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ISSUES.md

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Error and Issue Tracking

This document tracks all known issues in the Genesis-Sphere project that need to be addressed.

Athena Simulation Issues

1. Invalid Boundary Conditions

Problem: Athena rejects certain boundary condition types that are specified in input files.
Files Affected:

  • time_density_spherical.in
  • time_density_spherical_fixed.in
  • Other .in files with invalid boundary conditions

Error Message: FATAL ERROR related to boundary conditions
Solution: Use only valid boundary conditions supported by your Athena build:

  • reflecting - Working in most builds
  • outflow - Appears to work in some configurations
  • polar_wedge - For spherical coordinates
  • periodic - Works in most cases

2. Missing Output Files

Problem: Athena simulations complete but don't produce output files
Files Affected: All simulation output files
Symptoms: No .out* or .vtk files are generated despite successful execution
Solution:

  • Check that output directories exist and are writable
  • Verify the -o parameter has no space (e.g., -ooutput_name not -o output_name)
  • Add explicit out_dir parameter in the <output1> block

3. Simulation Configuration Issues

Problem: Some simulations fail to initialize or complete
Files Affected:

  • time_density_cartesian.in
  • time_density_spherical.in

Error Symptoms: Docker exits without proper error message
Solution:

  • Include required parameters for the chosen problem generator
  • For blast problems, ensure radius, center_x1, etc. are defined
  • For custom problems, add all required parameters

Docker Issues

4. Docker Path Mounting Problems

Problem: Windows path mounting in Docker sometimes fails
Files Affected: Docker execution scripts
Error Symptoms: "Cannot mount volume" or "No such file or directory"
Solutions:

  • Use absolute paths: -v "C:\full\path\to\directory:/workspace"
  • Replace backslashes with forward slashes
  • Try using Docker Desktop settings to share drives

5. Docker Permissions

Problem: Files created inside Docker containers have incorrect permissions
Files Affected: Output files from Docker runs
Symptoms: Cannot modify or delete files after Docker creates them
Solution:

  • Add appropriate user mapping to Docker run command
  • Fix permissions after creation: chmod -R 777 output_directory

Input File Issues

6. Missing Required Parameters

Problem: Input files missing required parameters for the chosen problem
Files Affected:

  • time_density_spherical.in
  • Other .in files

Error Symptoms: "Required parameter not found" or silent failures
Solution: Ensure all required parameters are present for each problem type:

  • For blast: Add radius, center_x1, center_x2, and pressure parameters
  • For time_density: Add matching parameters to meet expectations

7. Incorrect Time Integration

Problem: Some input files specify invalid time integrators
Files Affected: Multiple .in files
Error Symptoms: "Invalid integrator" or "Unknown integrator"
Solution: Use only valid integrators in the <time> block:

  • rk2 - 2nd-order Runge-Kutta (recommended)
  • Instead of vl2 use rk2

Analysis Script Issues

8. VTK Library Dependencies

Problem: Analysis scripts fail due to missing VTK library
Files Affected:

  • athena_analysis.py
  • fixed_analysis.py

Error Symptoms: ImportError for VTK module
Solution:

  • Install VTK: pip install vtk
  • Add error handling for missing VTK
  • Use conditional imports

9. Data Format Compatibility

Problem: Analysis scripts sometimes fail to read data files
Files Affected:

  • Analysis scripts
  • Output data files

Error Symptoms: "Error reading file" or KeyError for missing data
Solution:

  • Add better format detection and error handling
  • Support multiple file formats (VTK, HDF5, text)
  • Standardize on a single output format

Other Issues

10. Inconsistent Directory Structure

Problem: Scripts assume different directory structures
Files Affected: Multiple scripts and batch files
Symptoms: File not found errors, incorrect paths
Solution:

  • Standardize directory structure
  • Use relative paths consistently
  • Add configuration options for output directories

11. Python Environment Management

Problem: Dependencies aren't consistently managed across scripts
Files Affected: All Python scripts
Symptoms: Missing module errors, version conflicts
Solution:

  • Create and document a consistent environment setup
  • Use virtual environments
  • Maintain a single comprehensive requirements.txt

12. Documentation Gaps

Problem: Documentation doesn't cover all error scenarios
Files Affected: README.md and other docs
Symptoms: Users struggle to resolve errors
Solution:

  • Add troubleshooting section to README
  • Document common errors and solutions
  • Create example scripts with validated configurations

Priority Issues to Fix First

  1. Invalid Boundary Conditions - This is preventing simulations from running
  2. Missing Required Parameters - Causes silent failures in simulations
  3. Docker Path Mounting - Prevents Docker workflows from functioning
  4. Missing Output Files - Makes analysis impossible even when simulations run
  5. VTK Library Dependencies - Prevents analysis scripts from functioning

Next Steps

  1. Create a minimal working input file with validated parameters and boundary conditions
  2. Test Docker workflows with absolute paths to ensure consistent mounting
  3. Add better error handling to analysis scripts
  4. Document valid parameter combinations for each problem type
  5. Create a troubleshooting guide with common error messages and solutions