Skip to content

fix missing -lm -lpthread for SQLite 3.50.1 by setting $LIBS to empty string value #23374

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
SebastianAchilles merged 1 commit into from
Jul 10, 2025
Merged

fix missing -lm -lpthread for SQLite 3.50.1 by setting $LIBS to empty string value #23374

SebastianAchilles merged 1 commit into from
Jul 10, 2025

Conversation

@Thyre
Copy link
Collaborator

@Thyre Thyre commented Jul 10, 2025 •
edited
Loading

(created using eb --new-pr)

See discussion here for more information:

Basically, SQLite switched from passing @LIBS@ to @LDFLAGS_MATH@ and so on in their build system and sqlite3.pc. However, configure still honors the LIBS= we set with our toolchain.
This causes the following result:

== 2025-07-10 11:18:50,665 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previously undefined)
[...]
Loadable extension support enabled.
Checking libs for ceil...none needed
Enabling math SQL functions

Building then fails when not passing -lm -lpthread, as done in #23027.
However, while this fixes building SQLite, later packages requiring it can then fail with math linker errors, as seen in #23369.

To avoid this, simply unset LIBS= during configure. This causes the correct libraries to be picked up again.

@Thyre Thyre mentioned this pull request Jul 10, 2025
Merged
@SebastianAchilles SebastianAchilles added the 2025b issues & PRs related to 2025b common toolchains label Jul 10, 2025
@SebastianAchilles SebastianAchilles added this to the release after 5.1.1 milestone Jul 10, 2025
@SebastianAchilles
Copy link
Member

SebastianAchilles commented Jul 10, 2025

Test report by @SebastianAchilles
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bwd-rockylinux-100 - Linux Rocky Linux 10.0 (Red Quartz), x86_64, Intel(R) Core(TM) i7-6900K CPU @ 3.20GHz (broadwell), Python 3.12.9
See https://gist.github.com/SebastianAchilles/9a2c5bc9e72dc5250c3f4da4cd6a239c for a full test report.

@SebastianAchilles
Copy link
Member

SebastianAchilles commented Jul 10, 2025

@boegelbot please test @ jsc-zen3

@boegelbot
Copy link
Collaborator

boegelbot commented Jul 10, 2025

@SebastianAchilles: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=23374 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23374 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 7203

Test results coming soon (I hope)...

Details

- notification for comment with ID 3056660477 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

@boegelbot
Copy link
Collaborator

boegelbot commented Jul 10, 2025

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/6d2162e0e5c7004704db2683728ec6c7 for a full test report.

@Thyre Thyre changed the title {devel}[GCCcore/14.3.0] Fix missing -lm -lpthread for SQLite 3.50.1 {devel}[GCCcore/14.3.0] Fix missing -lm -lpthread for SQLite 3.50.1 Jul 10, 2025
SebastianAchilles
SebastianAchilles approved these changes Jul 10, 2025
View reviewed changes
Copy link
Member

@SebastianAchilles SebastianAchilles left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

lgtm

@SebastianAchilles
Copy link
Member

SebastianAchilles commented Jul 10, 2025

Going in, thanks @Thyre!

@SebastianAchilles SebastianAchilles merged commit c3ed227 into easybuilders:develop Jul 10, 2025
8 checks passed
@boegel boegel changed the title {devel}[GCCcore/14.3.0] Fix missing -lm -lpthread for SQLite 3.50.1 fix missing -lm -lpthread for SQLite 3.50.1 by setting $LIBS to empty string value Jul 31, 2025
@Crivella Crivella mentioned this pull request Sep 4, 2025
Merged
@boegel boegel added bug fix and removed change labels Sep 26, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@SebastianAchilles SebastianAchilles SebastianAchilles approved these changes

Assignees

No one assigned

Labels

2025b issues & PRs related to 2025b common toolchains bug fix

Projects

None yet

Milestone

5.1.2

Development

Successfully merging this pull request may close these issues.

4 participants

@Thyre @SebastianAchilles @boegelbot @boegel