Apply updates to 2025.06 compatibility layer (`lmod`, `ca-certificates`, `modules`) by bedroge · Pull Request #239 · EESSI/compatibility-layer

bedroge · 2026-10-27T11:38:45Z

No description provided.

bedroge · 2026-10-27T11:39:02Z

bot: build repo:eessi.io-2026.06-compat instance:eessi-bot-mc-aws for:arch=x86_64/generic

eessi-bot-aws-disabled-20261110 · 2026-10-27T11:39:11Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2026.06-compat
Building on: generic
Building for: x86_64/generic
Job dir: /project/def-users/SHARED/jobs/2026.10/pr_239/217164

date	job status	comment
Oct 27 11:39:09 UTC 2026	submitted	job id `217164` awaits release by job manager
Oct 27 11:39:29 UTC 2026	released	job awaits launch by Slurm scheduler
Oct 27 11:44:55 UTC 2026	running	job `217164` is running
Oct 27 11:47:08 UTC 2026	finished	job id `217164` was cancelled
Oct 27 11:48:39 UTC 2026	finished	🤷 UNKNOWN (click triangle for detailed information) Job results file `_bot_job217164.result` does not exist in job directory or reading it failed. No artefacts were found/reported.
Oct 27 11:48:39 UTC 2026	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job217164.test` does not exist in job directory or reading it failed.

bedroge · 2026-10-27T11:47:04Z

bot:cancel jobid:217164

bedroge · 2026-10-27T11:47:21Z

bot: build repo:eessi.io-2026.06-compat instance:eessi-bot-mc-aws for:arch=x86_64/generic

eessi-bot-aws-disabled-20261110 · 2026-10-27T11:47:30Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2026.06-compat
Building on: generic
Building for: x86_64/generic
Job dir: /project/def-users/SHARED/jobs/2026.10/pr_239/217170

date	job status	comment
Oct 27 11:47:29 UTC 2026	submitted	job id `217170` awaits release by job manager
Oct 27 11:48:23 UTC 2026	released	job awaits launch by Slurm scheduler
Oct 27 11:50:11 UTC 2026	running	job `217170` is running
Oct 27 11:55:32 UTC 2026	finished	job id `217170` was cancelled
Oct 27 11:56:38 UTC 2026	finished	🤷 UNKNOWN (click triangle for detailed information) Job results file `_bot_job217170.result` does not exist in job directory or reading it failed. No artefacts were found/reported.
Oct 27 11:56:38 UTC 2026	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job217170.test` does not exist in job directory or reading it failed.

bedroge · 2026-10-27T11:55:29Z

bot:cancel jobid:217170

bedroge · 2026-10-27T12:00:40Z

bot: build repo:eessi.io-2025.06-compat instance:eessi-bot-mc-aws for:arch=x86_64/generic

eessi-bot-aws-disabled-20261110 · 2026-10-27T12:00:49Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-compat
Building on: generic
Building for: x86_64/generic
Job dir: /project/def-users/SHARED/jobs/2026.10/pr_239/217190

date	job status	comment
Oct 27 12:00:48 UTC 2026	submitted	job id `217190` awaits release by job manager
Oct 27 12:01:34 UTC 2026	released	job awaits launch by Slurm scheduler
Oct 27 12:03:19 UTC 2026	running	job `217190` is running
Oct 27 12:07:08 UTC 2026	finished	job id `217190` was cancelled
Oct 27 12:08:25 UTC 2026	finished	🤷 UNKNOWN (click triangle for detailed information) Job results file `_bot_job217190.result` does not exist in job directory or reading it failed. No artefacts were found/reported.
Oct 27 12:08:25 UTC 2026	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job217190.test` does not exist in job directory or reading it failed.

bedroge · 2026-10-27T12:07:04Z

bot:cancel jobid:217190

bedroge · 2026-10-27T12:07:24Z

bot: build repo:eessi.io-2025.06-compat instance:eessi-bot-mc-aws for:arch=x86_64/generic

eessi-bot-aws-disabled-20261110 · 2026-10-27T12:07:33Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-compat
Building on: generic
Building for: x86_64/generic
Job dir: /project/def-users/SHARED/jobs/2026.10/pr_239/217203

date	job status	comment
Oct 27 12:07:32 UTC 2026	submitted	job id `217203` awaits release by job manager
Oct 27 12:07:57 UTC 2026	released	job awaits launch by Slurm scheduler
Oct 27 12:09:47 UTC 2026	running	job `217203` is running
Oct 27 12:10:20 UTC 2026	finished	job id `217203` was cancelled
Oct 27 12:11:32 UTC 2026	finished	🤷 UNKNOWN (click triangle for detailed information) Job results file `_bot_job217203.result` does not exist in job directory or reading it failed. No artefacts were found/reported.
Oct 27 12:11:32 UTC 2026	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job217203.test` does not exist in job directory or reading it failed.

bedroge · 2026-10-27T12:10:17Z

bot:cancel jobid:217203

bedroge · 2026-10-27T12:14:13Z

bot: build repo:eessi.io-2025.06-compat instance:eessi-bot-mc-aws for:arch=x86_64/generic

eessi-bot-aws-disabled-20261110 · 2026-10-27T12:14:22Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-compat
Building on: generic
Building for: x86_64/generic
Job dir: /project/def-users/SHARED/jobs/2026.10/pr_239/217204

date	job status	comment
Oct 27 12:14:21 UTC 2026	submitted	job id `217204` awaits release by job manager
Oct 27 12:15:41 UTC 2026	released	job awaits launch by Slurm scheduler
Oct 27 12:17:43 UTC 2026	running	job `217204` is running
Oct 27 12:22:54 UTC 2026	finished	job id `217204` was cancelled
Oct 27 12:24:38 UTC 2026	finished	🤷 UNKNOWN (click triangle for detailed information) Job results file `_bot_job217204.result` does not exist in job directory or reading it failed. No artefacts were found/reported.
Oct 27 12:24:38 UTC 2026	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job217204.test` does not exist in job directory or reading it failed.

bedroge · 2026-10-27T12:22:50Z

bot:cancel jobid:217204

bedroge · 2026-10-27T12:57:21Z

bot: build repo:eessi.io-2025.06-compat instance:eessi-bot-mc-aws for:arch=x86_64/generic

eessi-bot-aws-disabled-20261110 · 2026-10-27T12:57:30Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-compat
Building on: generic
Building for: x86_64/generic
Job dir: /project/def-users/SHARED/jobs/2026.10/pr_239/217210

date	job status	comment
Oct 27 12:57:28 UTC 2026	submitted	job id `217210` awaits release by job manager
Oct 27 12:58:41 UTC 2026	released	job awaits launch by Slurm scheduler
Oct 27 13:00:22 UTC 2026	running	job `217210` is running
Oct 27 16:14:29 UTC 2026	finished	job id `217210` was cancelled
Oct 27 16:15:42 UTC 2026	finished	🤷 UNKNOWN (click triangle for detailed information) Job results file `_bot_job217210.result` does not exist in job directory or reading it failed. No artefacts were found/reported.
Oct 27 16:15:42 UTC 2026	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job217210.test` does not exist in job directory or reading it failed.

bedroge · 2026-10-27T16:14:25Z

bot:cancel jobid:217210

bedroge · 2026-10-27T16:14:36Z

bot: build repo:eessi.io-2025.06-compat instance:eessi-bot-mc-aws for:arch=x86_64/generic

eessi-bot-aws-disabled-20261110 · 2026-10-27T16:14:45Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-compat
Building on: generic
Building for: x86_64/generic
Job dir: /project/def-users/SHARED/jobs/2026.10/pr_239/217242

date	job status	comment
Oct 27 16:14:43 UTC 2026	submitted	job id `217242` awaits release by job manager
Oct 27 16:15:03 UTC 2026	released	job awaits launch by Slurm scheduler
Oct 27 16:17:06 UTC 2026	running	job `217242` is running
Oct 27 18:48:27 UTC 2026	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-217242.out` ✅ no task failed ✅ found tarball Artefacts `eessi-2025.06-compat-linux-x86_64-1793126589.tar.gz` size: 2038 MiB (2137714430 bytes) entries: 196351
Oct 27 18:48:27 UTC 2026	test result	😢 FAILURE (click triangle for details) Reason Failed for unknown reason Details ✅ job output file `slurm-217242.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

bedroge · 2026-10-27T19:14:27Z

bot: build repo:eessi.io-2025.06-compat instance:eessi-bot-mc-aws for:arch=aarch64/generic

eessi-bot-aws-disabled-20261110 · 2026-10-27T19:14:37Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-compat
Building on: generic
Building for: aarch64/generic
Job dir: /project/def-users/SHARED/jobs/2026.10/pr_239/217277

date	job status	comment
Oct 27 19:14:36 UTC 2026	submitted	job id `217277` awaits release by job manager
Oct 27 19:15:08 UTC 2026	released	job awaits launch by Slurm scheduler
Oct 27 19:16:22 UTC 2026	running	job `217277` is running
Oct 27 21:48:57 UTC 2026	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-217277.out` ✅ no task failed ✅ found tarball Artefacts `eessi-2025.06-compat-linux-aarch64-1793137363.tar.gz` size: 1981 MiB (2077467478 bytes) entries: 196348
Oct 27 21:48:57 UTC 2026	test result	😢 FAILURE (click triangle for details) Reason Failed for unknown reason Details ✅ job output file `slurm-217277.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

bedroge · 2026-10-27T19:16:43Z

bot: build repo:eessi.io-2025.06-compat instance:eessi-bot-riscv-prod for:arch=riscv64/generic

riscv-eessi-io-bot · 2026-10-27T19:16:56Z

New job on instance eessi-bot-riscv-prod for repository eessi.io-2025.06-compat
Building on: generic
Building for: riscv64/generic
Job dir: /home/eessibot/production/shared/jobs/2026.10/pr_239/330722

date	job status	comment
Oct 27 19:16:53 UTC 2026	submitted	job id `330722` awaits release by job manager
Oct 27 19:17:21 UTC 2026	released	job awaits launch by Slurm scheduler
Oct 27 19:18:26 UTC 2026	running	job `330722` is running
Oct 27 23:42:46 UTC 2026	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-330722.out` ❌ some task failed ✅ found tarball Artefacts `eessi-2025.06-compat-linux-riscv64-1793141620.tar.gz` size: 2077 MiB (2178839829 bytes) entries: 196215
Oct 27 23:42:46 UTC 2026	test result	😢 FAILURE (click triangle for details) Reason EESSI test suite was not run, test step itself failed to execute. Details ✅ job output file `slurm-330722.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

bedroge · 2026-10-27T19:44:51Z

Just to be sure that it hasn't made additional/unwanted changes, I've extracted the $EPREFIX/etc/portage dir from the tarball and ran a diff:

$ diff -ru 2025.06/compat/linux/x86_64/etc/portage/ /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/etc/portage/
diff -ru 2025.06/compat/linux/x86_64/etc/portage/repos.conf/eessi.conf /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/etc/portage/repos.conf/eessi.conf
--- 2025.06/compat/linux/x86_64/etc/portage/repos.conf/eessi.conf	2026-10-27 16:16:52.000000000 +0000
+++ /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/etc/portage/repos.conf/eessi.conf	2025-06-20 00:13:40.000000000 +0000
@@ -3,5 +3,3 @@
 location = /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/var/db/repos/eessi
 sync-type = git
 sync-uri = https://github.com/EESSI/gentoo-overlay.git
-sync-git-clone-extra-opts = --branch main
-auto-sync = False

That change is okay / as expected, used to pin our checkout to a specific commit. Also the $EPREFIX/etc/resolv.conf symlink still looks fine.

Also the packages have been updates (modules because it's part of the set, that was done in an earlier step):

TASK [compatibility_layer : Update already installed packages] *****************
changed: [localhost] => (item={'name': 'sys-cluster/lmod', 'version': '9.4.5'})
changed: [localhost] => (item={'name': 'app-misc/ca-certificates', 'version': '20260816.3.131.1', 'environment': {'PYTHON_COMPAT_NO_STRICT': 1}})
ok: [localhost] => (item={'name': 'modules', 'version': '5.7.0'})

So, lgtm!

….06_updates

bedroge · 2026-10-28T11:09:33Z

The RISC-V build failed to install ReFrame:

Failed to build polars-runtime-32

:stderr:   error: subprocess-exited-with-error
  
  × Building wheel for polars-runtime-32 (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [34 lines of output]
      Running `maturin pep517 build-wheel -i /tmp/reframe_venv/bin/python3 --compatibility off`
      🍹 Building a mixed python/rust project
      🐍 Found CPython 3.13 at /tmp/reframe_venv/bin/python3
      🔗 Found pyo3 bindings with abi3-py3.10 support
      error: rustc 1.85.0 is not supported by the following packages:
        ar_archive_writer@0.5.3 requires rustc 1.88.0
        crc-fast@1.10.0 requires rustc 1.89
        home@0.5.12 requires rustc 1.88
        icu_collections@2.3.0 requires rustc 1.88
        icu_locale_core@2.3.0 requires rustc 1.88
        icu_normalizer@2.3.0 requires rustc 1.88
        icu_normalizer_data@2.3.0 requires rustc 1.88
        icu_normalizer_data@2.3.0 requires rustc 1.88
        icu_normalizer_data@2.3.0 requires rustc 1.88
        icu_properties@2.3.0 requires rustc 1.88
        icu_properties_data@2.3.0 requires rustc 1.88
        icu_properties_data@2.3.0 requires rustc 1.88
        icu_properties_data@2.3.0 requires rustc 1.88
        icu_provider@2.3.0 requires rustc 1.88
        idna_adapter@1.2.2 requires rustc 1.86
        libloading@0.9.0 requires rustc 1.88.0
        psm@0.1.32 requires rustc 1.88.0
        psm@0.1.32 requires rustc 1.88.0
        psm@0.1.32 requires rustc 1.88.0
        simd-json@0.17.3 requires rustc 1.88
        sysinfo@0.39.6 requires rustc 1.95
      Either upgrade rustc or select compatible dependency versions with
      `cargo update <name>@<current-ver> --precise <compatible-ver>`
      where `<compatible-ver>` is the latest version supporting rustc 1.85.0

I've looked into similar failures before (see e.g. #222), but don't have a solution yet. Maybe we should simply skip the tests for RISC-V for these older versions.

bedroge · 2026-10-28T11:17:41Z

Trying one more time with an older ReFrame, that worked for 2026.06.

bot: build repo:eessi.io-2025.06-compat instance:eessi-bot-riscv-prod for:arch=riscv64/generic

riscv-eessi-io-bot · 2026-10-28T11:17:52Z

New job on instance eessi-bot-riscv-prod for repository eessi.io-2025.06-compat
Building on: generic
Building for: riscv64/generic
Job dir: /home/eessibot/production/shared/jobs/2026.10/pr_239/330892

date	job status	comment
Oct 28 11:17:50 UTC 2026	submitted	job id `330892` awaits release by job manager
Oct 28 11:18:11 UTC 2026	released	job awaits launch by Slurm scheduler
Oct 28 12:07:00 UTC 2026	running	job `330892` is running
Oct 28 16:55:11 UTC 2026	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-330892.out` ✅ no task failed ✅ found tarball Artefacts `eessi-2025.06-compat-linux-riscv64-1793194098.tar.gz` size: 2003 MiB (2100681726 bytes) entries: 196210
Oct 28 16:55:11 UTC 2026	test result	😢 FAILURE (click triangle for details) Reason Failed for unknown reason Details ✅ job output file `slurm-330892.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Oct 29 16:11:03 UTC 2026	uploaded	transfer of `eessi-2025.06-compat-linux-riscv64-1793194098.tar.gz` to S3 bucket succeeded

bedroge · 2026-10-29T07:52:13Z

bot: build repo:eessi.io-2025.06-compat instance:eessi-bot-mc-aws for:arch=x86_64/generic
bot: build repo:eessi.io-2025.06-compat instance:eessi-bot-mc-aws for:arch=aarch64/generic

eessi-bot-aws-disabled-20261110 · 2026-10-29T07:52:24Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-compat
Building on: generic
Building for: x86_64/generic
Job dir: /project/def-users/SHARED/jobs/2026.10/pr_239/218991

date	job status	comment
Oct 29 07:52:22 UTC 2026	submitted	job id `218991` awaits release by job manager
Oct 29 07:52:26 UTC 2026	released	job awaits launch by Slurm scheduler
Oct 29 07:53:33 UTC 2026	running	job `218991` is running
Oct 29 11:32:37 UTC 2026	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-218991.out` ✅ no task failed ✅ found tarball Artefacts `eessi-2025.06-compat-linux-x86_64-1793261303.tar.gz` size: 1964 MiB (2059955677 bytes) entries: 196343
Oct 29 11:32:37 UTC 2026	test result	😢 FAILURE (click triangle for details) Reason Failed for unknown reason Details ✅ job output file `slurm-218991.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Oct 29 16:09:55 UTC 2026	uploaded	transfer of `eessi-2025.06-compat-linux-x86_64-1793261303.tar.gz` to S3 bucket succeeded

eessi-bot-aws-disabled-20261110 · 2026-10-29T07:52:31Z

New job on instance eessi-bot-mc-aws for repository eessi.io-2025.06-compat
Building on: generic
Building for: aarch64/generic
Job dir: /project/def-users/SHARED/jobs/2026.10/pr_239/218992

date	job status	comment
Oct 29 07:52:29 UTC 2026	submitted	job id `218992` awaits release by job manager
Oct 29 07:53:30 UTC 2026	released	job awaits launch by Slurm scheduler
Oct 29 07:59:44 UTC 2026	running	job `218992` is running
Oct 29 11:43:16 UTC 2026	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-218992.out` ✅ no task failed ✅ found tarball Artefacts `eessi-2025.06-compat-linux-aarch64-1793262030.tar.gz` size: 1907 MiB (1999816451 bytes) entries: 196341
Oct 29 11:43:16 UTC 2026	test result	😢 FAILURE (click triangle for details) Reason Failed for unknown reason Details ✅ job output file `slurm-218992.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Oct 29 16:10:42 UTC 2026	uploaded	transfer of `eessi-2025.06-compat-linux-aarch64-1793262030.tar.gz` to S3 bucket succeeded

boegel · 2026-10-29T21:28:47Z

staging PR merged

bedroge · 2026-10-30T08:10:02Z

$ source /cvmfs/software.eessi.io/versions/2025.06/init/lmod/bash
Modules purged before initialising EESSI
Module for EESSI/2025.06 loaded successfully
EESSI has selected x86_64/intel/haswell as the compatible CPU target for EESSI/2025.06
EESSI did not identify an accelerator on the system
(for debug information when loading the EESSI module, set the environment variable EESSI_MODULE_DEBUG_INIT)

{EESSI/2025.06} $ ml --version

Modules based on Lua: Version 9.4.5 2026-10-13 12:08 +01:00
    https://lmod.readthedocs.io

{EESSI/2025.06} $ qlist -Iv ca-certificates
app-misc/ca-certificates-20260816.3.131.1

{EESSI/2025.06} $ source /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/usr/share/Modules/init/bash
{EESSI/2025.06} $ ml --version
Modules Release 5.7.0 (2026-09-21)

ocaisa

LGTM, ignoring all those CI lint warnings

bedroge added 4 commits October 27, 2026 12:32

combine steps into a single one, don't use force

859b12b

add default for prefix_update_packages

6460b7f

allow overriding env vars when updating packages

719990a

update lmod, ca-certificates, modules

a5610f3

bedroge added 2 commits October 27, 2026 12:43

fix indentation

e9ef9a7

use specific commit of EESSI/gentoo-overlay

7a57dce

use correct variable name

0c4a5c6

bedroge added 2 commits October 27, 2026 12:58

rename variable

f2f7afc

pass EESSI version to script

ae08841

use empty dict for variable that's expected to be a dict

cceb834

use force for older versions

b60c3bc

revert changes, doesn't seem to work

2635937

skip SoftwareCleanupTest in some cases

05c67fa

boegel added the 2025.06-software.eessi.io 2025.06 version of software.eessi.io label Oct 27, 2026

bedroge marked this pull request as ready for review October 27, 2026 22:22

Merge branch 'main' of github.com:EESSI/compatibility-layer into 2025…

1356cc2

….06_updates

bedroge changed the title ~~Apply updates to 2025.06 compatibility layer~~ Apply updates to 2025.06 compatibility layer (lmod, ca-certificates, modules) Oct 28, 2026

fix deprecation warning

57fbf9d

bedroge added 2 commits October 28, 2026 12:15

stick to reframe 4.9.3

2a973fd

don't always clone again

21c990e

bedroge added 2 commits October 28, 2026 12:24

make linter happy

7d83967

make linter happy

061549d

boegel added the bot:deploy Ask bot to deploy built tarballs for compat layer label Oct 29, 2026

ocaisa approved these changes Oct 30, 2026

View reviewed changes

ocaisa merged commit 235be00 into EESSI:main Oct 30, 2026
1 check passed

bedroge deleted the 2025.06_updates branch October 30, 2026 08:37

bedroge mentioned this pull request Oct 30, 2026

Update ca-certificates in 2023.06 compatibility layer #240

Merged

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