Output log files are truncated.

I think the log file is not flushed before it is copied out of the temp directory and the original deleted so the output log files are truncated at the end, finishing mid word in many cases. Here are the last few lines of such a log file.

```
....
Before fftplan3d 6954MB free
After fftplan 6954MB free
re-transforming centerband
inserting centerband
centerband assembly completed
mo
```