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Thanks for catching the missing bin and bin_sgx directories.
It seems I messed up something with including eigen as a submodule.
The directory Include/eigen should contain a copy of the (unmodified) Eigen library which you can find here: https://github.com/eigenteam/eigen-git-mirror
The Makefile inside SGXDNN is for building the DNN library for use without SGX. So you shouldn't include eigen3_sgx, which is a slightly modified version of eigen with SGX-specific dependencies.
Your fix works for building SGXDNN without SGX, but you'll now have trouble building slalom for SGX because you modified eigen3_sgx.
I have attempted to build this in Ubuntu 16.04 LTS by following your build guideline, but found 3 errors.
On Makefile in SGXDNN directory, g++ include path must be ../Include/eigen3_sgx , not ../Include/eigen
You need to fix as following. (I just brought git diff)
You need to create ´bin´ and ´bin_sgx´ directory inside SGXDNN directory.
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