enhance `JuliaPackage` easyblock to avoid writing to `$HOME` & clean up `JuliaBundle` by Flamefire · Pull Request #4102 · easybuilders/easybuild-easyblocks

Flamefire · 2026-04-01T14:44:19Z

(created using eb --new-pr)

Some easyconfigs have sanity check commands that run e.g. julia -e ...

This will use the $JULIA_DEPOT_PATH set in the module which is something like :/foo:/bar where the leading colon means "including the user depot": https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH

That will write artifacts/cache files to $HOME/.julia or fail if that's not writable.

Similar to PythonPackage/PythonBundle use a temporary directory for that and end with a trailing colon for "excluding the user depot."

Additionally some empty methods on Juliabundle can be removed

…iaBundle

Flamefire · 2026-04-01T17:04:17Z

Test report by @Flamefire

Overview of tested easyconfigs (in order)

SUCCESS Circuitscape-5.12.3-Julia-1.9.2.eb
FAIL RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb (build issue)
(partial log available at https://gist.github.com/Flamefire/03cea4930daf40ee7031beee49666fa1)
SUCCESS Circuitscape-5.12.3-Julia-1.7.2.eb

Build succeeded for 2 out of 3 (total: 1 hour 12 mins 55 secs) (3 easyconfigs in total)
i7140 - Linux Rocky Linux 9.6, x86_64, AMD EPYC 7702 64-Core Processor (zen2), Python 3.9.21
See https://gist.github.com/Flamefire/d5fcfa06e0bfd1bbdfa15bf0e3ef2c6c for a full test report.

Flamefire · 2026-04-02T06:32:03Z

The only failure above is from a test failing due to German locale: "Warnung != Warning"
Fix in easybuilders/easybuild-easyconfigs#25666

boegel · 2026-04-08T14:35:30Z

@lexming Can you take a look at this?

…d_module` & cache results

Crivella · 2026-04-29T15:13:57Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--installpath=/tmp/ebpr-4102 IJulia-1.24.2-Julia-1.10.3.eb IJulia-1.23.3-Julia-1.6.7.eb IJulia-1.29.0-Julia-1.11.6.eb IJulia-1.24.0-Julia-1.8.5.eb Suppressor-0.2.4-Julia-1.9.2.eb Circuitscape-5.12.3-Julia-1.7.2.eb Circuitscape-5.12.3-Julia-1.9.2.eb RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb"

Crivella · 2026-04-29T15:24:48Z

Can confirm that with this PR neither ~/.julia is touched, nor you get a double compilation of packages under the install directory due to running Pkg.test in the sanity check commands

crivella@crivella-desktop:~$ cd .local/easybuild/software/Clearwood_stiffness_model/0.1.0-Julia-1.12.2
crivella@crivella-desktop:~/.local/easybuild/software/Clearwood_stiffness_model/0.1.0-Julia-1.12.2$ ls compiled/v1.12/Adapt
rUIgN_NQeV1.ji  rUIgN_NQeV1.so
crivella@crivella-desktop:~/.local/easybuild/software/Clearwood_stiffness_model/0.1.0-Julia-1.12.2$ ls ~/.julia
ls: cannot access '/home/crivella/.julia': No such file or directory
crivella@crivella-desktop:~/.local/easybuild/software/Clearwood_stiffness_model/0.1.0-Julia-1.12.2$

Test report by @Crivella

Overview of tested easyconfigs (in order)

SUCCESS Clearwood_stiffness_model-0.1.0-Julia-1.12.2.eb

Build succeeded for 1 out of 1 (total: 10 mins 0 secs) (1 easyconfigs in total)
crivella-desktop - Linux Ubuntu 22.04.5 LTS (Jammy Jellyfish), x86_64, 13th Gen Intel(R) Core(TM) i9-13900K (skylake), Python 3.11.14
See https://gist.github.com/Crivella/38f4d9e8d6378c1cb391182476f3c2bc for a full test report.

boegelbot · 2026-04-29T15:33:12Z

@Crivella: 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=4102 EB_ARGS="--installpath=/tmp/ebpr-4102 IJulia-1.24.2-Julia-1.10.3.eb IJulia-1.23.3-Julia-1.6.7.eb IJulia-1.29.0-Julia-1.11.6.eb IJulia-1.24.0-Julia-1.8.5.eb Suppressor-0.2.4-Julia-1.9.2.eb Circuitscape-5.12.3-Julia-1.7.2.eb Circuitscape-5.12.3-Julia-1.9.2.eb RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb" EB_CONTAINER= EB_REPO=easybuild-easyblocks EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_4102 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 10329

Test results coming soon (I hope)...

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Flamefire · 2026-04-29T15:57:42Z

I'm currently invetigating why the sanity check of Circuitscape/5.12.3-Julia-1.9.2 fails. Not sure if this is introduced by this or was there before.

boegelbot · 2026-04-29T16:48:26Z

Test report by @boegelbot

Overview of tested easyconfigs (in order)

FAIL IJulia-1.24.2-Julia-1.10.3.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/4e07aadf7df3367fc6625255d744eba4)
FAIL IJulia-1.23.3-Julia-1.6.7.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/1262b44bc7dc41f0434b05ded004e46b)
SUCCESS IJulia-1.29.0-Julia-1.11.6.eb
FAIL IJulia-1.24.0-Julia-1.8.5.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/0b72866a2ebc3d3d9fb9515ad7477545)
SUCCESS Suppressor-0.2.4-Julia-1.9.2.eb
FAIL Circuitscape-5.12.3-Julia-1.7.2.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/1d514660c0d0b43f976d66382746b608)
FAIL Circuitscape-5.12.3-Julia-1.9.2.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/4f366edf767ed663eac807d342ddc3e5)
FAIL RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/ea4ebbaa00d5608130a68b52bf9fb6f7)

Build succeeded for 2 out of 8 (total: 1 hour 14 mins 49 secs) (8 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.25
See https://gist.github.com/boegelbot/6ed33711b9b47d8e2591877581dd8ace for a full test report.

Crivella · 2026-05-01T08:08:44Z

Test report by @Crivella

Overview of tested easyconfigs (in order)

SUCCESS Clearwood_stiffness_model-0.1.0-Julia-1.12.2.eb

Build succeeded for 1 out of 1 (total: 9 mins 5 secs) (1 easyconfigs in total)
crivella-desktop - Linux Ubuntu 22.04.5 LTS (Jammy Jellyfish), x86_64, 13th Gen Intel(R) Core(TM) i9-13900K (skylake), Python 3.11.14
See https://gist.github.com/Crivella/ea92cb4b64ff929b6f8cc29d4cf6628e for a full test report.

Co-authored-by: Davide Grassano <34096612+Crivella@users.noreply.github.com>

Flamefire · 2026-05-01T08:26:04Z

mod_filepath = self.mod_filepath
AttributeError: 'JuliaPackage' object has no attribute 'mod_filepath'

That one is very weird: self.mod_filepath is set in the constructor/__init__

Looks like something else is off, seen that before when doing testing, but it disappeared. And now it's back again.
Will do some more investigation next week. Putting this on hold until then

Crivella · 2026-05-01T08:30:54Z

That one is very weird: self.mod_filepath is set in the constructor/init

Looks like something else is off, seen that before when doing testing, but it disappeared. And now it's back again.
Will do some more investigation next week. Putting this on hold until then

I assume it is coming from some extra stuff you have in framework (eg maybe you are on top of easybuilders/easybuild-framework#5185 ?)

I tested one of them on my workstation with develop as the framework branch and it works normally

Crivella · 2026-05-01T08:45:43Z

In ExtensionEasyblock the init of Easyblock is not always called

https://github.com/easybuilders/easybuild-framework/blob/632d4d24ca91f19077aaa52c52020791d82596a3/easybuild/framework/extensioneasyblock.py#L72-L100

Flamefire · 2026-05-01T08:54:01Z

True, I'm trying to always use all my open PRs in one tree for all builds so I detect issues. So indeed that PR was the cause: In some intermediate version I had an inverted condition in this (now fixed up) commit easybuilders/easybuild-framework@5ace95d
Basically: module creating in an extension doesn't work (and doesn't need to)

The job must have started before I applied that fix back on the cluster

Crivella · 2026-05-01T09:29:19Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--installpath=/tmp/ebpr-4102 IJulia-1.24.2-Julia-1.10.3.eb IJulia-1.23.3-Julia-1.6.7.eb IJulia-1.29.0-Julia-1.11.6.eb IJulia-1.24.0-Julia-1.8.5.eb Suppressor-0.2.4-Julia-1.9.2.eb Circuitscape-5.12.3-Julia-1.7.2.eb Circuitscape-5.12.3-Julia-1.9.2.eb RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb"

boegelbot · 2026-05-01T09:33:08Z

@Crivella: 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=4102 EB_ARGS="--installpath=/tmp/ebpr-4102 IJulia-1.24.2-Julia-1.10.3.eb IJulia-1.23.3-Julia-1.6.7.eb IJulia-1.29.0-Julia-1.11.6.eb IJulia-1.24.0-Julia-1.8.5.eb Suppressor-0.2.4-Julia-1.9.2.eb Circuitscape-5.12.3-Julia-1.7.2.eb Circuitscape-5.12.3-Julia-1.9.2.eb RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb" EB_CONTAINER= EB_REPO=easybuild-easyblocks EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_4102 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 10337

Test results coming soon (I hope)...

Details

- notification for comment with ID 4358702055 processed

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 · 2026-05-01T10:46:37Z

Test report by @boegelbot

Overview of tested easyconfigs (in order)

SUCCESS IJulia-1.24.2-Julia-1.10.3.eb
SUCCESS IJulia-1.23.3-Julia-1.6.7.eb
SUCCESS IJulia-1.29.0-Julia-1.11.6.eb
SUCCESS IJulia-1.24.0-Julia-1.8.5.eb
SUCCESS Suppressor-0.2.4-Julia-1.9.2.eb
SUCCESS Circuitscape-5.12.3-Julia-1.7.2.eb
SUCCESS Circuitscape-5.12.3-Julia-1.9.2.eb
FAIL RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb (build issue)
(partial log available at https://gist.github.com/boegelbot/60bdd755677ff2041beb32f9cc64490d)

Build succeeded for 7 out of 8 (total: 1 hour 13 mins 11 secs) (8 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.25
See https://gist.github.com/boegelbot/9960322651eee1f2c0af30ca38b2ba2b for a full test report.

Flamefire · 2026-05-01T10:56:14Z

FAIL RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb (build issue)
(partial log available at gist.github.com/boegelbot/60bdd755677ff2041beb32f9cc64490d)

That is caused by not listing all required packages, so an actual bug in the easyconfig we didn't catch before setting "offline" in the sanity check and hence the missing package was downloaded.
I have a fix for that but couldn't test it yet, due to the previous issue here with missing installdir

Crivella · 2026-05-01T11:14:46Z

We could probably also double check the other ECs with

Add functions to generate exts_list for a JuliaBundle starting from a Manifest.toml #4121

NOTE: It seems that AxisArrays is a weak (optional) dependency of RCall, but RCall's test suite does not skip/disable the test using it.

I am wondering if we should allow downloads for testing, right now we would need to install the test dependencies together with the normal ones.

In this case AxisArrays is also an optional deps so it would be fine but i do not think it is impossible to have a dep that is used only for testing

Flamefire · 2026-05-04T07:23:30Z

FAIL RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb (build issue)
(partial log available at gist.github.com/boegelbot/60bdd755677ff2041beb32f9cc64490d)

That is caused by not listing all required packages, so an actual bug in the easyconfig we didn't catch before setting "offline" in the sanity check and hence the missing package was downloaded. I have a fix for that but couldn't test it yet, due to the previous issue here with missing installdir

Fix in easybuilders/easybuild-easyconfigs#25903

We could probably also double check the other ECs with

As a good proxy we can run them as test reports for this PR. If the (now offline) sanity checks succeed there is a high chance they are complete.

NOTE: It seems that AxisArrays is a weak (optional) dependency of RCall, but RCall's test suite does not skip/disable the test using it.

I am wondering if we should allow downloads for testing, right now we would need to install the test dependencies together with the normal ones.

In this case AxisArrays is also an optional deps so it would be fine but i do not think it is impossible to have a dep that is used only for testing

If I understand the code directly it is not only for testing but an optional dependency allowing additional features. When they are not used nothing breaks. Only the tests assume they are available.
So IMO adding that is fine. Otherwise we'd need to disable those tests somehow.

Enabling downloads wouldn't be a good solution IMO. We already spend quite some time elsewhere in EasyBuild to allow fully offline builds.

Flamefire · 2026-05-04T11:42:16Z

Test report by @Flamefire

Overview of tested easyconfigs (in order)

SUCCESS Suppressor-0.2.4-Julia-1.9.2.eb
SUCCESS Julia-1.12.2.eb
SUCCESS Julia-1.11.7.eb
SUCCESS Julia-1.11.5.eb
SUCCESS Pluto-0.20.13-Julia-1.11.5.eb
FAIL PySR-1.5.8-gfbf-2024a.eb (build issue)
(partial log available at https://gist.github.com/Flamefire/d8ee9ddce37110b877cf4f5664db0db8)
SUCCESS IJulia-1.24.0-Julia-1.8.5.eb
SUCCESS IJulia-1.23.3-Julia-1.6.7.eb
SUCCESS IJulia-1.24.2-Julia-1.10.3.eb
SUCCESS IJulia-1.29.0-Julia-1.11.6.eb
SUCCESS Circuitscape-5.12.3-Julia-1.7.2.eb
SUCCESS Circuitscape-5.12.3-Julia-1.9.2.eb
SUCCESS RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb
SUCCESS ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb

Build succeeded for 13 out of 14 (total: 4 hours 17 mins 16 secs) (13 easyconfigs in total)
i7014 - Linux Rocky Linux 9.6, x86_64, AMD EPYC 7702 64-Core Processor (zen2), Python 3.9.21
See https://gist.github.com/Flamefire/f87390042a32ddd673a9ab411afa4b5c for a full test report.

Flamefire · 2026-05-04T13:42:29Z

PySR is tricky: It is a PythonBundle that uses some Julia stuff.

Added a fix in easybuilders/easybuild-easyconfigs#25909 that avoids the writes to $HOME in the sanity check.
Would be better if it had a dependency on the required Julia package(s?) instead/additionally so it doesn't download stuff in exts_filter, but works "enough" for now.

Crivella · 2026-05-05T08:40:00Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--buildpath=/tmp/ebpr-4102/build --installpath=/tmp/ebpr-4102/install --from-pr 25903,25909 RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb PySR-1.5.8-gfbf-2024a.eb"

boegelbot · 2026-05-05T08:53:09Z

@Crivella: 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=4102 EB_ARGS="--buildpath=/tmp/ebpr-4102/build --installpath=/tmp/ebpr-4102/install --from-pr 25903,25909 RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb PySR-1.5.8-gfbf-2024a.eb" EB_CONTAINER= EB_REPO=easybuild-easyblocks EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_4102 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 10355

Test results coming soon (I hope)...

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Message to humans: this is just bookkeeping information for me,
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Crivella · 2026-05-05T11:16:23Z

Test report for #4102 (comment) in the EC PR

Add missing (optional) dependencies to RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb easybuild-easyconfigs#25903 (comment)

Crivella · 2026-05-05T11:30:31Z

PySR is tricky: It is a PythonBundle that uses some Julia stuff.

Added a fix in easybuilders/easybuild-easyconfigs#25909 that avoids the writes to $HOME in the sanity check.
Would be better if it had a dependency on the required Julia package(s?) instead/additionally so it doesn't download stuff in exts_filter, but works "enough" for now.

This begs the question if we should always set JULIA_DEPOT_PATH to a tmpdir when Julia is a dependency.
Any package could depend on Julia and use it under the hood to do stuff which will end up producing artifacts in the user home

Flamefire · 2026-05-05T11:31:53Z

This begs the question if we should always set JULIA_DEPOT_PATH to a tmpdir when Julia is a dependency.
Any package could depend on Julia and use it under the hood to do stuff which will end up producing artifacts in the user home

This fits into the discussion of setting Python and Cargo variables in framework where the same applies

Flamefire added 4 commits April 1, 2026 16:44

Update JuliaPackage easyblock to avoid writing to $HOME & cleanup Jul…

0d31f6e

…iaBundle

Remove old method

bf4e97f

Make tmpdir creation lazy

9cddef3

Remove variable

ed67a9e

Flamefire mentioned this pull request Apr 2, 2026

Fix locale-dependent test failure in RCall 0.13.17 easybuilders/easybuild-easyconfigs#25666

Merged

1 task

boegel changed the title ~~Update JuliaPackage easyblock to avoid writing to $HOME & cleanup JuliaBundle~~ enhance JuliaPackage easyblock to avoid writing to $HOME & clean up JuliaBundle Apr 8, 2026

boegel added the enhancement label Apr 8, 2026

boegel added this to the release after 5.3.0 milestone Apr 8, 2026

Crivella requested changes Apr 28, 2026

View reviewed changes

Comment thread easybuild/easyblocks/generic/juliapackage.py Outdated

Comment thread easybuild/easyblocks/generic/juliapackage.py

Crivella requested changes Apr 28, 2026

View reviewed changes

Comment thread easybuild/easyblocks/generic/juliapackage.py Outdated

Flamefire and others added 4 commits April 28, 2026 18:08

Remove debug print

19e9487

Use prepare_julia_env instead of setting JULIA_DEPOT_PATH in `loa…

8b12a83

…d_module` & cache results

Use temporary folder as first folderin load_module

acae9a5

Disable downloads in load_module

b56cb13

Fix use of list of paths

7cf6413

Flamefire force-pushed the 20260401164416_new_pr_juliabundle branch from 08a7ece to 7cf6413 Compare April 29, 2026 15:20

Crivella requested changes Apr 29, 2026

View reviewed changes

Comment thread easybuild/easyblocks/generic/juliapackage.py

Keep installdir when cleaning DEPOT_PATH

ec598af

Crivella reviewed May 1, 2026

View reviewed changes

Comment thread easybuild/easyblocks/generic/juliapackage.py Outdated

Crivella reviewed May 1, 2026

View reviewed changes

Comment thread easybuild/easyblocks/generic/juliapackage.py

Apply suggestion from @Crivella

7faac3b

Co-authored-by: Davide Grassano <34096612+Crivella@users.noreply.github.com>

Flamefire marked this pull request as draft May 1, 2026 08:26

Flamefire marked this pull request as ready for review May 1, 2026 08:50

Keep installdir when cleaning LOAD_PATH

125342a

Flamefire force-pushed the 20260401164416_new_pr_juliabundle branch from 1b06f4e to 125342a Compare May 4, 2026 07:16

Flamefire mentioned this pull request May 4, 2026

Add missing (optional) dependencies to RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb easybuilders/easybuild-easyconfigs#25903

Merged

Flamefire mentioned this pull request May 4, 2026

Avoid writes to $HOME in sanity checks of PySR-1.5.8-gfbf-2024a.eb easybuilders/easybuild-easyconfigs#25909

Open

Crivella mentioned this pull request May 5, 2026

JuliaPackage can't really work with depedencies #4123

Open

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