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Tutorial: first SPIDER run

This page walks you through a minimal SPIDER run, from compile to quick visualization.

Prerequisites

  • You have installed PETSc and SPIDER by going through the installation guide.
  • You have a working C compiler.
  • Preferably: you are in a Conda environment with python version 3.12.

1. Run a known example

Use one of the provided options files:

./spider -options_file tests/opts/blackbody50.opts

This writes model output to the default output directory (typically output/).

Runtime

A first run on a laptop/workstation typically finishes in seconds to a few minutes, depending on CPU and PETSc settings.

To quickly verify output structure:

ls output
You should see text files with radial profiles and time-series data.

Expected signs of success:

  • output exists and is non-empty.
  • Multiple text files are produced (for example, interior profile and time-series outputs).
  • No PETSc crash/solver error is printed to terminal.

2. Make a quick plot

python py/plot_spider_lite.py -h
python py/plot_spider_lite.py -d output

The plotting script generates a basic figure of interior profiles from your run output inside the directory plots/.

3. Next steps

  • Try a different options file in tests/opts/.
  • Compare your run output against files in tests/expected_output/.

Common first-run issues

  • PETSC_DIR or PETSC_ARCH not set: Re-export them in your shell and rebuild.
  • ./spider not found: Build failed or you are not in the project root.
  • Plot script fails: Install Python dependencies from py/requirements.txt.