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It is not recommended to mix the operating systems for use in a single site even if they are seperated into different clusters.It was recommended that you should either choose Linux or Windows for your server environment and stick to that platform for all server deployment.Hope this helps.Cheers.
Any idea why or what that recommendation is based on? Two thoughts, first if the newly rewritten server is actually identical across the two OSs, I can't see a mounted file system for the configuration store being that great of an obstacle to setting up different OS based clusters. Second, It'd be a really tough sell in my opinion to say that if an organization needed a windows cluster to support some services based on .Net server object extensions, that they would be discouraged from setting up Linux machines to perform mapping, GP or geodata services.
Last week I was in a meeting with Eric Bader and Ismael Chivite from ESRI. Both of them indicated that mixing these is not supported. That makes sense to me because the fundamental design assumes a certain level of homogeneity. If you want to debate this then you will need to arrange a meeting with ESRI:)
Of course you are certainly free to setup as many systems as you want, e.g. you can have 5 Linux systems and 3 Windows systems.
I think just to close out the topic this video should help:
This video was taken at the dev summit and Ismael really breaks it down for us about deployments. There is a Q/A session at the end i believe which should touch some of the concerns brought up in this topic.