Comment 1 for bug 269966

I discovered the same issue. I think it is a serious memory leak.

For example, if the script you are running with "run" creates large arrays or images. In a typical situation, I am running the same script over and over as I improve and test it. Because of this bug, each script run leaks whatever memory is attached to the objects created by the script. This can add up to a large amount of memory in the sort of lengthy interactive session that IPython is so good at encouraging and supporting.

I tracked it down to IPython/Magic.py:1570 (in Ipython release 0.8.4) in the magic_run function. Here is an extract:

        if opts.has_key('i'):
            # Run in user's interactive namespace
            prog_ns = self.shell.user_ns
            __name__save = self.shell.user_ns['__name__']
            prog_ns['__name__'] = '__main__'
            main_mod = FakeModule(prog_ns)
        else:
            # Run in a fresh, empty namespace
            if opts.has_key('n'):
                name = os.path.splitext(os.path.basename(filename))[0]
            else:
                name = '__main__'
            main_mod = FakeModule()
            prog_ns = main_mod.__dict__
            prog_ns['__name__'] = name
            # The shell MUST hold a reference to main_mod so after %run exits,
            # the python deletion mechanism doesn't zero it out (leaving
            # dangling references)
            self.shell._user_main_modules.append(main_mod)

The last line appends the namespace of the script to a list. The list is only cleaned up if the user runs the %reset command. But that is overkill -- generally I want to keep the prompt's namespace but I am happy to overwrite the namespace when I re-run a script.

I found that commenting out the last line fixes the problem. I disagree with the comment above the last line.