License conflict?

It looks like the EIGENSOFT tools are meant to be linked with the GNU Scientific Library (GSL). The GSL is released under the terms of the GNU General Public License. According to the license terms, an application linking with the GSL should itself also be released under the GPL, yet according to the README it looks like EIGENSOFT is released under a license that prohibits commercial use, which makes it non-free software:

SOFTWARE COPYRIGHT NOTICE AGREEMENT
This software and its documentation are copyright (2010) by Harvard University 
and The Broad Institute. All rights are reserved. This software is supplied 
without any warranty or guaranteed support whatsoever. Neither Harvard 
University nor The Broad Institute can be responsible for its use, misuse, or 
functionality. The software may be freely copied for non-commercial purposes, 
provided this copyright notice is retained.

Could you please revise the license terms for EIGENSOFT or clarify the situation?

Review the README's licensing language and the SOFTWARE COPYRIGHT NOTICE quoted in the issue, then verify how the EIGENSOFT tools relate to the GNU Scientific Library's license. Done means the project's license terms are clarified or revised to address the stated GPL and non-commercial-use conflict.