Mode3 Top-20 Remote Debug (Linux, No SLURM)

This example records a real end-to-end validation run on 2026-04-08 for Surfacia Mode 3 with 20 molecules, focusing on reproducible debugging.

Goal

  • Verify that the PyPI package can be installed and used directly in a fresh conda environment.

  • Reproduce and fix the main runtime errors observed during ML analysis.

Run Context

  • Platform: remote Linux (SSH session)

  • Workflow scope: Step-7 (ml-analysis) validation on FinalFull_Mode3_20_168.csv

  • Execution mode: direct command line (no SLURM)

Environment Setup

conda create -n surfacia_mode3_test_20260408 python=3.10 -y
conda activate surfacia_mode3_test_20260408
pip install surfacia

Version sanity check:

python -c "import xgboost, shap; print('xgboost', xgboost.__version__, 'shap', shap.__version__)"

If needed, force compatible versions:

pip install --force-reinstall "xgboost==2.1.4" "shap==0.48.0"

Step-7 Command (Validated)

surfacia ml-analysis -i FinalFull_Mode3_20_168.csv \
  --max-features 1 --stepreg-runs 1 \
  --train-test-split 0.85 --epoch 32 --cores 8 \
  --test-samples "1,2,3"

Observed Errors and Fixes

Error 1: Input file '' not found!

  • Cause: shell variable (for example $finalfull) was not defined.

  • Fix: use an explicit filename or define variable first.

Error 2: Input file 'FinalFull_Mode3_20_168' not found!

  • Cause: missing file extension.

  • Fix: use FinalFull_Mode3_20_168.csv.

Error 3: surfacia: command not found

  • Cause: package not installed in current conda environment.

  • Fix: activate target env and run pip install surfacia.

Error 4: could not convert string to float: '[-3.2828572E0]' (or similar [-3.xxxE0])

  • Cause: environment dependency mismatch (xgboost / shap combination).

  • Fix: pin to validated versions:

    pip install --force-reinstall "xgboost==2.1.4" "shap==0.48.0"

Results Checklist

After fixes, the run should proceed through:

  1. baseline analysis

  2. stepwise regression

  3. output generation under Workflow_Analysis_<timestamp>/

This example is a practical deployment validation template for new users and new environments.