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is there a problem if an Extended Partition does not start on physical sector boundary?

Partition 4 does not start on physical sector boundary.

  ...
 /dev/sda4        639635454 1953521663 1313886210 626.5G  f W95 Ext'd (LBA)
 /dev/sda5        639635456  954208255  314572800   150G  7 HPFS/NTFS/exFAT
 ...

 Partition 4 does not start on physical sector boundary.

See also https://wiki.hetzner.de/index.php/Partition_Alignment:

On an Extended Partition no data will written, so is there any problem that it does not match the physical sector boundary?


Hint:

The Question fdisk warning message: (Extended) Partition does not start on physical sector boundary does not ask for the title info and answers only to

Partition table entries are not in disk order

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  • I think that out-dated operating systems such as Microsoft's Windows, will have problems. I don't know if they have fixed this bug. Commented Nov 18, 2018 at 16:16

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It depends on aligning logical blocks and physical sectors in new partition. If disk has 4K logical blocks that not aligned with 4K physical sectors, it can cause visible loss of performance. So fdisk just warns you not to do so.
In most cases no other problems will arise.

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  • yes, but does it cause a loss of performance because it is a extended partition?
    – User8461
    Commented Nov 18, 2018 at 22:29
  • In an extended partition no data will stored. /dev/sda5 is aligned correctly!
    – User8461
    Commented Nov 18, 2018 at 22:30
  • @User8461, fdisk knows nothing about your plans for this partition, fdisk only warns you. If you won't store any data in extended partition it won't affect performance of your system in any way. Commented Nov 18, 2018 at 22:49

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