I now remember that at some point during the sampling, the file system ran out of space on the partition containing the CmdStan output files (somewhere under /tmp). So I surmise that some samples weren’t written to the output file, and therefore at the end when the summary was to be made, the lists of samples were different lengths.
It’s kind of a bummer that Stan kept going after a write failed, when that would necessarily lead to a failure at the end … I would rather find out sooner rather than later. Also kind of a bummer that the output files were nuked at program termination; it would be pretty helpful to be able to inspect whatever was left. I don’t know what could be concluded from incomplete output files, but at any rate it would be better than having them simply vanish.