We have been trying to get to the bottom of this error message for quite some time without much success. I'm wondering whether anybody else has any insights or ideas from troubleshooting this message in a similar environment.
Oracle 12c, ArcSDE Geodatabase version 10.3
ArcGIS Server 10.3 and/or 10.4 (single server site)
We see it on most or all services when they need to spin up a new instance. Hardware resources are not likely the culprit. What makes it difficult to troubleshoot is that I can't reproduce the error very consistently. We're looking at a lot of variables but so far without too much consistent success.
Can you describe the problem a bit more? Only specific services fail to start or all of them? Is there any correlation to the source data location and which services fail to start? Are they query layers? If it only occurs for data coming from SDE, you'll need to take a look at Verbose or Debug logs and see which step it gets to when it stops spinning up, and compare that to a service that starts up successfully. I know you mentioned that resources aren't the problem, but how much RAM is on the machine, and how much of it is free when the problem happens? What about the page file size? Perhaps setting up PerfMon to capture that information and seeing what those values are when the problem happens is a good way to eliminate hardware issues.
If you think it may be a problem with the source of the data, you can also run an SDEINTERCEPT to see if there is a call or calls that take a long time.