Draft untested, nonreproducible, run-as-root apptainer backends

Author: imallona

Clustering.yaml

@@ -1,26 +1,30 @@
 id: clustering_example
-description: Clustering benchmark on Gagolewski's, true number of clusters plus minus 2.
-version: 1.1
+description: Clustering benchmark on Gagolewski's, true number of clusters plus minus 2. Caution dirty apptainer sifs.
+version: 1.1_root_apptainer
 benchmarker: "Izaskun Mallona, Daniel Incicau"
 storage: https://play.min.io
 benchmark_yaml_spec: 0.01
 storage_api: S3
 storage_bucket_name: clustering_example
-software_backend: conda
+software_backend: apptainer
 software_environments:
   clustbench:
     description: "clustbench on py3.12.6"
     conda: envs/clustbench.yml
     easyconfig: zlib-1.2.8.eb # clustbench.eb
+    apptainer: envs/clustbench.sif
   sklearn:
     description: "Daniel's on py3.12.6"
     conda: envs/sklearn.yml
+    apptainer: envs/sklearn.sif
   R:
     description: "Daniel's R with readr, dplyr, mclust, caret"
     conda: envs/r.yml
+    apptainer: envs/r.sif
   fcps:
     description: "CRAN's FCPS"
     conda: envs/fcps.yml
+    apptainer: envs/fcps.sif
 stages:
 
   ## clustbench data ##########################################################
@@ -47,16 +51,16 @@ stages:
           # - values: ["--dataset_generator", "wut", "--dataset_name", "mk3"]
           # - values: ["--dataset_generator", "wut", "--dataset_name", "mk4"]
           # - values: ["--dataset_generator", "wut", "--dataset_name", "olympic"]
-          - values: ["--dataset_generator", "wut", "--dataset_name", "smile"]
+          # - values: ["--dataset_generator", "wut", "--dataset_name", "smile"]
           # - values: ["--dataset_generator", "wut", "--dataset_name", "stripes"]
           # - values: ["--dataset_generator", "wut", "--dataset_name", "trajectories"]
           # - values: ["--dataset_generator", "wut", "--dataset_name", "trapped_lovers"]
-          - values: ["--dataset_generator", "wut", "--dataset_name", "twosplashes"]
+          # - values: ["--dataset_generator", "wut", "--dataset_name", "twosplashes"]
           # - values: ["--dataset_generator", "wut", "--dataset_name", "windows"]
-          - values: ["--dataset_generator", "wut", "--dataset_name", "x1"]
+          # - values: ["--dataset_generator", "wut", "--dataset_name", "x1"]
           # - values: ["--dataset_generator", "wut", "--dataset_name", "x2"]
           # - values: ["--dataset_generator", "wut", "--dataset_name", "x3"]
-          - values: ["--dataset_generator", "wut", "--dataset_name", "z1"]
+          # - values: ["--dataset_generator", "wut", "--dataset_name", "z1"]
           # - values: ["--dataset_generator", "wut", "--dataset_name", "z2"]
           # - values: ["--dataset_generator", "wut", "--dataset_name", "z3"]
     outputs:

README.md

@@ -7,7 +7,6 @@ A clustering example for omnibenchmark
 3. Move to the cloned repository `cd clustering_example`
 4. Run locally, somewhat in parallel `ob run benchmark -b Clustering.yaml  --local --threads 6` (do not use lots of threads, this version uses conda and filesystem latency can be a problem)
 
-
 # Clustbench attribution
 
 by Marek Gagolewski, modified by Izaskun Mallona
@@ -75,7 +74,7 @@ by Marek Gagolewski, modified by Izaskun Mallona
     - args: ["--method", "FCPS_Clara"]
     - args: ["--method", "FCPS_PAM"]
 - Metric providers (several metrics)
- - https://github.com/imallona/clustbench_metrics
+  - https://github.com/imallona/clustbench_metrics
     - args: ["--metric", "normalized_clustering_accuracy"]
     - args: ["--metric", "adjusted_fm_score"]
     - args: ["--metric", "adjusted_mi_score"]
@@ -89,14 +88,19 @@ by Marek Gagolewski, modified by Izaskun Mallona
     - args: ["--metric", "rand_score"]
 - Metric collector
   - https://github.com/imallona/clustering_report
-- Daniel
+- Daniel modules (independent from clustbench)
   - https://github.com/omnibenchmark-example/iris.git
   - https://github.com/omnibenchmark-example/penguins.git
   - https://github.com/omnibenchmark-example/kmeans.git
   - https://github.com/omnibenchmark-example/ward.git
   - https://github.com/omnibenchmark-example/ari.git
   - https://github.com/omnibenchmark-example/accuracy.git
 
+  
+# Software backends
+
+In `envs`: conda, apptainer, easybuild (lmod modules)
+
 # Warnings
 
 Mind we try to run clusterings specifying the true number of clusters +- 2. But sometimes the true number is k=3. Then we do `k=2, k=2, k=3, k=5, k=6` filling with k=2s as needed, and recomputing the same values multiple times (so runtimes are comparable across datasets, regardless of their true number of clusters).

envs/README.md

@@ -0,0 +1,35 @@
+## Conda
+
+### Files
+
+- `clustbench.yml`
+- `fcps.yml`
+- `r.yml`
+- `sklearn.yml`
+
+### How to build
+
+Lorem ipsum
+
+## Apptainer
+
+### Files
+
+- `clustbench_singularity.def`
+- `fcps_singularity.def`
+- `r_singularity.def`
+- `sklearn_singularity.def`
+
+### How to build
+
+- `build_singularity.sh`
+
+## Easybuild
+
+### Files
+
+- `clustbench.eb`
+
+### How to build
+
+Lorem ipsum

envs/build_singularity.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+sudo singularity build sklearn.sif sklearn_singularity.def
+
+sudo singularity build clustbench.sif clustbench_singularity.def
+
+sudo singularity build r.sif r_singularity.def
+
+sudo singularity build fcps.sif fcps_singularity.def

envs/clustbench_singularity.def

@@ -0,0 +1,38 @@
+Bootstrap: docker 
+From: ubuntu:jammy-20240911.1
+
+%labels
+
+    AUTHOR izaskun.mallona@gmail.com
+
+%post
+    
+    # Install python3.12
+    apt-get update
+    apt install -y build-essential zlib1g-dev libncurses5-dev libgdbm-dev libnss3-dev libssl-dev \
+        libreadline-dev libffi-dev libsqlite3-dev wget libbz2-dev python-is-python3 git
+
+    wget https://www.python.org/ftp/python/3.12.6/Python-3.12.6.tgz
+    tar -xf Python-3.12.6.tgz
+    cd Python-3.12.*/
+    ./configure --enable-optimizations
+    make -j 4
+    make altinstall
+
+    # virtualenv
+    cd /opt
+    python3.12 -m venv "default"
+    . default/bin/activate
+    
+    pip3 install "clustering-benchmarks==1.1.5" "wget" "fastcluster==1.2.6" "numpy==1.26.4" "scipy==1.14.1" \
+      "isodate" "pydantic-core"  \
+      "genieclust==1.1.6" "pandas==2.2.3" "gitpython==3.1.43"
+
+    echo '. /opt/default/bin/activate' >> $SINGULARITY_ENVIRONMENT
+
+%environment
+
+    . /opt/default/bin/activate
+    echo $PATH
+    python --version
+    python3.12 --version

envs/fcps_singularity.def

@@ -0,0 +1,21 @@
+Bootstrap: docker
+From: rocker/tidyverse:4.4
+
+%labels
+
+    AUTHOR izaskun.mallona@gmail.com
+
+%post
+
+    # Install python packages
+
+    apt-get update
+    apt-get -y install python3 python3-pip python3-dev python-is-python3 git
+    
+    pip3 install -U argparse gitpython isodate pydantic-core 
+
+    # Install R packages
+    
+    Rscript -e 'BiocManager::install(c("fcps", "dbscan", "protoclust", "energy", "argparse"))'
+
+%environment

envs/r_singularity.def

@@ -0,0 +1,23 @@
+Bootstrap: docker
+From: rocker/tidyverse:4.4
+
+%labels
+
+    AUTHOR izaskun.mallona@gmail.com
+
+%post
+
+    # Install python packages
+
+    apt-get update
+    apt-get -y install python3 python3-pip python3-dev python-is-python3 git
+    
+    pip3 install argparse gitpython isodate pydantic-core
+
+    #################################
+    # Install R packages
+    #################################
+    
+    Rscript -e 'BiocManager::install(c("mclust", "caret", "readr", "argparse"))'
+
+%environment

envs/sklearn_singularity.def

@@ -0,0 +1,33 @@
+Bootstrap: docker 
+From: ubuntu:jammy-20240911.1
+
+%labels
+
+    AUTHOR izaskun.mallona@gmail.com
+
+%post
+    
+    # Install python3.12
+    apt-get update
+    apt install -y build-essential zlib1g-dev libncurses5-dev libgdbm-dev libnss3-dev libssl-dev \
+        libreadline-dev libffi-dev libsqlite3-dev wget libbz2-dev python-is-python3 git
+
+    wget https://www.python.org/ftp/python/3.12.6/Python-3.12.6.tgz
+    tar -xf Python-3.12.6.tgz
+    cd Python-3.12.*/
+    ./configure --enable-optimizations
+    make -j 4
+    make altinstall
+
+    # virtualenv
+    cd /opt
+    python3.12 -m venv "default"
+    . default/bin/activate
+
+    pip3 install -U scikit-learn pandas argparse numpy scipy "isodate" "pydantic-core" "gitpython==3.1.43"
+
+    echo '. /opt/default/bin/activate' >> $SINGULARITY_ENVIRONMENT
+
+%environment
+
+    . /opt/default/bin/activate