At this point I always recommend separate instances for end users vs job/idoc processing etc. With virtualization this has become much easier. Its often not an issue with the hardware but that it seems you can only really tune Netweaver to be good at one or the other, not both at the same time. FWIW I have seen the same kinds of work distribution issues with PI systems and I believe SAP recommends the approach for Fiori implementations. I am not in the middle of it so I can't speak with any authority but I know SAP is adding some capability in the underlying Netweaver level to have some control over what nodes things run on etc. I also see some frustration with the way Netweaver wants to distribute work across nodes. For example instead of running 4 nodes at 20% each it wants to run one at 60%, one at 20% and idle the rest. Because it has no way to know the next job is a big memory hog it may stick the job on the 60% node and end up killing it. My comments are anecdotal and there may be a way to tune this behavior that I haven't discovered yet but in my experience separate instances does seem to be the way to go.
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