I am using JIRA 6.1, we wanted to achieve federation. I had referred https://confluence.atlassian.com/enterprise/federating-jira-managing-multiple-instances-461504624.html
This document doesn't provide clarity that how to achieve federation. Can anybody help me in this?
Also, Is it required that both JIRA instance have the same version?
Jira does not need to be the exact same versions. That document you linked does explain this:
The JIRA servers, thereby, do not need to run the exact same version as long as all versions contain the Application Links functionality.
It is the application links between Jira instances that provides the federation aspect. But there is also an understanding that you have some single sign-on mechanism between these Jira instances, such as Atlassian Crowd. That part allow you to use a single login between the different instances.
The application links don't technically have to be running the exact same version. However there are known incompatibilities between certain versions. These are documented in the top of the Application links version matrix.
Since you are running Jira 6.1, that means this version of Jira is using the applinks 4.0 package. You should be ok if your other version is on a closely related applink package.
However that document does indicate a well known limitation that:
Products using AppLinks 4.1 or earlier cannot be linked to products using AppLinks 5.0 or later
Because of this, we know that you won't be able to link your Jira 6.1.x version to any version of Jira 7.0.x or higher, Confluence, 5.9.x or higher, Bitbucket 4.x or higher, etc.
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