Limitation of upgrading filesystem from VMFS-3 to VMFS-5
While a VMFS-3 which is upgraded to VMFS-5 provides you with most of the capabilities as a newly created VMFS-5, there are some differences.
VMFS-5 upgraded from VMFS-3 continues to use the previous file-block size, which may be larger than the unified 1MB file-block size.
VMFS-5 upgraded from VMFS-3 continues to use 64KB sub-blocks and not the new 8KB sub-blocks. This can also lead to stranded/unused disk space. The upgraded VMFS-5 also continues to use the original number of sub-blocks from the VMFS-3.
VMFS-5 upgraded from VMFS-3 continues to have a file limit of 30,720 rather than new file limit of > 100,000 for newly created VMFS-5.
VMFS-5 upgraded from VMFS-3 continues to use MBR (Master Boot Record) partition type; when the VMFS-5 volume has grown beyond 2TB, it automatically and seamlessly switches from MBR to GPT (GUID Partition Table) with no impact on the running virtual machines.
VMFS-5 upgraded from VMFS-3 continues to have its partition starting on sector 128. Newly created VMFS-5 partitions will have their partition starting at sector 2048.
VMFS 5 Upgrade from VMFS 3
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Minimum H/W requirements for VMware vCenter Server 4.x and 5.x
Comparison and Difference between vSphere 5.1 and 5.5