prevent GObject-Introspection from setting EB-filtered environment variables by bedroge · Pull Request #646 · EESSI/software-layer

bedroge · 2024-07-19T11:32:46Z

This should properly fix #196. Instead of fixing it in all the packages that use GObject-Introspection to compile stuff, it changes GObject-Introspection itself and makes sure that it doesn't set $LD_LIBRARY_PATH (or any other variable) when EB is configured to filter it.

I initially checked in the hook if EB was configured to filter $LD_LIBRARY_PATH and then used one of the following sed commands:

# always sets runtime_path_envvar = []
sed -i "s/runtime_path_envvar = .* \(if not.*\)/runtime_path_envvar = [] \1/g"

and

# only remove $LD_LIBRARY_PATH from the list
sed -i "s/\(runtime_path_envvar = .*\)\('LD_LIBRARY_PATH', \)\(.*\)/\1\3/g"

But in the end I went for another solution (which I found a bit cleaner, though the sed command is a bit longer/more complex), which is always applied by the hook, but changes the original line:

`runtime_path_envvar = ['LD_LIBRARY_PATH', 'DYLD_FALLBACK_LIBRARY_PATH'] if not lib_dirs_envvar else [lib_dirs_envvar]`

to

            runtime_path_envvar = ['LD_LIBRARY_PATH', 'DYLD_FALLBACK_LIBRARY_PATH'] if not lib_dirs_envvar else [lib_dirs_envvar]
            runtime_path_envvar =  [x for x in runtime_path_envvar if not x in os.environ.get('EASYBUILD_FILTER_ENV_VARS', '').split(',')]

I.e. it will remove items from that list if they're also in $EASYBUILD_FILTER_ENV_VARS. Note that this may not always work outside of EESSI, e.g. someone could pass this list via a CLI argument instead of an environment variable. But for EESSI it should always work as we do use an environment variable.

I've tested this interactively and both GObject-Introspection itself installed without issues, but also the affected packages Pango, at-spi2-core, and GTK worked fine. I'll trigger some (re)builds here to verify this.

…rom being set if EB filters them

eessi-bot · 2024-07-19T11:32:50Z

Instance eessi-bot-mc-aws is configured to build for:

architectures: x86_64/generic, x86_64/intel/haswell, x86_64/intel/skylake_avx512, x86_64/amd/zen2, x86_64/amd/zen3, aarch64/generic, aarch64/neoverse_n1, aarch64/neoverse_v1
repositories: eessi.io-2023.06-compat, eessi-hpc.org-2023.06-software, eessi-hpc.org-2023.06-compat, eessi.io-2023.06-software

eessi-bot · 2024-07-19T11:32:50Z

Instance eessi-bot-mc-azure is configured to build for:

architectures: x86_64/amd/zen4
repositories: eessi-hpc.org-2023.06-compat, eessi-hpc.org-2023.06-software, eessi.io-2023.06-software, eessi.io-2023.06-compat

bedroge · 2024-07-19T11:52:33Z

bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3

eessi-bot · 2024-07-19T11:52:35Z

Updates by the bot instance eessi-bot-mc-aws (click for details)

received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3 from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- submitted job 14729, for details & status see prevent GObject-Introspection from setting EB-filtered environment variables #646 (comment)

eessi-bot · 2024-07-19T11:52:36Z

Updates by the bot instance eessi-bot-mc-azure (click for details)

received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3 from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- no jobs were submitted

eessi-bot · 2024-07-19T11:52:40Z

New job on instance eessi-bot-mc-aws for architecture x86_64-amd-zen3 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.07/pr_646/14729

date	job status	comment
Jul 19 11:52:39 UTC 2024	submitted	job id `14729` awaits release by job manager
Jul 19 11:53:25 UTC 2024	released	job awaits launch by Slurm scheduler
Jul 19 11:58:27 UTC 2024	running	job `14729` is running
Jul 19 12:11:40 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-14729.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-x86_64-amd-zen3-1721390463.tar.gz` size: 7 MiB (8249093 bytes) entries: 673 modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all `GObject-Introspection/1.74.0-GCCcore-12.2.0.lua` `GObject-Introspection/1.76.1-GCCcore-12.3.0.lua` `GObject-Introspection/1.78.1-GCCcore-13.2.0.lua` software under 2023.06/software/linux/x86_64/amd/zen3/software `GObject-Introspection/1.74.0-GCCcore-12.2.0` `GObject-Introspection/1.76.1-GCCcore-12.3.0` `GObject-Introspection/1.78.1-GCCcore-13.2.0` other under 2023.06/software/linux/x86_64/amd/zen3 `2023.06/init/easybuild/eb_hooks.py`
Jul 19 12:11:40 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 14/14 test case(s) from 14 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-14729.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eb_hooks.py

Co-authored-by: ocaisa <alan.ocais@cecam.org>

…re-layer into gobject_introspection_fix

bedroge · 2024-07-19T12:40:17Z

bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3

eessi-bot · 2024-07-19T12:40:20Z

Updates by the bot instance eessi-bot-mc-aws (click for details)

received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3 from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- submitted job 14730, for details & status see prevent GObject-Introspection from setting EB-filtered environment variables #646 (comment)

eessi-bot · 2024-07-19T12:40:20Z

Updates by the bot instance eessi-bot-mc-azure (click for details)

received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3 from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- no jobs were submitted

eessi-bot · 2024-07-19T12:40:24Z

New job on instance eessi-bot-mc-aws for architecture x86_64-amd-zen3 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.07/pr_646/14730

date	job status	comment
Jul 19 12:40:24 UTC 2024	submitted	job id `14730` awaits release by job manager
Jul 19 12:40:45 UTC 2024	released	job awaits launch by Slurm scheduler
Jul 19 12:41:47 UTC 2024	running	job `14730` is running
Jul 19 12:56:15 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-14730.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-x86_64-amd-zen3-1721393092.tar.gz` size: 11 MiB (11664497 bytes) entries: 1562 modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all `at-spi2-core/2.46.0-GCCcore-12.2.0.lua` `at-spi2-core/2.49.91-GCCcore-12.3.0.lua` `GObject-Introspection/1.74.0-GCCcore-12.2.0.lua` `GObject-Introspection/1.76.1-GCCcore-12.3.0.lua` `GObject-Introspection/1.78.1-GCCcore-13.2.0.lua` software under 2023.06/software/linux/x86_64/amd/zen3/software `at-spi2-core/2.46.0-GCCcore-12.2.0` `at-spi2-core/2.49.91-GCCcore-12.3.0` `GObject-Introspection/1.74.0-GCCcore-12.2.0` `GObject-Introspection/1.76.1-GCCcore-12.3.0` `GObject-Introspection/1.78.1-GCCcore-13.2.0` other under 2023.06/software/linux/x86_64/amd/zen3 `2023.06/init/easybuild/eb_hooks.py`
Jul 19 12:56:15 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 14/14 test case(s) from 14 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-14730.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

bedroge · 2024-07-19T12:42:47Z

bot: build repo:eessi.io-2023.06-software arch:aarch64/generic

eessi-bot · 2024-07-19T12:42:50Z

Updates by the bot instance eessi-bot-mc-aws (click for details)

received bot command build repo:eessi.io-2023.06-software arch:aarch64/generic from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/generic
handling command build repository:eessi.io-2023.06-software architecture:aarch64/generic resulted in:
- submitted job 14731, for details & status see prevent GObject-Introspection from setting EB-filtered environment variables #646 (comment)

eessi-bot · 2024-07-19T12:42:50Z

Updates by the bot instance eessi-bot-mc-azure (click for details)

received bot command build repo:eessi.io-2023.06-software arch:aarch64/generic from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/generic
handling command build repository:eessi.io-2023.06-software architecture:aarch64/generic resulted in:
- no jobs were submitted

eessi-bot · 2024-07-19T12:42:54Z

New job on instance eessi-bot-mc-aws for architecture aarch64-generic for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.07/pr_646/14731

date	job status	comment
Jul 19 12:42:53 UTC 2024	submitted	job id `14731` awaits release by job manager
Jul 19 12:43:49 UTC 2024	released	job awaits launch by Slurm scheduler
Jul 19 12:44:52 UTC 2024	running	job `14731` is running
Jul 19 13:20:40 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-14731.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-aarch64-generic-1721393683.tar.gz` size: 54 MiB (57002685 bytes) entries: 5825 modules under 2023.06/software/linux/aarch64/generic/modules/all `ATK/2.38.0-GCCcore-13.2.0.lua` `at-spi2-atk/2.38.0-GCCcore-13.2.0.lua` `at-spi2-core/2.46.0-GCCcore-12.2.0.lua` `at-spi2-core/2.49.91-GCCcore-12.3.0.lua` `at-spi2-core/2.50.0-GCCcore-13.2.0.lua` `FriBidi/1.0.13-GCCcore-13.2.0.lua` `Gdk-Pixbuf/2.42.10-GCCcore-13.2.0.lua` `GObject-Introspection/1.74.0-GCCcore-12.2.0.lua` `GObject-Introspection/1.76.1-GCCcore-12.3.0.lua` `GObject-Introspection/1.78.1-GCCcore-13.2.0.lua` `GTK3/3.24.39-GCCcore-13.2.0.lua` `libepoxy/1.5.10-GCCcore-13.2.0.lua` `Pango/1.51.0-GCCcore-13.2.0.lua` software under 2023.06/software/linux/aarch64/generic/software `ATK/2.38.0-GCCcore-13.2.0` `at-spi2-atk/2.38.0-GCCcore-13.2.0` `at-spi2-core/2.46.0-GCCcore-12.2.0` `at-spi2-core/2.49.91-GCCcore-12.3.0` `at-spi2-core/2.50.0-GCCcore-13.2.0` `FriBidi/1.0.13-GCCcore-13.2.0` `Gdk-Pixbuf/2.42.10-GCCcore-13.2.0` `GObject-Introspection/1.74.0-GCCcore-12.2.0` `GObject-Introspection/1.76.1-GCCcore-12.3.0` `GObject-Introspection/1.78.1-GCCcore-13.2.0` `GTK3/3.24.39-GCCcore-13.2.0` `libepoxy/1.5.10-GCCcore-13.2.0` `Pango/1.51.0-GCCcore-13.2.0` other under 2023.06/software/linux/aarch64/generic `2023.06/init/easybuild/eb_hooks.py`
Jul 19 13:20:40 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 14/14 test case(s) from 14 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-14731.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

bedroge · 2024-07-19T12:43:57Z

I've (temporarily) added Pango and GTK3 to the 2023b easystack (they were failing in #644), just to test if they can be built without issues. If they do, I'll remove them again.

bedroge · 2024-07-19T13:20:54Z

All the builds were successful, so I've reverted the commit that added Pango and GTK3. This is now ready for a final review, and I'll start builds for all targets.

bedroge · 2024-07-19T13:24:19Z

bot: build repo:eessi.io-2023.06-software arch:aarch64/generic
bot: build repo:eessi.io-2023.06-software arch:aarch64/neoverse_n1
bot: build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1
bot: build repo:eessi.io-2023.06-software arch:x86_64/generic
bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen2
bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3
bot: build repo:eessi.io-2023.06-software arch:x86_64/intel/haswell
bot: build repo:eessi.io-2023.06-software arch:x86_64/intel/skylake_avx512

eessi-bot · 2024-07-19T13:24:22Z

Updates by the bot instance eessi-bot-mc-aws (click for details)

received bot command build repo:eessi.io-2023.06-software arch:aarch64/generic from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/generic
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_n1 from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
received bot command build repo:eessi.io-2023.06-software arch:x86_64/generic from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/generic
received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen2 from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2
received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3 from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3
received bot command build repo:eessi.io-2023.06-software arch:x86_64/intel/haswell from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell
received bot command build repo:eessi.io-2023.06-software arch:x86_64/intel/skylake_avx512 from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/intel/skylake_avx512
handling command build repository:eessi.io-2023.06-software architecture:aarch64/generic resulted in:
- submitted job 14735, for details & status see prevent GObject-Introspection from setting EB-filtered environment variables #646 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1 resulted in:
- submitted job 14736, for details & status see prevent GObject-Introspection from setting EB-filtered environment variables #646 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- submitted job 14737, for details & status see prevent GObject-Introspection from setting EB-filtered environment variables #646 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/generic resulted in:
- submitted job 14738, for details & status see prevent GObject-Introspection from setting EB-filtered environment variables #646 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2 resulted in:
- submitted job 14739, for details & status see prevent GObject-Introspection from setting EB-filtered environment variables #646 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- submitted job 14740, for details & status see prevent GObject-Introspection from setting EB-filtered environment variables #646 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell resulted in:
- submitted job 14741, for details & status see prevent GObject-Introspection from setting EB-filtered environment variables #646 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/skylake_avx512 resulted in:
- submitted job 14742, for details & status see prevent GObject-Introspection from setting EB-filtered environment variables #646 (comment)

eessi-bot · 2024-07-19T13:24:22Z

Updates by the bot instance eessi-bot-mc-azure (click for details)

received bot command build repo:eessi.io-2023.06-software arch:aarch64/generic from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/generic
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_n1 from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
received bot command build repo:eessi.io-2023.06-software arch:x86_64/generic from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/generic
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- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2
received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3 from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3
received bot command build repo:eessi.io-2023.06-software arch:x86_64/intel/haswell from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell
received bot command build repo:eessi.io-2023.06-software arch:x86_64/intel/skylake_avx512 from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/intel/skylake_avx512
handling command build repository:eessi.io-2023.06-software architecture:aarch64/generic resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1 resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:x86_64/generic resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2 resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/skylake_avx512 resulted in:
- no jobs were submitted

eessi-bot · 2024-07-19T13:24:25Z

New job on instance eessi-bot-mc-aws for architecture aarch64-generic for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.07/pr_646/14735

date	job status	comment
Jul 19 13:24:25 UTC 2024	submitted	job id `14735` awaits release by job manager
Jul 19 13:24:43 UTC 2024	released	job awaits launch by Slurm scheduler
Jul 19 13:25:59 UTC 2024	running	job `14735` is running
Jul 19 13:54:54 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-14735.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-aarch64-generic-1721395748.tar.gz` size: 11 MiB (11537321 bytes) entries: 1562 modules under 2023.06/software/linux/aarch64/generic/modules/all `at-spi2-core/2.46.0-GCCcore-12.2.0.lua` `at-spi2-core/2.49.91-GCCcore-12.3.0.lua` `GObject-Introspection/1.74.0-GCCcore-12.2.0.lua` `GObject-Introspection/1.76.1-GCCcore-12.3.0.lua` `GObject-Introspection/1.78.1-GCCcore-13.2.0.lua` software under 2023.06/software/linux/aarch64/generic/software `at-spi2-core/2.46.0-GCCcore-12.2.0` `at-spi2-core/2.49.91-GCCcore-12.3.0` `GObject-Introspection/1.74.0-GCCcore-12.2.0` `GObject-Introspection/1.76.1-GCCcore-12.3.0` `GObject-Introspection/1.78.1-GCCcore-13.2.0` other under 2023.06/software/linux/aarch64/generic `2023.06/init/easybuild/eb_hooks.py`
Jul 19 13:54:54 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 14/14 test case(s) from 14 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-14735.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Jul 19 14:20:27 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-aarch64-generic-1721395748.tar.gz` to S3 bucket succeeded

eessi-bot · 2024-07-19T13:24:29Z

New job on instance eessi-bot-mc-aws for architecture aarch64-neoverse_n1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.07/pr_646/14736

date	job status	comment
Jul 19 13:24:28 UTC 2024	submitted	job id `14736` awaits release by job manager
Jul 19 13:24:45 UTC 2024	released	job awaits launch by Slurm scheduler
Jul 19 13:29:07 UTC 2024	running	job `14736` is running
Jul 19 13:59:00 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-14736.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-aarch64-neoverse_n1-1721395999.tar.gz` size: 11 MiB (11555873 bytes) entries: 1562 modules under 2023.06/software/linux/aarch64/neoverse_n1/modules/all `at-spi2-core/2.46.0-GCCcore-12.2.0.lua` `at-spi2-core/2.49.91-GCCcore-12.3.0.lua` `GObject-Introspection/1.74.0-GCCcore-12.2.0.lua` `GObject-Introspection/1.76.1-GCCcore-12.3.0.lua` `GObject-Introspection/1.78.1-GCCcore-13.2.0.lua` software under 2023.06/software/linux/aarch64/neoverse_n1/software `at-spi2-core/2.46.0-GCCcore-12.2.0` `at-spi2-core/2.49.91-GCCcore-12.3.0` `GObject-Introspection/1.74.0-GCCcore-12.2.0` `GObject-Introspection/1.76.1-GCCcore-12.3.0` `GObject-Introspection/1.78.1-GCCcore-13.2.0` other under 2023.06/software/linux/aarch64/neoverse_n1 `2023.06/init/easybuild/eb_hooks.py`
Jul 19 13:59:00 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 14/14 test case(s) from 14 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-14736.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Jul 19 14:20:47 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-aarch64-neoverse_n1-1721395999.tar.gz` to S3 bucket succeeded

eessi-bot · 2024-07-19T13:24:33Z

New job on instance eessi-bot-mc-aws for architecture aarch64-neoverse_v1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.07/pr_646/14737

date	job status	comment
Jul 19 13:24:32 UTC 2024	submitted	job id `14737` awaits release by job manager
Jul 19 13:24:47 UTC 2024	released	job awaits launch by Slurm scheduler
Jul 19 13:29:09 UTC 2024	running	job `14737` is running
Jul 19 13:50:45 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-14737.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-aarch64-neoverse_v1-1721395965.tar.gz` size: 11 MiB (11552407 bytes) entries: 1562 modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all `at-spi2-core/2.46.0-GCCcore-12.2.0.lua` `at-spi2-core/2.49.91-GCCcore-12.3.0.lua` `GObject-Introspection/1.74.0-GCCcore-12.2.0.lua` `GObject-Introspection/1.76.1-GCCcore-12.3.0.lua` `GObject-Introspection/1.78.1-GCCcore-13.2.0.lua` software under 2023.06/software/linux/aarch64/neoverse_v1/software `at-spi2-core/2.46.0-GCCcore-12.2.0` `at-spi2-core/2.49.91-GCCcore-12.3.0` `GObject-Introspection/1.74.0-GCCcore-12.2.0` `GObject-Introspection/1.76.1-GCCcore-12.3.0` `GObject-Introspection/1.78.1-GCCcore-13.2.0` other under 2023.06/software/linux/aarch64/neoverse_v1 `2023.06/init/easybuild/eb_hooks.py`
Jul 19 13:50:45 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 14/14 test case(s) from 14 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-14737.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Jul 19 14:21:09 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-aarch64-neoverse_v1-1721395965.tar.gz` to S3 bucket succeeded

eessi-bot · 2024-07-19T13:24:37Z

New job on instance eessi-bot-mc-aws for architecture x86_64-generic for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.07/pr_646/14738

date	job status	comment
Jul 19 13:24:36 UTC 2024	submitted	job id `14738` awaits release by job manager
Jul 19 13:24:51 UTC 2024	released	job awaits launch by Slurm scheduler
Jul 19 13:30:20 UTC 2024	running	job `14738` is running
Jul 19 13:48:36 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-14738.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-x86_64-generic-1721396102.tar.gz` size: 11 MiB (11661122 bytes) entries: 1562 modules under 2023.06/software/linux/x86_64/generic/modules/all `at-spi2-core/2.46.0-GCCcore-12.2.0.lua` `at-spi2-core/2.49.91-GCCcore-12.3.0.lua` `GObject-Introspection/1.74.0-GCCcore-12.2.0.lua` `GObject-Introspection/1.76.1-GCCcore-12.3.0.lua` `GObject-Introspection/1.78.1-GCCcore-13.2.0.lua` software under 2023.06/software/linux/x86_64/generic/software `at-spi2-core/2.46.0-GCCcore-12.2.0` `at-spi2-core/2.49.91-GCCcore-12.3.0` `GObject-Introspection/1.74.0-GCCcore-12.2.0` `GObject-Introspection/1.76.1-GCCcore-12.3.0` `GObject-Introspection/1.78.1-GCCcore-13.2.0` other under 2023.06/software/linux/x86_64/generic `2023.06/init/easybuild/eb_hooks.py`
Jul 19 13:48:36 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 14/14 test case(s) from 14 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-14738.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Jul 19 14:21:29 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-generic-1721396102.tar.gz` to S3 bucket succeeded

eessi-bot · 2024-07-19T13:24:41Z

New job on instance eessi-bot-mc-aws for architecture x86_64-amd-zen2 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.07/pr_646/14739

date	job status	comment
Jul 19 13:24:40 UTC 2024	submitted	job id `14739` awaits release by job manager
Jul 19 13:24:49 UTC 2024	released	job awaits launch by Slurm scheduler
Jul 19 13:30:16 UTC 2024	running	job `14739` is running
Jul 19 13:48:35 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-14739.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-x86_64-amd-zen2-1721396152.tar.gz` size: 11 MiB (11665057 bytes) entries: 1562 modules under 2023.06/software/linux/x86_64/amd/zen2/modules/all `at-spi2-core/2.46.0-GCCcore-12.2.0.lua` `at-spi2-core/2.49.91-GCCcore-12.3.0.lua` `GObject-Introspection/1.74.0-GCCcore-12.2.0.lua` `GObject-Introspection/1.76.1-GCCcore-12.3.0.lua` `GObject-Introspection/1.78.1-GCCcore-13.2.0.lua` software under 2023.06/software/linux/x86_64/amd/zen2/software `at-spi2-core/2.46.0-GCCcore-12.2.0` `at-spi2-core/2.49.91-GCCcore-12.3.0` `GObject-Introspection/1.74.0-GCCcore-12.2.0` `GObject-Introspection/1.76.1-GCCcore-12.3.0` `GObject-Introspection/1.78.1-GCCcore-13.2.0` other under 2023.06/software/linux/x86_64/amd/zen2 `2023.06/init/easybuild/eb_hooks.py`
Jul 19 13:48:35 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 14/14 test case(s) from 14 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-14739.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Jul 19 14:21:48 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-amd-zen2-1721396152.tar.gz` to S3 bucket succeeded

eessi-bot · 2024-07-19T13:24:45Z

New job on instance eessi-bot-mc-aws for architecture x86_64-amd-zen3 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.07/pr_646/14740

date	job status	comment
Jul 19 13:24:44 UTC 2024	submitted	job id `14740` awaits release by job manager
Jul 19 13:25:53 UTC 2024	released	job awaits launch by Slurm scheduler
Jul 19 13:27:02 UTC 2024	running	job `14740` is running
Jul 19 13:40:42 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-14740.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-x86_64-amd-zen3-1721395800.tar.gz` size: 11 MiB (11662002 bytes) entries: 1562 modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all `at-spi2-core/2.46.0-GCCcore-12.2.0.lua` `at-spi2-core/2.49.91-GCCcore-12.3.0.lua` `GObject-Introspection/1.74.0-GCCcore-12.2.0.lua` `GObject-Introspection/1.76.1-GCCcore-12.3.0.lua` `GObject-Introspection/1.78.1-GCCcore-13.2.0.lua` software under 2023.06/software/linux/x86_64/amd/zen3/software `at-spi2-core/2.46.0-GCCcore-12.2.0` `at-spi2-core/2.49.91-GCCcore-12.3.0` `GObject-Introspection/1.74.0-GCCcore-12.2.0` `GObject-Introspection/1.76.1-GCCcore-12.3.0` `GObject-Introspection/1.78.1-GCCcore-13.2.0` other under 2023.06/software/linux/x86_64/amd/zen3 `2023.06/init/easybuild/eb_hooks.py`
Jul 19 13:40:42 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 14/14 test case(s) from 14 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-14740.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Jul 19 14:20:07 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-amd-zen3-1721395800.tar.gz` to S3 bucket succeeded

eessi-bot · 2024-07-19T13:24:48Z

New job on instance eessi-bot-mc-aws for architecture x86_64-intel-haswell for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.07/pr_646/14741

date	job status	comment
Jul 19 13:24:48 UTC 2024	submitted	job id `14741` awaits release by job manager
Jul 19 13:25:54 UTC 2024	released	job awaits launch by Slurm scheduler
Jul 19 13:31:28 UTC 2024	running	job `14741` is running
Jul 19 13:49:41 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-14741.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-x86_64-intel-haswell-1721396165.tar.gz` size: 11 MiB (11666252 bytes) entries: 1562 modules under 2023.06/software/linux/x86_64/intel/haswell/modules/all `at-spi2-core/2.46.0-GCCcore-12.2.0.lua` `at-spi2-core/2.49.91-GCCcore-12.3.0.lua` `GObject-Introspection/1.74.0-GCCcore-12.2.0.lua` `GObject-Introspection/1.76.1-GCCcore-12.3.0.lua` `GObject-Introspection/1.78.1-GCCcore-13.2.0.lua` software under 2023.06/software/linux/x86_64/intel/haswell/software `at-spi2-core/2.46.0-GCCcore-12.2.0` `at-spi2-core/2.49.91-GCCcore-12.3.0` `GObject-Introspection/1.74.0-GCCcore-12.2.0` `GObject-Introspection/1.76.1-GCCcore-12.3.0` `GObject-Introspection/1.78.1-GCCcore-13.2.0` other under 2023.06/software/linux/x86_64/intel/haswell `2023.06/init/easybuild/eb_hooks.py`
Jul 19 13:49:41 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 14/14 test case(s) from 14 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-14741.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Jul 19 14:22:09 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-intel-haswell-1721396165.tar.gz` to S3 bucket succeeded

eessi-bot · 2024-07-19T13:24:52Z

New job on instance eessi-bot-mc-aws for architecture x86_64-intel-skylake_avx512 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.07/pr_646/14742

date	job status	comment
Jul 19 13:24:51 UTC 2024	submitted	job id `14742` awaits release by job manager
Jul 19 13:25:57 UTC 2024	released	job awaits launch by Slurm scheduler
Jul 19 13:31:30 UTC 2024	running	job `14742` is running
Jul 19 13:47:29 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-14742.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-x86_64-intel-skylake_avx512-1721396096.tar.gz` size: 11 MiB (11652475 bytes) entries: 1562 modules under 2023.06/software/linux/x86_64/intel/skylake_avx512/modules/all `at-spi2-core/2.46.0-GCCcore-12.2.0.lua` `at-spi2-core/2.49.91-GCCcore-12.3.0.lua` `GObject-Introspection/1.74.0-GCCcore-12.2.0.lua` `GObject-Introspection/1.76.1-GCCcore-12.3.0.lua` `GObject-Introspection/1.78.1-GCCcore-13.2.0.lua` software under 2023.06/software/linux/x86_64/intel/skylake_avx512/software `at-spi2-core/2.46.0-GCCcore-12.2.0` `at-spi2-core/2.49.91-GCCcore-12.3.0` `GObject-Introspection/1.74.0-GCCcore-12.2.0` `GObject-Introspection/1.76.1-GCCcore-12.3.0` `GObject-Introspection/1.78.1-GCCcore-13.2.0` other under 2023.06/software/linux/x86_64/intel/skylake_avx512 `2023.06/init/easybuild/eb_hooks.py`
Jul 19 13:47:29 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 14/14 test case(s) from 14 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-14742.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Jul 19 14:22:28 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-intel-skylake_avx512-1721396096.tar.gz` to S3 bucket succeeded

bedroge · 2024-07-19T13:26:58Z

Note that we shouldn't build for zen4 here, since it doesn't have all these versions (yet). It doesn't even have GCC 12.2.0 at all. I'll open a similar PR specifically for zen4.

ocaisa

Great work!

bedroge · 2024-07-19T14:23:05Z

Staging PRs shouldn't be merged yet, I'll use a manual ingestion procedure to make sure that the old installations are removed first:

cvmfs_server transaction software.eessi.io

rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/aarch64/generic/software/at-spi2-core
rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/aarch64/generic/software/GObject-Introspection

rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/aarch64/neoverse_n1/software/at-spi2-core
rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/aarch64/neoverse_n1/software/GObject-Introspection

rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/aarch64/neoverse_v1/software/at-spi2-core
rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/aarch64/neoverse_v1/software/GObject-Introspection

rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/generic/software/at-spi2-core
rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/generic/software/GObject-Introspection

rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/at-spi2-core
rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/GObject-Introspection

rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/skylake_avx512/software/at-spi2-core
rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/skylake_avx512/software/GObject-Introspection

rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen2/software/at-spi2-core
rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen2/software/GObject-Introspection

rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen3/software/at-spi2-core
rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen3/software/GObject-Introspection

cd /cvmfs/software.eessi.io/versions

tar -xzf /srv/tmp/tarballs/eessi-2023.06-software-linux-aarch64-generic-1721395748.tar.gz
tar -xzf /srv/tmp/tarballs/eessi-2023.06-software-linux-aarch64-neoverse_n1-1721395999.tar.gz
tar -xzf /srv/tmp/tarballs/eessi-2023.06-software-linux-aarch64-neoverse_v1-1721395965.tar.gz
tar -xzf /srv/tmp/tarballs/eessi-2023.06-software-linux-x86_64-generic-1721396102.tar.gz
tar -xzf /srv/tmp/tarballs/eessi-2023.06-software-linux-x86_64-amd-zen2-1721396152.tar.gz
tar -xzf /srv/tmp/tarballs/eessi-2023.06-software-linux-x86_64-amd-zen3-1721395800.tar.gz
tar -xzf /srv/tmp/tarballs/eessi-2023.06-software-linux-x86_64-intel-haswell-1721396165.tar.gz
tar -xzf /srv/tmp/tarballs/eessi-2023.06-software-linux-x86_64-intel-skylake_avx512-1721396096.tar.gz

cd

cvmfs_server diff --worktree software.eessi.io > PR646-diff.txt
cvmfs_server publish -m "rebuilds of GObject-Introspection and at-spi2-core, PR 646" software.eessi.io

bedroge · 2024-07-19T14:58:57Z

Manual ingestion has been done, we can now safely merge (or close) the staging PRs.

add a hook for GObject-Introspection that prevents environment vars f…

8a2eca3

…rom being set if EB filters them

rebuild all GObject-Introspection versions to apply new hook

62c1f7d

ocaisa reviewed Jul 19, 2024

View reviewed changes

eb_hooks.py Outdated Show resolved Hide resolved

ocaisa reviewed Jul 19, 2024

View reviewed changes

eb_hooks.py Outdated Show resolved Hide resolved

bedroge and others added 4 commits July 19, 2024 13:58

fix comment

6277bc3

Co-authored-by: ocaisa <alan.ocais@cecam.org>

remove the at-spi2-core hook

5593999

rebuild at-spi2-core with the rebuilt GObject-Introspection

46a9c85

Merge branch 'gobject_introspection_fix' of github.com:bedroge/softwa…

013e181

…re-layer into gobject_introspection_fix

bedroge force-pushed the gobject_introspection_fix branch from 9d3e5a3 to 013e181 Compare July 19, 2024 13:09

bedroge changed the title ~~[WIP] prevent GObject-Introspection from setting EB-filtered environment variables~~ prevent GObject-Introspection from setting EB-filtered environment variables Jul 19, 2024

bedroge added bug Something isn't working 2023.06-software.eessi.io 2023.06 version of software.eessi.io labels Jul 19, 2024

bedroge requested a review from ocaisa July 19, 2024 13:23

bedroge mentioned this pull request Jul 19, 2024

{zen4} prevent GObject-Introspection from setting EB-filtered environment variables #647

Merged

ocaisa approved these changes Jul 19, 2024

View reviewed changes

ocaisa added the bot:deploy Ask bot to deploy missing software installations to EESSI label Jul 19, 2024

bedroge mentioned this pull request Jul 19, 2024

{2023.06}[2023a] Paraver 4.11.4 #570

Merged

ocaisa merged commit efd3ad1 into EESSI:2023.06-software.eessi.io Jul 19, 2024

bedroge deleted the gobject_introspection_fix branch July 19, 2024 18:32

ocaisa mentioned this pull request Jul 22, 2024

Issues lurking with gobject-introspection #196

Closed

ocaisa mentioned this pull request Aug 21, 2024

{2023.06,a64fx}[foss/2023a] R-bundle-CRAN v2023.12 #680

Closed

Neves-P mentioned this pull request Aug 23, 2024

Rebuild GObject-Introspection/1.76.1-GCCcore-12.3.0 for A64FX #683

Merged

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