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I have also posted on superuser. But I recieved no response to my last two questions on superuser. So I am posting here.

I have a multi-os setup on a new HDD which was cloned from an old HDD. I used clonezilla "partition to partition" clone method.

old HDD setup : ubuntu 14.04 +ubuntu 16.04 + windows 7.windows on primary partition, rest on extended partition

new HDD setup : ubuntu 14.04 +ubuntu 16.04 all on extended partition(no primary partition)

The cloned system is much slower than the old one(both on ubuntu 16.04 and 14.04). Also the SWAP is not enabled by default. I have to manually enable it after login. Even after enabling SWAP, the new setup is very slow. The partition table on the new HDD is as follows:

I did some tests to check for disk partition allignment and I got that some mislignment is there.

sudo fdisk -l

Disk /dev/sdb: 2000.4 GB, 2000398934016 bytes
255 heads, 63 sectors/track, 243201 cylinders, total 3907029168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disk identifier: 0x22c8142a

   Device Boot      Start         End      Blocks   Id  System
 /dev/sdb1            2048  3907028991  1953513472    5  Extended
 /dev/sdb5            4096   552964095   276480000   83  Linux
 /dev/sdb6   *   552966144   972806143   209920000   83  Linux
 /dev/sdb7       972808192  1041416191    34304000   82  Linux swap /     Solaris
 /dev/sdb8      1041418240  3907028991  1432805376   83  Linux

sudo parted yields:

(parted) p                                                                
Model: ATA WDC WD20EARX-00P (scsi)
Disk /dev/sda: 2000GB
Sector size (logical/physical): 512B/4096B
Partition Table: msdos
Disk Flags: 

Number  Start   End     Size    Type      File system     Flags
 1      1049kB  2000GB  2000GB  extended
 5      2097kB  283GB   283GB   logical   ext4
 6      283GB   498GB   215GB   logical   ext4            boot
 7      498GB   533GB   35.1GB  logical   linux-swap(v1)
 8      533GB   2000GB  1467GB  logical   ext4

(parted) align-check optimal 1                                            
1 aligned
(parted) align-check optimal 5
5 aligned
(parted) align-check optimal 6
6 aligned
(parted) align-check optimal 7
7 aligned
(parted) align-check optimal 8
8 aligned
(parted)

So all disks are aligned.

user27665
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    Save the whole disk (instead of each partition separately) and then restore the image to the new HDD ! :) – cl-netbox Jan 09 '17 at 17:02
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    Could you test the performance of both disks before asking why the new one is slower? – Fabby Jan 09 '17 at 17:36
  • Ok I will do the performance test. The new HDD has no primary parition, only extended. Does it have any effect on speed? @cl-netbox: I want to only selectively have some paritions, hence cloning the whole disk is not applicable. – user27665 Jan 09 '17 at 18:02
  • Maybe the drives have different optimal configurations, which means that cloning is not the best method. But you should try cloning the whole drive before trying advanced methods (as suggested already). – sudodus Jan 09 '17 at 19:45
  • Use sudo fdisk -l for a quick check to see if your partitions are aligned. Use sudo parted align-check for a more thorough check. Edit your answer with the output. For swap, you need to sudo blkid and cat /etc/fstab to make sure that your UUIDs match, and your mount for swap is correct. – heynnema Jan 09 '17 at 22:43
  • ps: With a modern UEFI computer, and a 2TB disk, you should be using GPT partition tables and only primary partitions. And your swap partition is insanely large. – heynnema Jan 09 '17 at 23:06
  • @heynnema : I did sudo fdisk -l. Looks like the partitions are not alligned. I will do the parted align-check and update – user27665 Jan 10 '17 at 07:44

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