use clean_dir instead of remove_dir on installation directory in custom easyblock for Amber (+ AmberTools)

[smoors]

(created using eb --new-pr)

requires:

• add clean_dir function, use it to try to empty install dir if removing it fails easybuild-framework#4932

[smoors]

Test report by @smoors

Overview of tested easyconfigs (in order)

• SUCCESS AmberTools-24.10-foss-2024a.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
node601.hydra.os - Linux Rocky Linux 9.6, x86_64, AMD EPYC 9384X 32-Core Processor (zen4), Python 3.9.21
See https://gist.github.com/smoors/e84c2d6803da0d680af1b693a351ce37 for a full test report.

[boegel]

lgtm

[boegel]

@boegelbot please test @ jsc-zen3
CORE_CNT=16
EB_ARGS="--installpath /tmp/boegelbot/pr3935 AmberTools-25.2-foss-2025a.eb"

[boegelbot]

@boegel: 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=3935 EB_ARGS="--installpath /tmp/boegelbot/pr3935 AmberTools-25.2-foss-2025a.eb" EB_CONTAINER= EB_REPO=easybuild-easyblocks EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_3935 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 10055

Test results coming soon (I hope)...

Details

- notification for comment with ID 4090279387 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]

Test report by @boegelbot

Overview of tested easyconfigs (in order)

• FAIL AmberTools-25.2-foss-2025a.eb (build issue)
  (partial log available at https://gist.github.com/boegelbot/74b4ff6090ed8e138312aef4bbeb83ce)

Build succeeded for 0 out of 1 (total: 1 min 30 secs) (1 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/dea70ec5b4fbce4bcf97b911f76fdd8f for a full test report.

edit: failed with:

NoInternetAccess: Cannot connect to https://ambermd.org
Preparing to apply specific updates... please wait.

[boegel]

@smoors Can you sync this with develop after merge of #4093, and also submit a test report with Amber?

[smoors]

Test report by @smoors

Overview of tested easyconfigs (in order)

• SUCCESS AmberTools-25.2-foss-2025a.eb

Build succeeded for 1 out of 1 (total: 2 hours 8 mins 26 secs) (1 easyconfigs in total)
node604.hydra.os - Linux Rocky Linux 9.7, x86_64, AMD EPYC 9384X 32-Core Processor (zen4), Python 3.9.25
See https://gist.github.com/smoors/056ca4e432b7b7b666180d45b319f3e3 for a full test report.

[smoors]

Test report by @smoors

Overview of tested easyconfigs (in order)

• FAIL Amber-24.3-foss-2025a-CUDA-12.8.0-pmemd.eb (build issue)
  (partial log available at https://gist.github.com/smoors/cccb89ac801a194279b901a66e977e89)

Build succeeded for 0 out of 1 (total: 8 mins 43 secs) (1 easyconfigs in total)
node407.hydra.os - Linux Rocky Linux 9.7, x86_64, AMD EPYC 7282 16-Core Processor (zen2), 1 x NVIDIA NVIDIA A100-PCIE-40GB, 590.48.01, Python 3.9.25
See https://gist.github.com/smoors/2b59b0bed0174c24b72c5b61a148e48c for a full test report.

(out of memory)

[smoors]

Test report by @smoors

Overview of tested easyconfigs (in order)

• SUCCESS Amber-24.3-foss-2025a-CUDA-12.8.0-pmemd.eb

Build succeeded for 1 out of 1 (total: 44 mins 10 secs) (1 easyconfigs in total)
node404.hydra.os - Linux Rocky Linux 9.7, x86_64, AMD EPYC 7282 16-Core Processor (zen2), 1 x NVIDIA NVIDIA A100-PCIE-40GB, 590.48.01, Python 3.9.25
See https://gist.github.com/smoors/57dfef3f926c59fe90a51173168a1504 for a full test report.

[boegel]

@boegelbot please test @ jsc-zen3
CORE_CNT=16
EB_ARGS="--installpath /tmp/boegelbot/pr3935 AmberTools-25.2-foss-2025a.eb"

[boegelbot]

@boegel: 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=3935 EB_ARGS="--installpath /tmp/boegelbot/pr3935 AmberTools-25.2-foss-2025a.eb" EB_CONTAINER= EB_REPO=easybuild-easyblocks EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_3935 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 10095

Test results coming soon (I hope)...

Details

- notification for comment with ID 4132628968 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]

Test report by @boegelbot

Overview of tested easyconfigs (in order)

• SUCCESS AmberTools-25.2-foss-2025a.eb

Build succeeded for 1 out of 1 (total: 1 hour 48 mins 42 secs) (1 easyconfigs in total)
jsczen3c4.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/7b00607b096bac082a644adfe5bb2fa1 for a full test report.