Upgrading from HPC Pack 2008 to HPC Pack 2012 R2 Update 3 requires lots of upgrades and really easy to fail, it includes:
Upgrade to HPC Pack 2008 R2 (refer to https://technet.microsoft.com/en-us/library/ff872108(v=ws.10).aspx)
1. First windows system upgrade from Server 2008 to Server 2008 R2
2. SQL upgrade
3. Upgrade HPC Pack
4. etc
Then upgrade to HPC Pack 2012, for this, you have to do migration, please refer to https://technet.microsoft.com/en-us/library/jj945407(v=ws.11).aspx
then you patching all the way to HPC Pack 2012 R2 Update 3
I would recommend you do a new installation of HPC Pack 2012 R2 Update 3 (and applying QFEs), and moving workloads to the new cluster.
Qiufang Shi