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

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SebastianAchilles merged 1 commit intoeasybuilders:developfrom
Thyre:20250710114037_new_pr_SQLite3501
Jul 10, 2025
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fix missing -lm -lpthread for SQLite 3.50.1 by setting $LIBS to empty string value#23374
SebastianAchilles merged 1 commit intoeasybuilders:developfrom
Thyre:20250710114037_new_pr_SQLite3501

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@Thyre Thyre commented Jul 10, 2025 •
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(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
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@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
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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.

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SebastianAchilles commented Jul 10, 2025

@boegelbot please test @ jsc-zen3

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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)...

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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).

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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
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SebastianAchilles approved these changes Jul 10, 2025
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lgtm

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SebastianAchilles commented Jul 10, 2025

Going in, thanks @Thyre!

@SebastianAchilles SebastianAchilles merged commit c3ed227 into easybuilders:develop Jul 10, 2025
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@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
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@boegel boegel added bug fix and removed change labels Sep 26, 2025
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