Site collection administrators have god like power within a site collection, They can add/delete sites, content, users, etc for any site within a site collection.
In SharePoint 2010 primary, secondary site collection administrators are set from Central Administration >> Application Management >> Change site collection administrators under Site Collection.
To change primary site owner, secondary site owner in MOSS 2007, we use stsadm with siteowner switch.
stsadm -o siteowner -url https://my.brightpoint.com/personal/brightpoint_markh -ownerlogin domain\user -secondarylogin global\salaudeen"
You can find site collection Primary and Secondary administrators under site collection administrators group (Site Actions >> Site Settings >> Site collection administrators) along with other site collection administrators. But Primary and Secondary Administrators are the only users who receive e-mail notifications for events, such as the quota reached, Site usage confirmation, etc.
To change primary administrator in SharePoint site with object model code C#:
This code sets SharePoint primary site collection administrator
In SharePoint 2010 onwards PowerShell cmdlets makes it much simpler:
To get Primary and Secondary Site collection Administrators:
Similarly, to set Site collection Primary and secondary owners, we can use the powershell cmdlet: Set-SPSite
This will change SharePoint 2010 primary site collection administrator and secondary site collection administrator.
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