1. Introduction

When it comes to managing data on Linux systems, understanding and maintaining filesystems is crucial. As Linux enthusiasts and system administrators, one common issue we may encounter is a bad geometry error in the Fourth Extended (ext4) filesystem. This problem can prevent a filesystem from mounting correctly, leading to potential data inaccessibility.

In this tutorial, we’ll dive into ext4 filesystems, specifically focusing on how to address and resolve the bad geometry error. First, we’ll understand the ext4 filesystem and its geometry. Then, we’ll discuss common causes, preliminary checks, and detailed troubleshooting steps to get our system back on track if the bad geometry problem happens. Let’s get started!

2. Understanding ext4 Filesystem and Its Geometry

ext4 is the default filesystem for many Linux distributions. It’s known for its robustness and common usage in various environments, from personal computers to large servers. ext4 introduces several improvements over its predecessors like increased maximum volumes and file sizes, reduced fragmentation, and improved performance.

Filesystem geometry refers to how the system organizes and manages data within the filesystem. In the context of ext4, this involves understanding how the system arranges blocks, inodes, and other structural elements. Each filesystem has a specific way of allocating and managing these resources, which is crucial for the efficient operation of the system.

A clear grasp of these basics is vital when troubleshooting issues like bad geometry.

Typically, bad geometry means that there’s a mismatch or corruption in the filesystem’s metadata – the data that describes the structure and health of the filesystem itself. This could manifest as incorrect block counts, damaged superblocks, or inconsistencies in the inode tables. Understanding these components helps in diagnosing the root cause of the issue.

3. Common Causes of Bad Geometry in ext4

Encountering bad geometry in an ext4 filesystem can be a daunting issue. Understanding the common causes and adopting a practical approach to each is crucial in troubleshooting and resolving these problems. Let’s discuss some key ones.

3.1. Improper Resizing of Filesystems or Partitions

Resizing a filesystem, such as ext4, is a complex operation that modifies its structure. When this process is done incorrectly – perhaps due to using unsuitable tools or not adhering to proper procedures – the filesystem’s metadata, which includes information about its size and layout, can become misaligned with its actual physical structure.

Also, if we interrupt the resizing process, it can lead to discrepancies between the filesystem’s metadata and its actual size.

3.2. Faulty Disk or Partition Table Issues

The health and integrity of the underlying disk are critical to the filesystem’s stability.

Faults in the disk or errors in the partition table (the scheme that defines how the system organizes data on the disk) can manifest as bad geometry in the filesystem. This is particularly common in situations where disk cloning or imaging is done inaccurately, leading to mismatches between the expected and actual disk layout.

3.3. Unsuccessful Filesystem Checks or Repairs

Filesystem maintenance tools, like filesystem check (fsck), identify and correct filesystem errors.

However, in cases where the filesystem is severely damaged, or these tools are used inappropriately, they may fail to repair the filesystem adequately. Moreover, repeated unsuccessful attempts to fix the filesystem can further corrupt its structure, complicating the issue.

3.4. Power Failures or Improper Shutdowns

ext4, like many other filesystems, is vulnerable to disruptions caused by power failures or improper shutdowns. Such incidents can interrupt ongoing write operations, leaving the filesystem in an inconsistent state. This inconsistency often manifests as bad geometry, where the logical structure of the filesystem doesn’t align with its physical data.

3.5. Hardware Compatibility Issues

Sometimes, the root cause of bad geometry lies not in the filesystem itself but in the compatibility between the hardware components.

Older or incompatible hardware, particularly disk drives, motherboards, and disk controllers, can report inaccurate disk geometry information. This misreporting can mislead the filesystem, leading to discrepancies in how the disk organizes and accesses stored data.

Understanding these causes is a vital step in troubleshooting bad geometry in ext4 filesystems. With this knowledge, we can proceed with targeted diagnostics and apply effective remedies.

4. Preliminary Checks and Preparations

Before we dive into the intricate troubleshooting process of the bad geometry error on the filesystem, it’s essential to lay the groundwork with several preliminary checks and preparations. These initial steps are not just routine procedures; they’re critical measures that can significantly prevent data loss and ensure a smoother and more effective resolution process.

4.1. Data Backup

The paramount concern in any form of system repair or troubleshooting is the safety and integrity of our data.

Therefore, first and foremost, we should ensure that we back up all critical data on the affected filesystem. This is a crucial step, as some repair procedures can potentially lead to data loss. If the filesystem is partially accessible, we should try to copy the important files to another storage device.

However, if the ext4 filesystem isn’t mountable due to bad geometry or other issues, it’s essential to consider data recovery tools capable of reading the filesystem in its raw state.

Here are some notable tools for this purpose:

  • TestDisk – A powerful open-source tool to recover lost partitions and make non-booting disks bootable again. TestDisk is particularly effective for cases involving corrupted partition tables and can also gather data from raw filesystems.
  • PhotoRec – Another powerful tool that specializes in file recovery. Despite its name, it’s not limited to photo recovery and can retrieve various file types. PhotoRec ignores the filesystem and goes after the underlying data, making it a good choice for recovering files from a damaged ext4 filesystem.
  • R-Linux – A free file recovery utility specifically designed for the ext filesystem family (ext2, ext3, ext4). It’s user-friendly and useful for recovering lost files due to virus attack, system crash, or disk reformatting.
  • Foremost – A forensic program to recover lost files. It works on the principle of carving, which involves searching for file headers and footers in the raw data of the disk, making it a handy tool for ext4 filesystems that cannot be mounted.

Each of these tools has its unique strengths and application scenarios. For instance, if the goal is to recover specific file types like documents or media files, PhotoRec and Foremost are excellent choices. On the other hand, for more comprehensive partition recovery, TestDisk might be the preferred option.

4.2. Checking Disk and Partition Health

It’s also important to assess the health of our disk and partitions. This step helps in identifying if the problem lies with the filesystem or with the physical storage itself.

To do this, first, we can use fdisk -l with administrative privileges (sudo) to list all the partitions on all disks:

$ sudo fdisk -l
Disk /dev/sda: 500 GiB, 536870912000 bytes, 1048576000 sectors
Disk model: XYZ123
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: gpt
Disk identifier: D3B8AC2B-1234-5678-91AB-CDEF12345678

Device         Start       End   Sectors   Size Type
/dev/sda1       2048   1050623   1048576   512M EFI System
/dev/sda2    1050624 500000000 498949377 237.8G Linux filesystem

Our output reveals basic information about the disk(s).

However, we should focus on the Start and End columns, as these columns show the starting and ending sectors of the partition. Alignments here are critical, as inconsistencies might suggest a partitioning issue. In this example, the consistency in the start and end values indicates a green light.

4.3. Checking for Disk Errors With smartctl

The Self-Monitoring, Analysis, and Reporting Technology (SMART) data provides insights into the health and operational status of a disk.

We can use the smartctl command from the smartmontools package to inspect the SMART data of our hard drive:

$ sudo smartctl -a /dev/sda
smartctl 7.1 2019-12-30 r5022 [x86_64-linux-5.4.0-42-generic] (local build)
Copyright (C) 2002-20, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Model Family:     XYZ Solid State Drives
Device Model:     XYZ SSD Plus 240GB
Serial Number:    123456789ABC
LU WWN Device Id: 5 123456 789abcdef
Firmware Version: XYZ123
User Capacity:    240,057,409,536 bytes [240 GB]
Sector Size:      512 bytes logical/physical
Rotation Rate:    Solid State Device
Form Factor:      2.5 inches

=== START OF READ SMART DATA SECTION ===
SMART overall-health self-assessment test result: PASSED

ID# ATTRIBUTE_NAME          FLAG     VALUE WORST THRESH TYPE      UPDATED  WHEN_FAILED RAW_VALUE
  5 Reallocated_Sector_Ct   0x0033   100   100   010    Pre-fail  Always       -       0
  9 Power_On_Hours          0x0032   095   095   000    Old_age   Always       -       2200
 12 Power_Cycle_Count       0x0032   099   099   020    Old_age   Always       -       1050
...

In this example, the SMART data provides insights into the health and operational status of a disk (/dev/sda, which we can replace with any disk revealed by fdisk -l from our previous interaction).

From our output, we should keep an eye on the SMART Health Status and any attributes where the VALUE is close to or below the THRESH value, as this might indicate potential or imminent drive failure. Also, unusual RAW_VALUE readings can be indicators of drive issues.

5. Using fsck for Filesystem Checks

Our first line of defense against bad geometry due to filesystem corruption is the fsck command. It’s a powerful tool we can use to check and repair filesystem inconsistencies.

We can use fsck on an ext4 filesystem and fix the bad geometry problem.

Furthermore, with the -p flag, we automatically repair any problems that can be safely fixed without user intervention:

$ sudo fsck.ext4 -p /dev/sda1
Pass 1: Checking inodes, blocks, and sizes
Pass 2: Checking directory structure
Pass 3: Checking directory connectivity
Pass 4: Checking reference counts
Pass 5: Checking group summary information

/dev/sda1: 11/65536 files (0.0% non-contiguous), 10485/262144 blocks

The output of fsck can be extensive, but it typically includes information about the inode count, block count, and any errors found and fixed.

As we can see, the final line of our output provides a summary:

  • 11/65536 files – indicates that there are 11 files and the filesystem has 65536 inodes in total
  • (0.0% non-contiguous) – shows the percentage of non-contiguous files, which is 0.0% in this case, indicating good file fragmentation
  • 10485/262144 blocks – indicates that 10485 blocks are used out of 262144 total blocks

In short, our output here indicates that the filesystem has been checked and, if -p was effective, necessary repairs have been made automatically.

6. Addressing Partition Table Issues

When fsck from our previous interaction fails to resolve filesystem issues, the problem may lie with the partition table.

The partition table is a critical data structure on a disk that defines how the system divides a disk into partitions. This table holds the information about the size and location of each partition. If this table is corrupt or misconfigured, it can lead to a range of disk-related problems, including issues that fsck cannot fix and thus problems like “bad geometry.”

6.1. Using sfdisk for Partition Table Analysis

sfdisk is a versatile tool for dealing with partition tables in Linux.

Using sfdisk with the -d option dumps the current partition table, allowing for inspection and backup:

$ sudo sfdisk -d /dev/sda > sda.txt

Here, we save the partition table of /dev/sda to a file sda.txt.

Now, we can inspect the saved file sda.txt with the cat command:

$ cat sda.txt
label: dos
label-id: 0x0007c45d
device: /dev/sda
unit: sectors

/dev/sda1 : start=        2048, size=    2097152, type=83
/dev/sda2 : start=     2099200, size=   10485760, type=83

This dumped data is crucial for analyzing the current state of the partition table.

6.2. Restoring the Partition Table

After inspecting the partition table, if we notice discrepancies or errors and we have a correct and valid backup (probably sda_backup.txt), we can also restore it using sfdisk:

$ sudo sfdisk /dev/sda < sda_backup.txt
Checking that no-one is using this disk right now ... OK

Disk /dev/sda: 500 GiB, 536870912000 bytes, 1048576000 sectors
Disk model: XYZ123
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: gpt
Disk identifier: D3B8AC2B-1234-5678-91AB-CDEF12345678

Old situation:

New situation:
Disklabel type: dos
Partition 1 does not start on physical sector boundary.

The partition table has been altered.
Calling ioctl() to re-read partition table.
Syncing disks.

From our output, the line “Partition 1 does not start on physical sector boundary.” is a warning that can occur, especially with older partitioning schemes, indicating potential misalignment. This might not be an issue for modern systems but could impact performance on older ones.

Finally, the message “The partition table has been altered.” confirms that the changes have been made. Then, the system calls ioctl() to make the operating system re-read the partition table. The last line, “Syncing disks,” ensures that all pending changes to disk structures are written out from memory to disk.

7. Addressing Physical Disk Damage

In some instances, ext4 filesystem issues like bad geometry transcend the realm of simple fixes and enter more complex territories, such as physical disk damage or severe corruption.

Physical damage to a disk, like bad sectors, head crashes, or motor failures, can have severe consequences, including filesystem corruption and bad geometry errors. Bad sectors are areas of the disk that are physically damaged and cannot reliably hold and store data.

With tools like badblocks, we can identify bad sectors:

$ sudo badblocks -sv /dev/sda
Checking blocks 0 to 976762583
Checking for bad blocks (read-only test): done                                                 
Pass completed, 5 bad blocks found. (5/0/0 errors)

Our output shows that badblocks is performing a read-only test, scanning each block to see if it can be read successfully.

Then, it completes the scan and identifies 5 bad blocks. The (5/0/0 errors) breakdown shows that all 5 errors are read errors, with no write or corruption errors detected.

In cases like this, continued use of the disk with bad blocks might cause further harm. It’s crucial to stop using the disk.

7.1. Using ddrescue for Disk Cloning

When dealing with a failing disk, especially one with bad sectors or physical damage, cloning the disk to a healthy one is a prudent step. This process can help salvage data that might otherwise be lost.

We can clone a disk to a healthy one using tools like ddrescue. This process creates a bit-by-bit copy of the drive, potentially circumventing bad sectors:

$ sudo ddrescue /dev/sda /dev/sdb /path/to/logfile.log
GNU ddrescue 1.25
Press Ctrl-C to interrupt
rescued:     10240 kB,  errsize:       0 B,  current rate:    20480 kB/s
   ipos:     10240 kB,   errors:       0,    average rate:    15360 kB/s
   opos:     10240 kB, run time:       1 s,  successful read:       0 s ago

This clones the disk /dev/sda to /dev/sdb, with the progress and error log being saved to /path/to/logfile.log.

Let’s better understand our output from ddrescue:

  • rescued – amount of data successfully copied so far
  • errsize – size of the data that has not been successfully copied (due to errors, etc.)
  • current rate/average rate – current and average data transfer rates
  • ipos/opos – input and output positions (i.e., how far along the source and destination disks ddrescue has processed)
  • errors – number of errors encountered so far
  • run time – current duration of the ddrescue process
  • successful read – time since the last successful read operation

A successful ddrescue operation will show a growing amount of rescued data and ideally a low or zero errsize. The presence of errors (errors count) indicates problem areas on the source disk. A completed run without errors suggests a successful clone.

7.2. Importance of the Log File

The log file in ddrescue is crucial, especially for large or damaged drives.

If the process is interrupted (for example, due to power failure), we can resume ddrescue without starting over, using the same log file. This makes recovery from large or severely damaged drives more feasible.

8. Preventing Future ext4 Geometry Issues

In filesystem management, particularly with the ext4 format, ensuring the long-term integrity of our filesystems often hinges on adopting proactive measures and best practices.

One of the most pivotal practices is the regular backing up of data. This strategy stands as a robust safeguard against potential data loss due to filesystem corruption or hardware failure. Automated backup solutions, which methodically and consistently back up critical data, can be a cornerstone in our data protection strategy.

Also, we can’t overstate the importance of safe system practices. Ensuring that we always shut down our system properly plays a crucial role in maintaining filesystem health. Abrupt power losses or forced restarts can leave our filesystem in an inconsistent state, heightening the risk of corruption. This is particularly true for journaled filesystems like ext4, where unexpected interruptions can disrupt the journaling process, leading to potential filesystem inconsistencies.

Moreover, the value of regular filesystem checks stands as a proactive measure to catch and address issues early. Tools like fsck are instrumental in this regard, offering a means to routinely check for and repair filesystem inconsistencies. It’s particularly wise to run these checks following any improper shutdowns or unexpected system crashes, as these incidents are common precursors to filesystem problems.

Lastly, when it comes to partitioning drives, precision and foresight are key. We must ensure that partitions are correctly aligned and sized appropriately. Misaligned partitions can lead to inefficient disk usage and a heightened risk of filesystem errors. Employing reliable tools like gparted for partition management helps in maintaining optimal partition structures, thereby fostering a healthy filesystem environment.

9. Conclusion

In this article, we discussed the complexities of resolving bad geometry errors in ext4 filesystems, a common yet challenging issue in the Linux environment. From understanding the fundamentals of ext4 and its geometry to diving deep into troubleshooting methods, we’ve covered a comprehensive range of strategies to address this problem.

We began by identifying common causes of bad geometry, such as improper resizing or physical disk issues. Then, we moved on to preliminary checks to ensure the safety and readiness for troubleshooting.

Beyond the basic troubleshooting, we explored advanced solutions for more complex scenarios, like dealing with physical disk damage and cloning the failed disk into a new one. Recognizing the importance of proactive measures, we also discussed best practices in partitioning, filesystem management, and regular maintenance tips to prevent future occurrences of ext4 geometry issues.

Comments are closed on this article!