How to fix "Partition does not start on physical sector boundary" warning?
Mia Lopez 
I have one HDD on my laptop, with two partitions (one ext3 with Ubuntu 12.04 installed and one swap).
fdisk is giving me the following warning:
Partition 1 does not start on physical sector boundaryWhat is the cause and do I need to fix it? If so, how?
This is sudo fdisk -l:
Disk /dev/sda: 750.2 GB, 750156374016 bytes
255 testine, 63 settori/tracce, 91201 cilindri, totale 1465149168 settori
Unità = settori di 1 * 512 = 512 byte
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Identificativo disco: 0x5a25087f
Dispositivo Boot Start End Blocks Id System
/dev/sda1 * 63 1448577023 724288480+ 83 Linux
Partition 1 does not start on physical sector boundary.
/dev/sda2 1448577024 1465147391 8285184 82 Linux swap / SolarisThis is sudo lshw related result:
*-disk description: ATA Disk product: WDC WD7500BPKT-0 vendor: Western Digital physical id: 0 bus info: scsi@0:0.0.0 logical name: /dev/sda version: 01.0 serial: WD-WX21CC1T0847 size: 698GiB (750GB) capabilities: partitioned partitioned:dos configuration: ansiversion=5 signature=5a25087f *-volume:0 description: EXT3 volume vendor: Linux physical id: 1 bus info: scsi@0:0.0.0,1 logical name: /dev/sda1 logical name: / version: 1.0 serial: cc5c562a-bc59-4a37-b589-805b27b2cbd7 size: 690GiB capacity: 690GiB capabilities: primary bootable journaled extended_attributes large_files recover ext3 ext2 initialized configuration: created=2010-02-27 09:18:28 filesystem=ext3 modified=2012-06-23 18:33:59 mount.fstype=ext3 mount.options=rw,relatime,errors=remount-ro,user_xattr,barrier=1,data=ordered mounted=2012-06-28 00:20:47 state=mounted *-volume:1 description: Linux swap volume physical id: 2 bus info: scsi@0:0.0.0,2 logical name: /dev/sda2 version: 1 serial: 16a7fee0-be9e-4e34-9dc3-28f4eeb61bf6 size: 8091MiB capacity: 8091MiB capabilities: primary nofs swap initialized configuration: filesystem=swap pagesize=4096These are related /etc/fstab lines:
UUID=cc5c562a-bc59-4a37-b589-805b27b2cbd7 / ext3 errors=remount-ro,user_xattr 0 1
UUID=16a7fee0-be9e-4e34-9dc3-28f4eeb61bf6 none swap sw 0 08 Answers
Your hard disk has Advanced Format 4096-byte sectors to which the partition is not perfectly aligned
This line explains the warning:
Sector size (logical/physical): 512 bytes / 4096 bytes
- Your hard disk is one of the newer models which uses the Advanced Format of 4096 bytes per physical sector instead of the older 512 bytes/sector.
- These HDDs can still provide a "legacy" emulation of 512 bytes/sector, which is why you see the logical sector size as 512.
- In fact,
lshwshows it's a Western Digital drive, the first company to switch to AF. They have an extensive page with lots of information on it, which you may wish to look at.
Thus, the warning occurs because partition 1 starts at logical sector 63 = byte 32256, a number not divisible by 4096; in fact it's near the end of the 7th physical sector (position 7.875 to be exact :)
Should you fix it? If so, how? [always backup!]
In theory this sort of partitioning may affect read/write IO rates somewhat, depending on your drive's firmware. If you are happy with the performance now, ignore the warning, and no need to do anything. If not, backup all important data first, and then use Gparted to move the partition so that it starts at 4096-byte sector; setting the start boundary at 1 MiB is an easy way to do it.
- Technically, you can set the start to any logical sector which is a multiple of 8, e.g. 64 is good, 256 is good, etc., but 63, 255... are not.
For your new HDD, first create partitions using gparted as per your wish.
Then, access your HDD using sudo fdisk device_name.m command in fdisk will print help menu.
npcompete@npcompete-desktop:~$ sudo fdisk /dev/sda
The device presents a logical sector size that is smaller than
the physical sector size. Aligning to a physical sector (or optimal
I/O) size boundary is recommended, or performance may be impacted.
Command (m for help): p
Disk /dev/sda: 1000.2 GB, 1000204886016 bytes
255 heads, 63 sectors/track, 121601 cylinders, total 1953525168 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: 0x0008e009 Device Boot Start End Blocks Id System
/dev/sda1 2048 209717247 104857600 83 Linux
/dev/sda2 209717248 1953525167 871903960 5 Extended
/dev/sda5 600349113 795667319 97659103+ 83 Linux
Partition 5 does not start on physical sector boundary.
/dev/sda6 795667383 990985589 97659103+ 83 Linux
Partition 6 does not start on physical sector boundary.
/dev/sda7 990985653 1953520064 481267206 83 Linux
Partition 7 does not start on physical sector boundary.
/dev/sda8 209719296 600349112 195314908+ 83 Linux
Partition table entries are not in disk order
Command (m for help): d
Partition number (1-8): 5
Command (m for help): p
Disk /dev/sda: 1000.2 GB, 1000204886016 bytes
255 heads, 63 sectors/track, 121601 cylinders, total 1953525168 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: 0x0008e009 Device Boot Start End Blocks Id System
/dev/sda1 2048 209717247 104857600 83 Linux
/dev/sda2 209717248 1953525167 871903960 5 Extended
/dev/sda5 795667383 990985589 97659103+ 83 Linux
Partition 5 does not start on physical sector boundary.
/dev/sda6 990985653 1953520064 481267206 83 Linux
Partition 6 does not start on physical sector boundary.
/dev/sda7 209719296 600349112 195314908+ 83 Linux
Partition table entries are not in disk order
Command (m for help): w
The partition table has been altered!
Calling ioctl() to re-read partition table.
Syncing disks.
npcompete@npcompete-desktop:~$ sudo fdisk /dev/sda
The device presents a logical sector size that is smaller than
the physical sector size. Aligning to a physical sector (or optimal
I/O) size boundary is recommended, or performance may be impacted.
Command (m for help): n
Partition type: p primary (1 primary, 1 extended, 2 free) l logical (numbered from 5)
Select (default p): l
Adding logical partition 8
First sector (600351161-1953525167, default 600352768):
Using default value 600352768
Last sector, +sectors or +size{K,M,G} (600352768-795667382, default 795667382):
Using default value 795667382
Command (m for help): p
Disk /dev/sda: 1000.2 GB, 1000204886016 bytes
255 heads, 63 sectors/track, 121601 cylinders, total 1953525168 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: 0x0008e009 Device Boot Start End Blocks Id System
/dev/sda1 2048 209717247 104857600 83 Linux
/dev/sda2 209717248 1953525167 871903960 5 Extended
/dev/sda5 795667383 990985589 97659103+ 83 Linux
Partition 5 does not start on physical sector boundary.
/dev/sda6 990985653 1953520064 481267206 83 Linux
Partition 6 does not start on physical sector boundary.
/dev/sda7 209719296 600349112 195314908+ 83 Linux
/dev/sda8 600352768 795667382 97657307+ 83 Linux
Partition table entries are not in disk order
Command (m for help): w
The partition table has been altered!
Calling ioctl() to re-read partition table.
Syncing disks.Now delete the partition which gives warning using d option in fdisk.
First Command d, then the partition number (mentioned in the warning).
Now write the changes to the disk using w command. It will exit from the fdisk.
Second time access your HDD using sudo fdisk device_name.
Now create a new partition using the free space(previously we have deleted a partition, that will be the free space or unallocated space) using n command in fdisk.
In New partition command don't enter any value for First and Last Sector, just press Enter. it will take the default value.
Now write the changes to the disk using w command. It will exit from the fdisk.
Do the above steps for all the partitions. After finishing this format your newly created partitions, using gparted. (That's what I did worked for me. No warnings in fdisk -l output.)
0As pointed out by izx:
your hard disk has Advanced Format 4096-byte sectors to which the partition is not perfectly aligned.
The advanced format specification and its impact on user-side hard drive partitioning practices is explained nicely by this article.
To fix this issue you must backup your data and then:
- Either resize the erroneously sized partition to the proper size;
- Or delete the erroneously sized partition and create a new partition of the proper size.
To accomplish this using the graphical hard-drive partitioning software that is called GParted then you can:
Launch the Gparted application with super-user privileges; exercise caution!
gksudo gpartedSelect the storage device containing the erroneously sized partition from the pull-down menu in the upper right hand corner of the GParted menu.
Select the erroneously-sized partition by clicking on it in the rectangular partition map.
Now you may choose to delete and create a new partition or you may choose to resize the existing partition. Regardless of your choice you will reach a menu that allows you to set the size of the partition. You must clear the "Round to cylinders" checkbox and set the size of the free space preceding to 1MiB. It will look similar to
.
By switching the "u" units. The default sector size will show up when you create the partition. If you are starting to partition a new disk and you get this error, you can.
- create a partion with the defaut.
- n,p,1,Enter, Enter
- Display and get the partition error message. "p".
- switch units "u"
- delete the partition. "d"
- Now create again. this time the defaults will show the correct sector. (in my case it was 1024).
Command (m for help): p
Disk /dev/sdb: 599.9 GB, 599932844032 bytes
255 heads, 63 sectors/track, 72937 cylinders
Units = cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 262144 bytes / 524288 bytes
Disk identifier: 0x2016bdc5 Device Boot Start End Blocks Id System
Command (m for help): n
Command action e extended p primary partition (1-4)
p
Partition number (1-4): 1
First cylinder (1-72937, default 1): 1
Last cylinder, +cylinders or +size{K,M,G} (1-72937, default 72937):
Using default value 72937
Command (m for help): p
Disk /dev/sdb: 599.9 GB, 599932844032 bytes
255 heads, 63 sectors/track, 72937 cylinders
Units = cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 262144 bytes / 524288 bytes
Disk identifier: 0x2016bdc5 Device Boot Start End Blocks Id System
/dev/sdb1 1 72937 585866421 83 Linux
Partition 1 does not start on physical sector boundary.
Command (m for help): u
Changing display/entry units to sectors
Command (m for help): p
Disk /dev/sdb: 599.9 GB, 599932844032 bytes
255 heads, 63 sectors/track, 72937 cylinders, total 1171743836 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 262144 bytes / 524288 bytes
Disk identifier: 0x2016bdc5 Device Boot Start End Blocks Id System
/dev/sdb1 63 1171732904 585866421 83 Linux
Partition 1 does not start on physical sector boundary.
Command (m for help): d
Selected partition 1
Command (m for help): p
Disk /dev/sdb: 599.9 GB, 599932844032 bytes
255 heads, 63 sectors/track, 72937 cylinders, total 1171743836 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 262144 bytes / 524288 bytes
Disk identifier: 0x2016bdc5 Device Boot Start End Blocks Id System
Command (m for help): n
Command action e extended p primary partition (1-4)
p
Partition number (1-4): 8
Value out of range.
Partition number (1-4): 1
First sector (63-1171743835, default 1024):
Using default value 1024
Last sector, +sectors or +size{K,M,G} (1024-1171743835, default 1171743835):
Using default value 1171743835
Command (m for help): p
Disk /dev/sdb: 599.9 GB, 599932844032 bytes
255 heads, 63 sectors/track, 72937 cylinders, total 1171743836 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 262144 bytes / 524288 bytes
Disk identifier: 0x2016bdc5 Device Boot Start End Blocks Id System
/dev/sdb1 1024 1171743835 585871406 83 Linux
Command (m for help): w
The partition table has been altered!Just delete all partitions and do this with fdisk:
Command (m for help): c
DOS Compatibility flag is not set
Command (m for help): u
Changing display/entry units to sectors1. Solve it
I also encounter this problem, and this is how I suppress the annoying warning!
The key point is: set the start to any logical sector, which is a multiple of 8.
I set 204800 (because I can only choose from 65535-976773167).
step1 fdisk
$ fdisk /dev/sdf
The device presents a logical sector size that is smaller than
the physical sector size. Aligning to a physical sector (or optimal
I/O) size boundary is recommended, or performance may be impacted.
欢迎使用 fdisk (util-linux 2.23.2)。
更改将停留在内存中，直到您决定将更改写入磁盘。
使用写入命令前请三思。
命令(输入 m 获取帮助)：d
已选择分区 1
分区 1 已删除
命令(输入 m 获取帮助)：p
磁盘 /dev/sdf：500.1 GB, 500107862016 字节，976773168 个扇区
Units = 扇区 of 1 * 512 = 512 bytes
扇区大小(逻辑/物理)：512 字节 / 4096 字节
I/O 大小(最小/最佳)：4096 字节 / 33553920 字节
磁盘标签类型：dos
磁盘标识符：0xa2254a70 设备 Boot Start End Blocks Id System
命令(输入 m 获取帮助)：n
Partition type: p primary (0 primary, 0 extended, 4 free) e extended
Select (default p): p
分区号 (1-4，默认 1)：1
# the key point
# ⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬⏬
起始 扇区 (65535-976773167，默认为 65535)： 204800 （chose a multiple of 8）
Last 扇区, +扇区 or +size{K,M,G} (204800-976773167，默认为 976773167)：
将使用默认值 976773167
分区 1 已设置为 Linux 类型，大小设为 465.7 GiB
# 🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼🔼
命令(输入 m 获取帮助)：w
The partition table has been altered!
Calling ioctl() to re-read partition table.
正在同步磁盘。step2 format the disk
$ mkfs.ext4 /dev/sdf1
mke2fs 1.42.9 (28-Dec-2013)
文件系统标签=
OS type: Linux
块大小=4096 (log=2)
分块大小=4096 (log=2)
Stride=0 blocks, Stripe width=8191 blocks
30523392 inodes, 122071046 blocks
6103552 blocks (5.00%) reserved for the super user
第一个数据块=0
Maximum filesystem blocks=2271215616
3726 block groups
32768 blocks per group, 32768 fragments per group
8192 inodes per group
Superblock backups stored on blocks: 32768, 98304, 163840, 229376, 294912, 819200, 884736, 1605632, 2654208, 4096000, 7962624, 11239424, 20480000, 23887872, 71663616, 78675968, 102400000
Allocating group tables: 完成
正在写入inode表: 完成
Creating journal (32768 blocks): 完成
Writing superblocks and filesystem accounting information: 完成step3 the result
And, finally the warning is disappear.
$ fdisk -l /dev/sdf
磁盘 /dev/sdf：500.1 GB, 500107862016 字节，976773168 个扇区
Units = 扇区 of 1 * 512 = 512 bytes
扇区大小(逻辑/物理)：512 字节 / 4096 字节
I/O 大小(最小/最佳)：4096 字节 / 33553920 字节
磁盘标签类型：dos
磁盘标识符：0xa2254a70 设备 Boot Start End Blocks Id System
/dev/sdf1 204800 976773167 488284184 83 Linux
$ lsblk
NAME MAJ:MIN RM SIZE RO TYPE MOUNTPOINT
sda 8:0 0 223.6G 0 disk
├─sda1 8:1 0 500M 0 part /boot/efi
├─sda2 8:2 0 1G 0 part /boot
└─sda3 8:3 0 170G 0 part ├─centos--sda-root 253:0 0 100G 0 lvm / ├─centos--sda-swap 253:1 0 20G 0 lvm └─centos--sda-home 253:2 0 50G 0 lvm /home
sdb 8:16 0 1.8T 0 disk /data2
sdc 8:32 0 1.8T 0 disk
sdd 8:48 0 1.8T 0 disk /data1
sde 8:64 0 1.8T 0 disk /home
sdf 8:80 0 465.8G 0 disk
└─sdf1 8:81 0 465.7G 0 part2.How this problem looks like
Show disk
[root@dt120 data1]# lsblk
NAME MAJ:MIN RM SIZE RO TYPE MOUNTPOINT
sda 8:0 0 223.6G 0 disk
├─sda1 8:1 0 500M 0 part /boot/efi
├─sda2 8:2 0 1G 0 part /boot
└─sda3 8:3 0 170G 0 part ├─centos--sda-root 253:0 0 100G 0 lvm / ├─centos--sda-swap 253:1 0 20G 0 lvm └─centos--sda-home 253:2 0 50G 0 lvm /home
sdb 8:16 0 1.8T 0 disk /data2
sdc 8:32 0 1.8T 0 disk
sdd 8:48 0 1.8T 0 disk /data1
sde 8:64 0 1.8T 0 disk /home
sdf 8:80 0 465.8G 0 disk
└─sdf1 8:81 0 465.7G 0 partfdisk
$ fdisk /dev/sdf
欢迎使用 fdisk (util-linux 2.23.2)。
更改将停留在内存中，直到您决定将更改写入磁盘。
使用写入命令前请三思。
Device does not contain a recognized partition table
使用磁盘标识符 0xff020bf0 创建新的 DOS 磁盘标签。
The device presents a logical sector size that is smaller than
the physical sector size. Aligning to a physical sector (or optimal
I/O) size boundary is recommended, or performance may be impacted.
命令(输入 m 获取帮助)：p
磁盘 /dev/sdf：500.1 GB, 500107862016 字节，976773168 个扇区
Units = 扇区 of 1 * 512 = 512 bytes
扇区大小(逻辑/物理)：512 字节 / 4096 字节
I/O 大小(最小/最佳)：4096 字节 / 33553920 字节
磁盘标签类型：dos
磁盘标识符：0xff020bf0 设备 Boot Start End Blocks Id System
命令(输入 m 获取帮助)：n
Partition type: p primary (0 primary, 0 extended, 4 free) e extended
Select (default p): p
分区号 (1-4，默认 1)：1
起始 扇区 (65535-976773167，默认为 65535)：
将使用默认值 65535
Last 扇区, +扇区 or +size{K,M,G} (65535-976773167，默认为 976773167)：
将使用默认值 976773167
分区 1 已设置为 Linux 类型，大小设为 465.7 GiB
命令(输入 m 获取帮助)：p
磁盘 /dev/sdf：500.1 GB, 500107862016 字节，976773168 个扇区
Units = 扇区 of 1 * 512 = 512 bytes
扇区大小(逻辑/物理)：512 字节 / 4096 字节
I/O 大小(最小/最佳)：4096 字节 / 33553920 字节
磁盘标签类型：dos
磁盘标识符：0x2b6ce6ea 设备 Boot Start End Blocks Id System
/dev/sdf1 65535 976773167 488353816+ 83 Linux
Partition 1 does not start on physical sector boundary.
命令(输入 m 获取帮助)：w
The partition table has been altered!
Calling ioctl() to re-read partition table.
正在同步磁盘。
$ lsblk
NAME MAJ:MIN RM SIZE RO TYPE MOUNTPOINT
sda 8:0 0 223.6G 0 disk
├─sda1 8:1 0 500M 0 part /boot/efi
├─sda2 8:2 0 1G 0 part /boot
└─sda3 8:3 0 170G 0 part ├─centos--sda-root 253:0 0 100G 0 lvm / ├─centos--sda-swap 253:1 0 20G 0 lvm └─centos--sda-home 253:2 0 50G 0 lvm /home
sdb 8:16 0 1.8T 0 disk /data2
sdc 8:32 0 1.8T 0 disk
sdd 8:48 0 1.8T 0 disk /data1
sde 8:64 0 1.8T 0 disk /home
sdf 8:80 0 465.8G 0 disk
└─sdf1 8:81 0 465.7G 0 partformat
$ mkfs.ext4 /dev/sdf1
mke2fs 1.42.9 (28-Dec-2013)
/dev/sdf1 alignment is offset by 512 bytes.
This may result in very poor performance, (re)-partitioning suggested.
文件系统标签=
OS type: Linux
块大小=4096 (log=2)
分块大小=4096 (log=2)
Stride=0 blocks, Stripe width=8191 blocks
30523392 inodes, 122088454 blocks
6104422 blocks (5.00%) reserved for the super user
第一个数据块=0
Maximum filesystem blocks=2271215616
3726 block groups
32768 blocks per group, 32768 fragments per group
8192 inodes per group
Superblock backups stored on blocks: 32768, 98304, 163840, 229376, 294912, 819200, 884736, 1605632, 2654208, 4096000, 7962624, 11239424, 20480000, 23887872, 71663616, 78675968, 102400000
Allocating group tables: 完成
正在写入inode表: 完成
Creating journal (32768 blocks): 完成
Writing superblocks and filesystem accounting information: 完成the problem
Partition 1 does not start on physical sector boundary.
$ fdisk -l /dev/sdf
磁盘 /dev/sdf：500.1 GB, 500107862016 字节，976773168 个扇区
Units = 扇区 of 1 * 512 = 512 bytes
扇区大小(逻辑/物理)：512 字节 / 4096 字节
I/O 大小(最小/最佳)：4096 字节 / 33553920 字节
磁盘标签类型：dos
磁盘标识符：0xa2254a70 设备 Boot Start End Blocks Id System
/dev/sdf1 65535 976773167 488353816+ 83 Linux
Partition 1 does not start on physical sector boundary.I complete other excellent answers in this thread with an example of how to fix the warning numerically.
I could do all these operations from a live USB stick:
it provides the terminal, a calculator and, of course, GParted.
The problem is to adjust the start boundary of the partition.
Givens
For my case sudo fdisk -l signalled a few important things:
- The problematic partition started at the sector 12001278;
Sector size (logical/physical): 512 bytes / 4096 bytes;- The units of its display:
Units: sectors of 1 * 512 = 512 bytes.
Requirements
The requirement behind the warning
Partition X does not start on physical sector boundaryis that the partition boundary should be be at the beginning of a logical sector (individual size 512 B) and of a physical sector (individual size 4096 B). Therefore, the disk space in bytes before the beginning of the offending partition must be such that
n_L * 512 = n_P * 4096where n_L is the logical-sector count (the output of fdisk) and n_P is the physical-sector count. Both counts must be integers. Since 4096/512=8, this explains why 8 must be an integer divisor of n_L.
Action
In my case: 12001278/8 = 1500159.75, so the decimals spoil the party. I have then the choice to move the start of the partition to the left (making it larger) or to the right (making it smaller). The choice depends on what is convenient for you with the current partition table. Either way, Gparted will ask you to move the partition using MiB as units. So it is necessary to compute the displacement.
I chose to move the partition start to the left and round down the ratio 1500159.75:
- To obtain
n_L/8 = 1500159, you needn_L = 12001272. Compare with 12001278, so move the partition's start 6 logical sectors to the left. - Since the each logical sector is 512 B, I ask GParted to move the start of the partition 3 MiB before the current position. You may need to make space for this by shrinking the neighbouring partition.
After this displacement of 3 MiB, the warning disappeared. Of course: 12001272 * 512 = 4096 * 1500159.
If you have a windows dual boot you can use MiniTool Partition Wizard. This thing has saved my ass multiple times. Just right click the partition and click align. Don't forget to click apply.
