easybuild using system cmake

[LukeLabrie]

When I run

eb ~/.local/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.3-GCCcore-11.3.0.eb --robot

I get the following error:

cmake: ~/.local/easybuild/software/GCCcore/11.3.0/lib64/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /usr/lib/libicuuc.so.72)
 (at easybuild/tools/run.py:641 in parse_cmd_output)

After some investigation, I realized that this is because when the cmake command is invoked, it's using /usr/bin/cmake, i.e. my system cmake (3.24.3). But you can see that in the easybuild file for libjpeg-turbo that it is explicitly specified to use 3.23.1, which would not require GLIBCXX_3.4.30 (see below from ~/.local/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.3-GCCcore-11.3.0.eb)

builddependencies = [
    ('CMake', '3.23.1'),
    ('binutils', '2.38'),
]

Any indication on whether this is a bug or just an issue with my implementation? This is a standard easyconfig file that ships with easybuild.

edit:

Perhaps what would help me would be an explanation of how, and in which scripts, the framework normally handles invocation of cmake within the module so I can poke around and see what's going on

[boegel]

@LukeLabrie What may be happening is that you have EasyBuild configured to filter out the CMake build dependency as specified by EasyBuild, via --filter-deps (in which case the installation will use the cmake from the OS, if available).
You can easily check your active EasyBuild configuration using --show-config.

[LukeLabrie]

Currently I'm not using using the --filter-deps option. Output of eb --show-config

#
# Current EasyBuild configuration
# (C: command line argument, D: default value, E: environment variable, F: configuration file)
#
buildpath      (D) = /home/luke/.local/easybuild/build
containerpath  (D) = /home/luke/.local/easybuild/containers
installpath    (D) = /home/luke/.local/easybuild
repositorypath (D) = /home/luke/.local/easybuild/ebfiles_repo
robot-paths    (D) = /home/luke/.local/easybuild/easyconfigs
sourcepath     (D) = /home/luke/.local/easybuild/sources

[boegel]

@LukeLabrie That's quite strange... Can you provide the full EasyBuild log file for this (preferably a debug log, created using eb --debug)

[LukeLabrie]

Sure. See attached.
easybuild-GCCcore-11.3.0-20230103.191459.CAOvN.log

[boegel]

@LukeLabrie The log you shared is for the installation of GCCcore/11.3.0, i.e. the GCC compiler that is used as a toolchain to install libjpeg-turbo (not the installation of libjpeg-turbo itself). There's no trace of cmake in that log (as I would expect).

The error you mentioned is there though:

msgfmt -o fr.mo ../../../../libstdc++-v3/po/fr.po
msgfmt: /home/luke/.local/easybuild/build/GCCcore/11.3.0/system-system/gcc-11.3.0/stage3_obj/x86_64-pc-linux-gnu/libstdc++-v3/src/.libs/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /usr/lib/libicuuc.so.72)
make[5]: *** [Makefile:556: de.mo] Error 1

The problem here is probably that you're letting EasyBuild use your home directory as location for build directories.
What type of filesystem is your home directory on?

If it is any type of parallel filesystem (NFS, GPFS, Lustre, etc.), that's a bad idea, it often causes weird build failures because the filesystem is too slow (the compiler expects files to be there already, but can't find them); see also https://easybuilders.github.io/easybuild-tutorial/2022-isc22/configuration/#build-path

[LukeLabrie]

Hi @boegel, revisiting this issue.

No I'm not running on a parallel filesystem, everything is being done natively. I tried changing the build directory as suggested to /tmp/$USER, but this did not resolve the issue.