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I am fairly new to SharePoint, but we have 1 department site (we have 40 or so total) that keeps going down every 3-4 days it seems (screen just says "Working on it...."). They have a LOT of workflows(we use Nintex) on the site (30-40) and roughly 15-20 that run daily. We bring the site back up by resetting iis on the 2 SharePoint servers. This isn't ideal obviously, so we are trying to find the root cause and the logs don't really show anything.

I noticed in IIS App Pools that the Workflow Management pool has a idle-timeout of 20 minutes and a recycle time of every 29 hours instead of daily at 3:00 or so. Should these settings be changed to idle-timeout of 0 and recycle at 3:00am daily? Could this be causing the site to hang? All of our other pools have a 0 for idle-timeout and sometime early in the morning for recycle times.

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No, do not adjust Application Pool settings. Is the pool crashing or is just having to spin up the following day?

If it is just having to spin up, then don't use multiple app pools. Create a single pool for all Service Apps (PowerPoint Conversion Service being an outlier - it requires the Farm Admin to run the pool). This way the amount of time it takes to JIT the workflow binaries is minimal while the bigger SharePoint binaries are already JIT'ed, which is the longest part of the startup process for a SharePoint App Pool of any type.

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