As far as a workaround in concerned, that scipy archive post says you can disable threads in numpy.
Sorry can't help more, I don't know much about how to bypass such GIL issues.

-=- Olivier

2011/10/3 Yang Zhang <yanghatespam@gmail.com>
It turns out that there's a long-standing problem in numpy that
prevents it from being used in embedded CPython environments:

http://stackoverflow.com/questions/7592565/when-embedding-cpython-in-java-why-does-this-hang/7630992#7630992
http://mail.scipy.org/pipermail/numpy-discussion/2009-July/044046.html
Is there any fix or workaround for this?  Thanks.
--
Yang Zhang
http://yz.mit.edu/
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