Ok I solved it. It seems the order in which you set the variables maters. So I set the prefix first then the boost directory. Also the -D has to have a space after it for it to work. It also seems the prefix doesnt work as stated on the build from source webpage. I changed the prefix while running "ccmake ." And changed the option there. Here is what worked for me:

cmake -D CMAKE_INSTALL_PREFIX:PATH=/storage/alps/2.1.1 -D Boost_ROOT_DIR:PATH=/root/Cluster/alps-2.1.1-r6176-src-with-boost/boost /root/Cluster/alps-2.1.1-r6176-src-with-boost/alps

But I suspect that removing the prefix would work. Also I added the :PATH to the prefix because that is what seemed to work for the Boost. But either way (online or this way) doesnt seem to change anything. Thanks for the help. What tipped me was what German said. When i switched the boost and the prefix these errors went away. I noticed this error changed when i removed and added space behind the -D tag. Hope this helps someone else out.

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