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Are you using the UI to initiate the client task, or the web API? Sounds like just the UI. In that case I would make two comments:
1) it's almost always preferable to assign the task, and let it complete after the next time the agent dials in. For run now to be successful, the agents have to be online, have wakeup enabled in policy, and reachable from the server. It's great for troubleshooting but the traditional client task assignment is best for deployments, generally.
2) if you are using the 'run now' in the UI, there is a second tab on the bottom labeled 'Options' that contains several fields you may want to modify, including # of attempts to contact the agent, a retry interval, and an expiration timer. You might play with upping the number of attempts, choosing 'all agent handlers' (if you have more than one), and bumping up the retry interval.
Thank you for your reply, I've just arrived at work now so I'll check all listed posibilities again and try to RDP to a machine with the UI, currently I am mobile a lot so the website has been my only access to controling anything.
I thought it might have been better to get to a UI machine but due to time limits, being mobile, ect, I thought it best to ask here in case it was a known (in the KB) issue.
Neither of those solutions helped, have tried to wake them up one by one and then test them just to see if we can get a result but no, nothing. I'm sure some of these must be machines not in use, about 1160 of them, at the time of the deployments but I was wondering if there could be other issues effecting the expired machines that I wouldn't know of yet.