It might be that you have introduced some modifications to the psf2gdml.py script. You need to make sure that the .gdml file is fine and that you are configuring your simulation properly. The following represents a non-exhausting list of typical culprits that you should make sure to avoid.

• The GDML file has a core (SDID 0), a crust (SDID 1), at least one gas layer, and a loss volume (SDID LAST).
• Extract from the GDML file the radius of the uppermost sensitive detector. Use this as the radius of your source surface in your macro file.
• Make sure that between the upper most sensitive detector and the loss layer there is a gap of at least 1m. If there is an overlap between the source surface and the loss volume, the simulation will typically finish much quicker then expected.
• Ensure that the whole planet fits within the square world box. Check the size of the box vs the radius of the outermost volume.
• Check that the crust and core compositions are correct.
• Check that the SDIDs in the GDML file are increasing from 0 to LAST without any gaps.