_systools_lstopo_version}.tar.bz2'],
'source_urls': [f'https://www.open-mpi.org/software/hwloc/v{local_systools_lstopo_version_mm}/downloads/'],
'checksums': ['52e936afb6ebd80f171f763fcf14f7b1f5ce98b125af5dd2f328b873b1fd0dab'],
'start_dir': f'hwloc-{local_systools_lstopo_version}',
'pre_configure_opts': 'LDFLAGS="-L$EBROOTSYSLIBS/lib -lncurses $LDFLAGS"',
'configure_opts': ' '.join([
'--with-rocm=/opt/rocm',
'--disable-shared',
'--enable-static',
'--disable-libxml2',
'--disable-cairo',
'--without-x',
]),
'install_opts': ' && mkdir -p %(installdir)s/share/licenses/%(name)s' +
' && cp AUTHORS COPYING NEWS README %(installdir)s/share/licenses/%(name)s',
}),
('PRoot', local_systools_PRoot_version, {
'sources': [ { # https://github.com/haampie/libtree/archive/refs/tags/v3.1.1.tar.gz
'download_filename': 'v%(version)s.zip',
'filename': SOURCELOWER_ZIP,
'source_urls': ['https://github.com/proot-me/proot/archive/refs/tags']
} ],
'checksums': ['8812f3a6c224bdd6a316f13689377e7543e7e3cebcdef6ec98827abee60fa327'],
'start_dir': '%(namelower)s-%(version)s/src',
'skip_steps': [ 'configure' ],
'pre_build_opts': 'sed -e "s/.*GIT_.*//" -i GNUmakefile && ',
'build_opts': 'proot V=1 CFLAGS="-O2 -march=znver1" VERSION="%(version)s"',
'install_opts': 'V=1 PREFIX="%(installdir)s"' +
' && mkdir -p %(installdir)s/share/licenses/%(name)s' +
' && cd ..' +
' && cp AUTHORS CHANGELOG.rst COPYING README.rst %(installdir)s/share/licenses/%(name)s',
}),
]
post_install_cmds = [
'/bin/rm -r %(installdir)s/bin/hwloc* %(installdir)s/include %(installdir)s/lib %(installdir)s/lib64 %(installdir)s/sbin',
'/bin/rm -r %(installdir)s/share/doc %(installdir)s/share/hwloc',
'/bin/rm -r %(installdir)s/share/man/man1/hwloc* %(installdir)s/share/man/man3 %(installdir)s/share/man/man7',
]
sanity_check_paths = {
'files': ['bin/gpp', 'share/man/man1/gpp.1', 'share/licenses/GPP/COPYING', 'share/licenses/GPP/COPYING.LESSER'] +
['bin/htop', 'share/man/man1/htop.1', 'share/licenses/htop/COPYING'] +
['bin/pbzip2', 'share/man/man1/pbzip2.1'] +
['bin/libtree', 'share/man/man1/libtree.1', 'share/licenses/libtree/LICENSE'] +
['bin/tree', 'share/man/man1/tree.1', 'share/licenses/tree/LICENSE'] +
['bin/proot', 'share/licenses/PRoot/COPYING'],
'dirs': []
}
sanity_check_cmds = [
'gpp --version',
'htop --version',
'pbzip2 -h 2>&1 | grep "Parallel BZIP2 v%(version)s"'
'libtree --help',
'libtree -v -p %(installdir)s/bin/libtree',
'tree --version',
'lstopo',
'proot --version'
]
env_mod_lua_footer = f"""
extensions( "GPP/{local_systools_GPP_version}, htop/{local_systools_htop_version}, pbzip2/{local_systools_pbzip2_version}, " ..
"libtree/{local_systools_libtree_version}, tree/{local_systools_tree_version}, lstopo/{local_systools_lstopo_version}, " ..
"PRoot/{local_systools_PRoot_version}" )
"""
env_mod_category = 'tools'