It looks like in the newer version the memory problem has been solved regarding the Windows 32-bit version though it might be a good idea to install the 64-bit version (Note: there is also a 5.0.0 version available). Under Cygwin this memory problem was not present. So I think the problem is that with the 2.38.0 version I ran into a 32-bit memory problem and that you might have had the same problem with the 2.50.0 version generating gif files. The size of the mentioned graph is very large and in my opinion useless due to the fact that everything is very small, I think a better choice might be to have the interactive svg as indicated before. When I ran, under Windows, with dot 4.0.0 all went well as well.
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