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Micromamba activate error fix#66

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jo-basevi merged 1 commit intomainfrom
test-micromamba-activate-fix
Apr 17, 2026
Merged

Micromamba activate error fix#66
jo-basevi merged 1 commit intomainfrom
test-micromamba-activate-fix

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@jo-basevi jo-basevi commented Apr 17, 2026

Currently micromamba issue is happening at build time when creating module inserts, and failing to run micromamba activate

@jo-basevi jo-basevi temporarily deployed to Gadi Prerelease April 17, 2026 03:06 — with GitHub Actions Inactive
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Same error:

info     libmamba ****************** Backtrace Start ******************
debug    libmamba Loading configuration
trace    libmamba Compute configurable 'create_base'
trace    libmamba Compute configurable 'no_env'
trace    libmamba Compute configurable 'no_rc'
trace    libmamba Compute configurable 'rc_files'
trace    libmamba Compute configurable 'root_prefix'
critical libmamba Could not use default root_prefix "/home/srv/**/.local/share/mamba": Directory exists, is not empty and not a conda prefix. Please set explicitly `MAMBA_ROOT_PREFIX` to "/home/srv/**/.local/share/mamba" to skip this error.
info     libmamba ****************** Backtrace End ********************

Will try setting MAMBA_ROOT_PREFIX to avoid defaulting to $HOME directory.

@jo-basevi jo-basevi force-pushed the test-micromamba-activate-fix branch from 8940bd8 to d391675 Compare April 17, 2026 03:30
@jo-basevi jo-basevi temporarily deployed to Gadi Prerelease April 17, 2026 03:31 — with GitHub Actions Inactive
@jo-basevi jo-basevi temporarily deployed to Gadi Prerelease April 17, 2026 03:50 — with GitHub Actions Inactive
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jo-basevi commented Apr 17, 2026

Setting MAMBA_ROOT_PREFIX seems to solve the issue. I noticed MAMBA_ROOT_PREFIX is also now needed for the tests.

I've copied the generated tar file for the payu/dev build (/g/data/vk83/testing/admin/conda_containers/prerelease/staging/conda_base.payu-dev.tar) and confirmed that the module file insert has been generated.

Succesful workflow pbs logs:

# Build
/g/data/vk83/testing/admin/conda_containers/prerelease/logs/build_payu-dev.e166302120
# Test
/g/data/vk83/testing/admin/conda_containers/prerelease/logs/test_payu-dev.o166302289

…ests

This is to prevent micromamba defaulting to using a root dir in the $HOME directory
@jo-basevi jo-basevi force-pushed the test-micromamba-activate-fix branch from c057b90 to 1282fc6 Compare April 17, 2026 04:11
@jo-basevi jo-basevi changed the title Test micromamba activate fix Micromamba activate error fix Apr 17, 2026
@jo-basevi jo-basevi requested a review from atteggiani April 17, 2026 04:47
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The changes look good.

I left one comment, but feel free to disregard it.

Comment thread scripts/test.sh
@jo-basevi jo-basevi merged commit 97d5db4 into main Apr 17, 2026
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2 participants