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Update easyconfigs / yaml-spec-free changes #48

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11 changes: 9 additions & 2 deletions envs/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -87,13 +87,20 @@ eb --robot fcps.eb --job-cores=10
eb --robot clustbench.eb --job-cores=10
```

Running a benchmark:
Running a benchmark assuming the modules were installed within the `MODULE_BASEPATH`/software/modules/all path (perhaps `MODULE_BASEPATH` equals `$EASYBUILD_PREFIX`):

```bash
# during a debugging session, this was `/home/mark/envmodules_debug/.local/easybuild/`
MODULE_BASEPATH='updateme'
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Copilot AI Jan 27, 2026

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The variable name should use consistent formatting. In line 94, it's set to 'updateme', but this placeholder value should be more clearly documented or use a more conventional placeholder like '/path/to/your/easybuild/prefix' to avoid confusion.

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MODULE_BASEPATH='updateme'
MODULE_BASEPATH='/path/to/your/easybuild/prefix'

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source /cvmfs/software.eessi.io/versions/2025.06/init/lmod/bash ## if not loaded
module load EESSI-extend/2025.06-easybuild ## if not loaded
export MODULEPATH="$EASYBUILD_PREFIX"/software/modules/all:"$MODULEPATH"
export MODULEPATH="$MODULE_BASEPATH"/software/modules/all:"$MODULEPATH"
module use $MODULEPATH
echo $MODULEPATH

# during a debugging session, the resulting $MODULEPATH contained both the MODULE_BASEPATH and EESSI's injections
# /home/mark/envmodules_debug/.local/easybuild/software/modules/all:/home/mark/eessi/versions/2025.06/software/linux/x86_64/amd/zen2/modules/all:/cvmfs/software.eessi.io/host_injections/2025.06/software/linux/x86_64/amd/zen2/modules/all:/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/amd/zen2/modules/all:/cvmfs/software.eessi.io/versions/2025.06/init/modules

ob run benchmark -b Clustering_envmodules.yml --local-storage --cores 30
```
11 changes: 5 additions & 6 deletions envs/clustbench.eb
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Expand Up @@ -23,8 +23,7 @@ builddependencies = [
dependencies = [
('Python', '3.12.3'),
('SciPy-bundle', '2024.05'),
('matplotlib', '3.9.2'),
('scikit-learn', '1.6.1')
('matplotlib', '3.9.2')
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Removal of scikit-learn 1.6.1 from the dependencies list. Verify that scikit-learn is not needed as a dependency by other packages in the dependencies list (SciPy-bundle, matplotlib) and that building it as an extension (version 1.4.2) in exts_list is the correct approach.

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]

sanity_pip_check = True
Expand All @@ -46,10 +45,10 @@ exts_list = [
('fastcluster', '1.2.6', {
'checksums': ['aab886efa7b6bba7ac124f4498153d053e5a08b822d2254926b7206cdf5a8aa6'],
}),
## ('scikit-learn', '1.6.1', {
## 'modulename': 'sklearn',
## 'source_urls' : [PYPI_SOURCE]
## }),
('scikit-learn', '1.4.2', {
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Moving scikit-learn from dependencies to exts_list changes the installation approach. The version is also downgraded from 1.6.1 to 1.4.2. Please verify that: 1) scikit-learn 1.4.2 is compatible with the other dependencies and with clustering_benchmarks 1.1.6, and 2) the version 1.6.1 was removed from dependencies because it's not compatible or because it should be built as part of this bundle instead.

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('scikit-learn', '1.4.2', {
('scikit-learn', '1.6.1', {

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'modulename': 'sklearn',
'source_urls' : [PYPI_SOURCE]
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The scikit-learn package entry is missing a checksum. For consistency and to ensure package integrity, a checksum should be added.

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'source_urls' : [PYPI_SOURCE]
'source_urls' : [PYPI_SOURCE],
'checksums': ['aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa']

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}),
('genieclust', '1.1.6', {
'source_urls': ['https://github.com/gagolews/genieclust/archive/refs/tags/'],
'sources': ['v1.1.6.tar.gz'],
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