1. Introduction

When managing partitions on a Linux system, we might occasionally encounter a warning that says, “Partition does not start on physical sector boundary.” This message can appear intimidating, especially if we’re not sure what it means or how it impacts our system.

In this tutorial, we’ll dive into the nitty-gritty of this warning, exploring its causes and how it affects our system’s performance, particularly the storage drives. First, we’ll explore the technical aspects of this warning, why alignment matters, and, most importantly, how to resolve it.

Whether we’re seasoned Linux enthusiasts or just getting started in Linux system administration, understanding this issue is crucial, as proper partition alignment plays a key role in ensuring optimal disk performance and longevity. Let’s get started!

2. Understanding the Warning

At its core, this warning is essentially an alert about misalignment during disk partitioning or inspection in Linux environments. This misalignment occurs between the logical start of a partition and the physical sectors of the hard disk.

To better understand this, let’s briefly recap the concept of sectors.

A sector is the smallest unit that can be accessed on a disk. Traditionally, these sectors were 512 bytes in size. However, as technology evolved with the advent of modern drives, especially those with Advanced Format technology, the physical sector size has increased to 4096 bytes (or 4 KiB).

2.1. Logical vs. Physical Sector Sizes

This increase in sector size is where the root of our warning lies. Modern hard drives now often use a combination of physical sectors (4096 bytes) and logical sectors (512 bytes). The logical sector size is maintained for compatibility with older systems that expect 512-byte sectors. However, the actual physical storage on the disk is organized in 4096-byte sectors.

A partition is considered misaligned when it starts on a logical sector that doesn’t coincide with the beginning of a physical sector. This misalignment can cause inefficiencies.

For instance, if a partition begins at logical sector 63, it corresponds to byte 32256 on the disk. However, since this number isn’t divisible by 4096, the partition starts near the end of the 7th physical sector. This means the data is spread across more physical sectors than necessary, thus leading to potential performance issues due to increased read/write operations.

Misalignment not only affects performance but can also lead to increased wear and tear on the disk. Each read/write operation now involves multiple physical sectors, leading to more mechanical movement in traditional Hard Disk Drives (HDDs) and more wear in Solid-State Drives (SSDs) due to increased read-modify-write cycles.

2.2. The Impact of Misalignment on System Performance

When a partition is misaligned in a Linux system, the effects on system performance can be quite significant, particularly in scenarios involving high input/output (I/O) operations.

Misalignment causes the system to potentially read or write to two physical sectors instead of one for the same amount of data. This doubling of I/O operations for a given data size leads to several consequences.

Firstly, there’s a noticeable slowdown in data transfer speeds. The need to engage more physical sectors for each operation means that data moves slower than it would in a well-aligned system. This is especially evident in tasks that involve large amounts of data transfer.

Additionally, increased latency is another outcome of misalignment. The system takes more time to read or write data because it effectively handles more operations than necessary. This added delay can be particularly problematic in environments where speed and efficiency are paramount, such as database management or file servers.

Moreover, there’s an uptick in Central Processing Unit (CPU) usage. The processor has to deal with an increased load due to the additional processing required for these extra I/O operations. This can lead to a general slowdown of the system, as the CPU is preoccupied with disk-related tasks, leaving less processing power available for other applications and processes.

Finally, for SSDs, misalignment can lead to a decrease in the drive’s endurance. SSDs suffer from more write amplification in a misaligned scenario, meaning that they have to write more data than necessary. This excessive writing accelerates the wear and tear on the SSD, potentially shortening its lifespan.

3. Identifying Misaligned Partitions

The significance of understanding and resolving partition misalignment is clear. It’s not just a matter of maintaining optimal performance but also of preserving the health and longevity of the storage device.

However, in some cases, particularly with older systems or where performance is not a critical factor, we might choose to ignore this warning. If our system is running smoothly with utmost satisfaction, the urgency to resolve this warning diminishes. But, for systems where disk performance is critical, such as servers or high-performance computing platforms, addressing misalignment is essential.

Let’s explore some ways to identify these misaligned partitions.

3.1. Using fdisk

We can use the fdisk tool to see detailed information about our disk’s partitions and their alignment:

$ sudo fdisk -l
Disk /dev/sda: 1.8 TiB, 2000398934016 bytes, 3907029168 sectors
Disk model: XYZ123
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disklabel type: gpt
Disk identifier: ABCD-EFGH

Device       Start       End   Sectors  Size Type
/dev/sda1     2048   2099199   2097152    1G Linux filesystem
/dev/sda2  2099200 3907028991 3904929792  1.8T Linux filesystem

As we can see, the fdisk command lists the partitions on all our disks, along with crucial details like the Start and End sectors. We should look for the warning about partitions not starting on a physical sector boundary, as this indicates a potential misalignment.

Here, the Start column lists the starting sectors for each partition. For optimal alignment, these numbers should be divisible by 8 (since 4096 bytes/512 bytes = 8). In this example, both partitions start at sectors that are multiples of 8, suggesting a proper alignment and no need for concern.

3.2. Using lshw

For a more detailed and concise analysis, especially regarding the hardware specifications, we can use the lshw command:

$ sudo lshw -class disk -class storage
  *-disk
       description: ATA Disk
       product: XYZ123
       physical id: 0
       bus info: scsi@0:0.0.0
       logical name: /dev/sda
       version: AB12
       serial: 12345678
       size: 1.82TiB (2TB)
       capabilities: partitioned partitioned:dos
       configuration: ansiversion=5 sectorsize=4096 signature=00012345

Here, our output is more focused on the disk hardware. The sectorsize detail is crucial as it shows the physical sector size.

In this example, a 4096-byte sector size is shown. This confirms the physical sector size, which is essential when assessing alignment. As we stated earlier, correctly aligned partitions should start on a sector number that is a multiple of the ratio between physical and logical sector sizes.

4. Fixing Misalignment With fdisk

To easily fix a misaligned partition with fdisk, we’ll need to delete and recreate it. Therefore, our first step is to backup important data on the partition and, if possible, the entire drive. Once we have a secure backup, we can proceed with confidence.

After backing up our data, let’s launch fdisk and use ‘p‘ to check for existing partitions:

$ sudo fdisk /dev/sda
[...]
Command (m for help): p
Disk /dev/sda: 1.8 TiB, 2000398934016 bytes, 3907029168 sectors
Device     Start       End   Sectors  Size Type
/dev/sda1  2048   2099199   2097152    1G Linux filesystem
/dev/sda2  1050625 3907028991 3905978367 1.8T Linux filesystem

Here, we can notice that /dev/sda2 starts at 1050625, which isn’t divisible by 8, indicating a misalignment.

Now, let’s delete /dev/sda2 for recreation.

4.1. Deleting the Misaligned Partition

To delete a partition, we use ‘d‘ in fdisk, then enter the number of the partition we want to delete (in this example, 2):

[...]
Command (m for help): d
Partition number (1,2, default 2): 2

To reiterate, this will erase the partition (sda2) and its data.

After deleting the misaligned partition (sda2), we can now recreate a new partition with ‘n‘:

Command (m for help): n
Partition type
   p   primary
   e   extended
Select (default p): p
Partition number (2-4, default 2): 2
First sector (2099200-3907029167, default 2099200): 2099200
Last sector, +/-sectors or +/-size{K,M,G,T,P} (2099200-3907029167, default 3907029167): 

We should ensure the first sector is divisible by 8. Here, we use the default (2099200).

If required, we can also set the partition type with ‘t‘:

Command (m for help): t
Partition number (1,2, default 2): 2
Hex code (type L to list all codes): 83

Here, we use 83 for the Linux filesystem.

Finally, we can write the changes to the disk using ‘w‘:

Command (m for help): w

If we want, we can format and mount the partition with mkfs:

$ sudo mkfs.ext4 /dev/sda2
mke2fs 1.45.6 (20-Mar-2020)
Creating filesystem with 488247040 4k blocks and 122101760 inodes
Filesystem UUID: 5f4ec43e-7dfb-4658-8267-d72bbaae30f5
Superblock backups stored on blocks: 
    32768, 98304, 163840, 229376, 294912, 819200, 884736, 1605632, 2654208, 
    4096000, 7962624, 11239424, 20480000, 23887872

Allocating group tables: done                            
Writing inode tables: done                            
Creating journal (262144 blocks): done
Writing superblocks and filesystem accounting information: done

After this operation, the system formats /dev/sda2 with an ext4 filesystem and is ready to be mounted and used.

Convincingly, we can run the fdisk -l /dev/sda command again to verify our new change and see that /dev/sda2 now starts at the correct sector.

4.2. Alternatives to fdisk

Apart from fdisk to fix partition realignment, we can use other tools like GParted and KDE Partition Manager to help us resize and realign our partitions.

While these alternatives exist, the process of realigning partitions, especially without deleting them, can be complex, and we must tread carefully.

5. Advanced Considerations for Partition Alignment

When we dive deeper into the realm of partition alignment in Linux, several advanced aspects warrant our attention. These not only enhance our understanding but also provide more nuanced solutions to complex scenarios.

5.1. The Impact on Different Filesystems

Various filesystems can react differently to misalignment. For example, filesystems like ext4 or XFS are designed to be more resilient to misalignment issues compared to older filesystems like ext3.

However, no filesystem is completely immune to the performance penalties that can arise from misalignment. We must consider the type of filesystem in use when addressing partition alignment issues.

5.2. Alignment in SSDs and Hybrid Drives

SSDs and hybrid drives, which combine SSD and HDD technology, also require careful consideration regarding alignment.

SSDs, in particular, have a different architecture compared to traditional HDDs, and misalignment can significantly impact their performance and lifespan. The wear-leveling algorithms in SSDs work best when data is evenly distributed, which is facilitated by proper alignment.

5.3. The Role of Advanced Partitioning Schemes

Advanced partitioning schemes like the GUID Partition Table (GPT) offer more flexibility and resilience than the traditional Master Boot Record (MBR) scheme.

For instance, GPT is better suited for modern, large drives and typically aligns partitions correctly by default.

Understanding and utilizing these advanced partitioning schemes can be a proactive step in preventing alignment issues.

6. Conclusion

In this article, we explored the complexities of the “Partition does not start on physical sector boundary” warning in Linux. Starting from the basics of understanding sector sizes and alignment, we delved into practical steps for identifying and resolving alignment issues using tools like fdisk. We covered not just the how-tos but also the whys, emphasizing the importance of alignment for optimal disk performance and longevity.

Additionally, we touched upon advanced considerations like the impact on different filesystems, the specifics of SSDs and hybrid drives, and the advantages of modern partitioning schemes like GPT.

Finally, we must remember that the key to successful disk management is caution and a good backup strategy.

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