See this GMT.jl issue.
This is something that can only occur from externals, and maybe not from PyGMT because it restarts the GMT API very often. But in Julia or Matlab, where the GMT API structure is kept alive all the time, the error happens when we call a module that creates virtual files for > ~250000 times.
Now this clearly looks like a limit of something. Either in C compiler or system-limits. Anyone has an idea of what it might be? @ES-Solar?