set JULIA_DEPOT_PATH in Julia easyconfigs with default value #17976

lexming · 2023-05-25T14:36:40Z

(created using eb --new-pr)

As reported in #17455, user depot should be the top entry in JULIA_DEPOT_PATH. This PR fixes that issue by simply setting JULIA_DEPOT_PATH to :, which is the default value with user's depot as top entry.

Having JULIA_DEPOT_PATH defined in the base Julia easyconfigs is needed for the changes in easybuilders/easybuild-easyblocks#2935 to fix #17961

lexming · 2023-05-25T14:52:24Z

@boegelbot: please test @ generoso

boegelbot · 2023-05-25T14:55:11Z

@lexming: Request for testing this PR well received on login1

PR test command 'EB_PR=17976 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17976 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10873

Test results coming soon (I hope)...

- notification for comment with ID 1563049751 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 · 2023-05-25T15:00:22Z

Test report by @boegelbot
SUCCESS
Build succeeded for 10 out of 10 (10 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/ef180f142967815ecbfe003c42c731c0 for a full test report.

lexming · 2023-05-26T11:36:33Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-05-26T11:37:08Z

@lexming: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=17976 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17976 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2668

Test results coming soon (I hope)...

- notification for comment with ID 1564258426 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 · 2023-05-26T11:40:05Z

Test report by @boegelbot
SUCCESS
Build succeeded for 10 out of 10 (10 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/0e4a2fff3b7fc1712aee896eb68707aa for a full test report.

exaexa · 2023-05-31T10:45:51Z

Hi all,
I just created #17995 which might be similar or straight out duplicated of this (didn't check the list properly, sorry).

One point to discuss: do we really want to point to the "shared" julia depots? Since 1.9.0 Julia will actually recompile much of the base packages anyway (depending on dependency updates etc), so I'd say that any attempts to push a package directory to it might be completely vain. The other concern is that the ..../share/julia directory that EB now points the depots to is not a proper julia depot and can't really be used for anything (at least on all Julia versions I tried).

And one note: I'm not sure if ~ in the configs here works as intended (especially for the history dir -- see the other PR).

Thanks!

Conflicts: easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb

lexming · 2023-07-07T23:26:15Z

@exaexa I checked your PR #17995 and as I commented there, entirely unsetting JULIA_DEPOT_PATH is not an option because then any other JuliaPackage loaded on top of Julia will reset the DEPOT_PATH and disable the user's depot.

I agree with you that using ~ is dangerous, so I simplified my approach by just setting JULIA_DEPOT_PATH to :. This is equivalent to use the default DEPOT_PATH and is compatible with loading JuliaPackages distributed with EasyBuild.

Let me know if this approach works for you.

lexming · 2023-07-07T23:28:43Z

@boegelbot: please test @ generoso

boegelbot · 2023-07-07T23:30:09Z

@lexming: Request for testing this PR well received on login1

PR test command 'EB_PR=17976 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17976 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11224

Test results coming soon (I hope)...

- notification for comment with ID 1626357996 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 · 2023-07-07T23:35:42Z

Test report by @boegelbot
SUCCESS
Build succeeded for 11 out of 11 (11 easyconfigs in total)
cns3 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/8a4f5f7066f923b6d8c30ac55c620e42 for a full test report.

…asyconfigs into 20230525163634_new_pr_Julia161

lexming · 2023-07-17T09:39:38Z

@boegelbot: please test @ generoso

boegelbot · 2023-07-17T09:45:12Z

@lexming: Request for testing this PR well received on login1

PR test command 'EB_PR=17976 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17976 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11256

Test results coming soon (I hope)...

- notification for comment with ID 1637704075 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 · 2023-07-17T09:51:17Z

Test report by @boegelbot
SUCCESS
Build succeeded for 12 out of 12 (12 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/0e63558493555f31846b01c61c64380f for a full test report.

lexming · 2023-07-17T09:53:32Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-07-17T09:57:08Z

@lexming: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=17976 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17976 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2998

Test results coming soon (I hope)...

- notification for comment with ID 1637739029 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 · 2023-07-17T10:00:18Z

Test report by @boegelbot
SUCCESS
Build succeeded for 12 out of 12 (12 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/6aa5f7868100cf46978034c1b17b415c for a full test report.

branfosj · 2023-07-17T12:35:19Z

Test report by @branfosj
SUCCESS
Build succeeded for 12 out of 12 (12 easyconfigs in total)
bear-pg0105u03a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/5ce7226cec7a9240b112197fbc33dd99 for a full test report.

branfosj · 2023-07-17T12:36:53Z

Going in, thanks @lexming!

set user depot ~/.julia as top entry in JULIA_DEPOT_PATH

b427b48

lexming added the bug fix label May 25, 2023

boegel added this to the release after 4.7.2 milestone May 26, 2023

exaexa mentioned this pull request May 31, 2023

[Julia-1.8.5] Prevent setting environment that breaks Julia #17995

Closed

boegel changed the title ~~set user depot ~/.julia as top entry in JULIA_DEPOT_PATH~~ set user depot ~/.julia as top entry in $JULIA_DEPOT_PATH Jun 7, 2023

boegel modified the milestones: 4.8.0, release after 4.8.0 Jul 6, 2023

lexming added 2 commits July 8, 2023 01:07

set JULIA_DEPOT_PATH with default value

149cdfd

Merge branch 'develop' into 20230525163634_new_pr_Julia161

d006be1

Conflicts: easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb

lexming changed the title ~~set user depot ~/.julia as top entry in $JULIA_DEPOT_PATH~~ set JULIA_DEPOT_PATH in Julia easyconfigs with default value Jul 7, 2023

lexming added 2 commits July 17, 2023 11:37

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

155aec7

…asyconfigs into 20230525163634_new_pr_Julia161

set JULIA_DEPOT_PATH with default value in Julia v1.9.2

59176b1

branfosj approved these changes Jul 17, 2023

View reviewed changes

branfosj merged commit e371b23 into easybuilders:develop Jul 17, 2023

lexming deleted the 20230525163634_new_pr_Julia161 branch July 17, 2023 12:37

lexming mentioned this pull request Jul 21, 2023

Julia: user depot not accessible with Pkg.add #17455

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set JULIA_DEPOT_PATH in Julia easyconfigs with default value #17976

set JULIA_DEPOT_PATH in Julia easyconfigs with default value #17976

lexming commented May 25, 2023 •

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set JULIA_DEPOT_PATH in Julia easyconfigs with default value #17976

set JULIA_DEPOT_PATH in Julia easyconfigs with default value #17976

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