MacPro with10.7.3. running a Python script in terminal I see a : "There is no more application memory available on your startup disk". Python uses 10G of 16G RAM and  VM =238G with 1TB free. Log: macx-swapon FAILED - 12. It only happens with larger inputs

On my MacPro with10.7.3. while running a Python script in terminal, after a while, in several hours actually,  I see a system message for the Terminal app: "There is no more application memory available on your startup disk". Both RAM and VM appear to be fine at this point, i.e. Python uses only 10G of 16G RAM and  VM =238G with ~1TB free. Log reads: " macx-swapon FAILED - 12" multiple times. Furthermore, other terminal windows can be opened and commands run there. It only happens with larger inputs (text files), but with inputs that are about half the size everything runs smoothly.  So the issue must be the memory indeed, but where to look for the problem/fix?

http://liulab.dfci.harvard.edu/MACS/README.html
Have you tried with the --diag flag for diagnostics? Or changing verbose to 3 to show debug messages? Clearly one of three things is happening;
1. You ARE running out of disk space, but once it errors out the space is reclaimed if the output file is deleted on error. When it fails, does your output have the content generated up to the point of termination?
2. The application (Terminal) is allocated memory that you are exceeding
3. The task within Terminal is allocated memory that you are exceeding
I don't know anything about what this does but is there a way to maybe run a smaller test run of it? Something that takes 10 minutes? Just to see if it works.

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