OK, I read the full setup output and realized that I was building the program using the -m64 flag in a 32bit system. Building with proper compiler flags works perfectly but the clusterer still crashes. This has been reported already so I guess there isn't much I can do about it.

I installed EPD but running setup.py with it (ipython) gives the same BLAS/MKL error. Should I include a link to the EPD lib directory somewhere? I tried adding '-L/.../lib' to the extra_link_args list on setup.py, but that doesn't help. I installed the program anyway and tried to run the tutorial, ...

Thanks for the quick answer!
I'm using the ubuntu system python. I tried modifying the setup.py file but that doesn't seem to help. If I install EPD python, how should I modify the setup.py file to include its MKL libraries?

Hi, I'm trying to build MSM Builder for the first time and I can't figure out how to solve this error: The C extension 'LPRMSD' could not be compiled. This may be due to a failure to find the BLAS/MKL libraries. I'm using Ubuntu; I installed the BLAS and LAPACK libraries from the repositories (packa...