Skip to content

fix postinstallcmds in shovill easyconfigs#17279

Merged
lexming merged 1 commit intoeasybuilders:developfrom
Flamefire:fix-shovill-ecs
Feb 11, 2023
Merged

fix postinstallcmds in shovill easyconfigs#17279
lexming merged 1 commit intoeasybuilders:developfrom
Flamefire:fix-shovill-ecs

Conversation

@Flamefire
Copy link
Copy Markdown
Contributor

@Flamefire Flamefire commented Feb 9, 2023 •
edited
Loading

  • Create the script containing the (unexpanded) $EBROOT* variables.
  • Quote string to be echoed to make it easier to read and avoid the escaping

Extracted from #11149

$ cat software/shovill/1.1.0-gompi-2021b/bin/{pilon,trimmomatic}
exec java -jar "$EBROOTPILON"/pilon-*.jar "$@"
exec java -jar "$EBROOTTRIMMOMATIC"/trimmomatic-*.jar "$@"

@jfgrimm @boegel

@Flamefire
Fix shovill postinstallcmds
5f1e8df 
- Create the script containing the (unexpanded) $EBROOT* variables.
- Quote string to be echoed to make it easier to read and avoid the escaping
@Flamefire Flamefire mentioned this pull request Feb 9, 2023
Merged
1 task
@Flamefire Flamefire marked this pull request as ready for review February 9, 2023 15:44
@Flamefire
Copy link
Copy Markdown
Contributor Author

Flamefire commented Feb 9, 2023

Test report by @Flamefire
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
taurusi6403.taurus.hrsk.tu-dresden.de - Linux RHEL 7.9, x86_64, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz (haswell), Python 2.7.5
See https://gist.github.com/affc8dafd48f91aa5c86dc0ade1b73bb for a full test report.

@jfgrimm jfgrimm added this to the 4.x milestone Feb 9, 2023
@jfgrimm
Copy link
Copy Markdown
Member

jfgrimm commented Feb 9, 2023

Test report by @jfgrimm
FAILED
Build succeeded for 44 out of 51 (3 easyconfigs in total)
himem06.pri.viking.alces.network - Linux CentOS Linux 7.9.2009, x86_64, Intel(R) Xeon(R) Platinum 8160 CPU @ 2.10GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/b9ff7d7d00a18ffeeff71932002b5d53 for a full test report.

@Flamefire
Copy link
Copy Markdown
Contributor Author

Flamefire commented Feb 9, 2023

@jfgrimm I noticed URLs for MEGAHIT and Velvet have changed (see Slack) and downloaded them manually. Might be worth fixing the ECs but as I don't have the old archives I couldn't compare them. Installation did work though.

@boegel boegel added the bug fix label Feb 9, 2023
@boegel boegel modified the milestones: 4.x, next release (4.7.1?) Feb 9, 2023
@boegel boegel changed the title Fix shovill postinstallcmds fix postinstallcmds in shovill easyconfigs Feb 10, 2023
@lexming
Copy link
Copy Markdown
Contributor

lexming commented Feb 11, 2023

@boegelbot: please test @ generoso
EB_ARGS="shovill-1.1.0-gompi-2021b.eb"

@boegelbot
Copy link
Copy Markdown
Collaborator

boegelbot commented Feb 11, 2023

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

PR test command 'EB_PR=17279 EB_ARGS="shovill-1.1.0-gompi-2021b.eb" EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17279 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 10211

Test results coming soon (I hope)...

Details

- notification for comment with ID 1426701005 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
Copy link
Copy Markdown
Collaborator

boegelbot commented Feb 11, 2023

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/f935bdac86b6b6c36f8c32226a382fd0 for a full test report.

@lexming
Copy link
Copy Markdown
Contributor

lexming commented Feb 11, 2023

Test report by @lexming
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node306.hydra.os - Linux CentOS Linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, Python 3.6.8
See https://gist.github.com/a087afea8d5d8622d800f733826285c6 for a full test report.

lexming
lexming approved these changes Feb 11, 2023
View reviewed changes
Copy link
Copy Markdown
Contributor

@lexming lexming left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM

@lexming
Copy link
Copy Markdown
Contributor

lexming commented Feb 11, 2023

Going in, thanks @Flamefire !

@lexming lexming merged commit b54598f into easybuilders:develop Feb 11, 2023
@Flamefire Flamefire deleted the fix-shovill-ecs branch February 11, 2023 14:00
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@lexming lexming lexming approved these changes

Assignees

No one assigned

Labels

bug fix

Projects

None yet

Milestone

4.7.1

Development

Successfully merging this pull request may close these issues.

5 participants

@Flamefire @jfgrimm @lexming @boegelbot @boegel