We installed a Domino Partition Server without Checking the Domino Partition server setup during first time install.
Steps we followed
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Install & Configure Domino as a Standalone Server: In this case the Notes.ini is in C:\Lotus\Domino folder.
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Bring up the domino server it works correctly.
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Copy the data folder in C:\Lotus\Domino Folder and name it as Data2
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Copy the Notes.ini from C:\lotus\Domino Folder and copy one in C:\Lotus\Domino\Data and the other in C:\Lotus\Domino\Data2 folder
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Open Notes.ini in Data2 folder and remove some of the notes.ini entry.
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Launch Server Setup for second partition and configure the other setup.
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Open the other server from Domino Administrator and create a database, replicate a database. The other server works as it is a configured Domino partition.
Is the above method, correct way of setting up Domino Partition?