add patch for Python 3.13 to fix test failure that may occur when collecting performance profile for profile-guided optimization (PGO)

[boegel]

(created using eb --new-pr)

see also EESSI/software-layer#1227

Strictly speaking the same problem also exists for older Python versions, but only Python 3.13+ requires that the tests that are run to guide PGO are passing, see python/cpython#110295 .

[boegel]

@boegelbot please test @ jsc-zen3
CORE_CNT=16
EB_ARGS="--installpath /tmp/$USER/pr24189"

[boegelbot]

@boegel: 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=24189 EB_ARGS="--installpath /tmp/$USER/pr24189" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24189 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 8264

Test results coming soon (I hope)...

Details

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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).

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen3c3.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/45a3d3ad341269b63469855d1b2b0aaa for a full test report.

[bedroge]

Test report by @bedroge
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 25.04 (Plucky Puffin), x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.13.3
See https://gist.github.com/bedroge/b2f2719e3180b7eca596d9657716a3c6 for a full test report.

/home/bob/.local/easybuild/build/Python/3.13.1/GCCcore-14.2.0/Python-3.13.1/Python/condvar.h:74:(.text+0x2579e3): undefined reference to `__pthread_cond_timedwait64'

I also just tried the existing easyconfig, but that resulted in the same error, so this does not seem in any way related to this PR.

[boegel]

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node4210.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor (zen4), Python 3.9.21
See https://gist.github.com/boegel/8deb6614bfa64bdf2431fb9dce4b6597 for a full test report.

[bedroge]

Test report by @bedroge
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
interactive1 - Linux Rocky Linux 8.10, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.6.8
See https://gist.github.com/bedroge/d9d879af9a4ccc89473a7146d008a888 for a full test report.

[Micket]

lgtm

[boegel]

tested extensively in EESSI build environment via:

• {2025.06}[2025a] Python 3.13.1 EESSI/software-layer#1232
  which confirms that the problem that triggered me to figure this out is indeed fixed:
• build failure for Python 3.13 in EESSI 2025.06 due to missing __gcov_indirect_call for test_embed during profile-guided optimization EESSI/software-layer#1227