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add -lpthread to configure options for Parallel-Hashmap v2.0.0#24094

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jfgrimm merged 1 commit intoeasybuilders:developfrom
nd996:20251002120413_new_pr_Parallel-Hashmap200
Oct 2, 2025
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add -lpthread to configure options for Parallel-Hashmap v2.0.0#24094
jfgrimm merged 1 commit intoeasybuilders:developfrom
nd996:20251002120413_new_pr_Parallel-Hashmap200

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@nd996 nd996 commented Oct 2, 2025 •
edited by jfgrimm
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Explicitly include -lpthread in configopts due to multiple 'undefined reference' errors in build on Rocky 8

(created using eb --new-pr)

@github-actions github-actions Bot added the change label Oct 2, 2025
@Thyre Thyre added the 2024a issues & PRs related to 2024a common toolchains label Oct 2, 2025
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jfgrimm commented Oct 2, 2025

@boegelbot: please test @ jsc-zen3

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boegelbot commented Oct 2, 2025

@jfgrimm: 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=24094 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24094 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 8129

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 Oct 2, 2025

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/3a70328ce01788f041f3f19a64a60d48 for a full test report.

@jfgrimm jfgrimm changed the title Explicitly include -lpthread in configopts due to multiple 'undefined reference' errors in build on Rocky 8 add -lpthread to configure options for Parallel-Hashmap v2.0.0 Oct 2, 2025
@jfgrimm jfgrimm added this to the next release (5.2.0?) milestone Oct 2, 2025
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jfgrimm commented Oct 2, 2025

Test report by @jfgrimm
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node072.viking2.yor.alces.network - Linux Rocky Linux 8.10, x86_64, AMD EPYC 7643 48-Core Processor, Python 3.6.8
See https://gist.github.com/jfgrimm/a011db9eca6821f9eda4264ddc70b838 for a full test report.

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jfgrimm approved these changes Oct 2, 2025
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lgtm

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jfgrimm commented Oct 2, 2025

Going in, thanks @nd996!

@jfgrimm jfgrimm merged commit 5e236d8 into easybuilders:develop Oct 2, 2025
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@jfgrimm jfgrimm added bug fix and removed change labels Oct 2, 2025
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jfgrimm commented Oct 2, 2025

in case anyone else hits this, the linking error was:

[ 38%] Linking CXX executable test_hash_policy_testing
/opt/apps/eb/software/CMake/3.29.3-GCCcore-13.3.0/bin/cmake -E cmake_link_script CMakeFiles/test_hash_policy_testing.dir/link.txt --verbose=1
/tmp/eb-u9njhowj/tmphe_qxgk5/rpath_wrappers/gxx_wrapper/g++ -O2 -ftree-vectorize -march=native -fno-math-errno -O3 -DNDEBUG -L/opt/apps/eb/software/googletest/1.15.2-GCCcore-13.3.0/lib64 -L/opt/apps/eb/software/googletest/1.15.2-GCCcore-13.3.0/lib -L/opt/apps/eb/software/binutils/2.42-GCCcore-13.3.0/lib64 -L/opt/apps/eb/software/binutils/2.42-GCCcore-13.3.0/lib -L/opt/apps/eb/software/GCCcore/13.3.0/lib64 -L/opt/apps/eb/software/GCCcore/13.3.0/lib CMakeFiles/test_hash_policy_testing.dir/tests/hash_policy_testing_test.cc.o -o test_hash_policy_testing  -lgmock_main -lgmock -lgtest
/opt/apps/eb/software/binutils/2.42-GCCcore-13.3.0/bin/ld: /opt/apps/eb/software/googletest/1.15.2-GCCcore-13.3.0/lib64/libgmock.a(gmock-all.cc.o): in function `testing::InSequence::InSequence()':
gmock-all.cc:(.text+0xba5d): undefined reference to `pthread_getspecific'
/opt/apps/eb/software/binutils/2.42-GCCcore-13.3.0/bin/ld: gmock-all.cc:(.text+0xbad4): undefined reference to `pthread_setspecific'
/opt/apps/eb/software/binutils/2.42-GCCcore-13.3.0/bin/ld: gmock-all.cc:(.text+0xbb4a): undefined reference to `pthread_getspecific'
/opt/apps/eb/software/binutils/2.42-GCCcore-13.3.0/bin/ld: gmock-all.cc:(.text+0xbc45): undefined reference to `pthread_setspecific'
/opt/apps/eb/software/binutils/2.42-GCCcore-13.3.0/bin/ld: /opt/apps/eb/software/googletest/1.15.2-GCCcore-13.3.0/lib64/libgmock.a(gmock-all.cc.o): in function `testing::InSequence::~InSequence()':
gmock-all.cc:(.text+0xbd37): undefined reference to `pthread_getspecific'

@nd996 nd996 deleted the 20251002120413_new_pr_Parallel-Hashmap200 branch October 6, 2025 08:02
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