One problem that we have seen several times now is the issues of mixed skus in a farm. So the scenario is that a customer wants to make use of some of the features of Microsoft Office SharePoint Server 2007 (MOSS) as well as Microsoft Office Project Server 2007 (PS). The misconception is that you can add a "Project Server" to a farm that is an Office Server farm - so you just want one Project machine in your farm - just load Project Server on a machine and join the farm! WRONG! The way it works is that ALL servers in the farm need to have all the bits loaded for all the different server products. So if your farm has 2 application servers and 2 web front end servers then each of these needs to have the applicable installation (complete or web front end) for both MOSS and PS. You can then choose which services are running on which server - and you could have the MOSS services on one and the PS services on the other - but both applications need to be loaded on all servers. There is a new document which includes details of this mixed server installation available at http://go.microsoft.com/fwlink/?LinkId=79599. Page 105 onward gives details steps of the why and how you can get these server products working together.
Remember - it is not that Project needs anything from MOSS for it to work - but in a farm environment you just cannot have different servers with different sets of binaries. One other option would be to have Project Server in its own farm - but you would then lose some of the capabilities of MOSS to work with PS - particularly regarding search across project workspaces.
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