Applications such as finance or ERP software would need to be rewritten, and currently are more suited to converged infrastructure.
"When you get to things like Oracle or SAP or the big enterprise apps they don't really run very well on hyper-converged yet," says 451 Research's Abbott.
"It is not such an obvious fit - you need to do a lot more optimisation and administration work with all of those non-distributed traditional enterprise apps with high transaction processing layers and things like that."
According to VCE's Moulton: "If you think of an application like an ERP system or something like Oracle financials, if either of those applications can't see the attached database, they stop working. And in most enterprise organisations that is a heart-stopping moment if it happens."
Another challenge for businesses is a change to the procurement model.
"Some people can't get their head around buying their storage and servers in one," says 451 Research's Abbott.
"Storage and compute does not necessarily evolve at the same pace, so if some new disk drives come out, you might want to buy those. It depends what your lifecycle of purchases is as well."
He adds that while one of the benefits of the hyper-converged model is the "modularity and simplicity", by offering more models and configurations to customers there is a "risk of introducing complexity".
And lock-in remains an issue.
"It depends how you view it," says Abbott. "Nutanix and others say that you are just buying a standard storage and server and that in some ways that's open because it's basically standard - it is not proprietary as such.
"But you have to buy it all from them and you have to rely on whether all vendors are going to be around over the next few years - so that is a problem.
"The ideal would be a separate software layer that you could run any hardware underneath and turn it into a hyper-converged system."
Hyper-converged infrastructure: What does the future hold?
Nevertheless, it is clear that hyper-converged vendors are targeting all manner of applications.
Simplivity's St Laurent says that while VDI has been a good entry point to target early adoption, the company has always been focused on the "core of the data centre".
He says Simplivity customers are already running a wide variety of software, including SQL Server, Exchange, Sharepoint and Oracle, as well as VDI.
It is not quite there yet, though. "Hyper-convergence needs to continue to evolve in terms of the area of IT it can cover," he says.
"Can you hold your seven-year retention deep archive data on these environments? Can you run your absolute mission-critical, sub-millisecond response time on these environments?
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