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I am using a Windows VPS with Windows Web Server 2008 R2. The server is running IIS and MSSQL Server 2008 R2.

Every 12 hours I have performance issues on this server. This occurs every 12 hours after a reboot of the server.

Is there a default process running on a server the occurs every 12 hours?

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Do you have any Anti Virus running? – Dan Feb 8 '12 at 8:35
Yes, AVG , but as far as I know there is no process that occurs every 12 hours – Jan Feb 8 '12 at 8:47
Anything in the logs? – Bart De Vos Feb 8 '12 at 8:57
I'd uninstall AVG and see if it makes a difference, personally. – Dan Feb 8 '12 at 8:59
Agree. Possibly IO overlaod by ignorant / bad / outdated virus scanner. Servers have little use for a virus scanner unless you allow peopel to uplload stuff. – TomTom Feb 8 '12 at 9:04

If it happening almost every 12 hours as you mentioned you should you should create a user defined data collector set using the system performance template. Configure a Custom Schedule using the guest-immated time around when you think it's happening to grab a list of proccess that are using the most resources. For the Stop condition you can use specify it by max file size you want the log to grow or run it for X amount minutes/hours/days

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Maybe another (not yours) VPS running on the same physical computer is using a lot of IO — for example creates a backup. Only your hosting provider can check this. VPS performance can be variable depending on physical computer load.

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Unlikely. Note his timing. it is 12 hours aftea reboot, not at specific times. This manes anothervps VERY unluikely - most will basically have batches at specific times. – TomTom Feb 8 '12 at 9:04
You're right — if it depends on time or reboot then it can not be another VPS. I bet on antivirus updating virus definitions. Maybe it can be configured to update at more appropriate time, when there's the least traffic. – Tometzky Feb 8 '12 at 9:35

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