Starr Hazard wrote: > Here are the last lines of a typical log file. This run stopped after > reading 236 files out of 1000 loop files. I have finished all of what I > wanted to do by reading the files in smaller batches. In all cases the > log files record a similar memory problem
Yes, you're absolutely right: Modeller is running out of memory. This is because the Python interface is creating some circular references, so the objects aren't being cleaned up properly. You have three options:
1. Do what you did already - split the job into smaller batches. 2. Do what I suggested - move the creation of the mdl and aln objects outside of the loop. 3. Apply the (attached) patch to your Modeller 8v1 distribution, which should fix the problem.
Ben Webb, Modeller Caretaker