I read in the content bible that films aren't usually split into multiple parts. But I think there's a case for this film to be split in a similar way to Nymphomaniac. Let me provide some information:

1. My DVD copy of the film splits it into 4 parts: Rust part1 (up to the intermission), Rust part2 (intermission to the end credits), Remnants, Rails
2. Although all parts of the film were released together, I think it's clear that it's meant to be a multiple part film. See wikipedia and the NYT review of the film. Each of the three parts has an opening title card, and closing credits.
3. The official(?) US release of this film offers it in either:

• A 3-part DVD set
• 3 Separate DVDs with separate listings:
• Rust
• Remnants
• Rails

However, I think there's also a case for leaving this film as a single 9-hour entry:

1. Most news articles describe this film as a single, 9-hour film. (See here and here).
2. Most screenings of this film have shown all 3 parts in one day, typically with 3 intermission breaks (example).
3. Wikipedia lists this film on it's List of Longest Films article (see the talk page for further discussion of whether this is a single film or 3 separate parts).