Prometheus does not have a dedicated repair command because its storage engine is designed to be self-healing through compaction and garbage collection. To resolve data corruption or index issues, you must stop the service, remove affected block directories from the tsdb path, and restart Prometheus to force a fresh reload of healthy data.
Understanding Prometheus Storage Integrity
The Prometheus time-series database stores data in blocks on disk. Each block represents a two-hour window of retention and contains compressed chunks of metrics data along with an index file. Unlike traditional relational databases, Prometheus does not perform in-place updates. Instead, it appends new data and periodically compacts older blocks into larger ones for efficient long-term storage. This append-only design means that "repair" is rarely a matter of fixing a single record; it is usually about removing corrupted segments so the system can rebuild them from source.
Corruption typically arises from unexpected shutdowns, disk I/O errors, or insufficient storage space during write operations. When a block is partially written or its index becomes inconsistent, Prometheus may fail to scrape or query that specific time range. In severe cases, the entire server might refuse to start if the head block is corrupted. Understanding this architecture is crucial because it dictates that recovery involves deletion rather than editing.
Assessing the Damage
Before taking any action, you need to identify which blocks are problematic. You can inspect the status of your local storage by checking the Prometheus web interface under the Status > Targets menu, but this only shows scraping health, not storage integrity. For deeper inspection, use the administrative API endpoint at /api/v1/status/tsdb. This JSON response provides details about each block, including its min and max timestamps, size, and whether it is compacted. Look for blocks marked as corrupt or those that have failed to load. If the API itself fails to respond, the corruption is likely in the active head block, requiring immediate intervention.
Step-by-Step Repair Procedure
The standard procedure for repairing Prometheus involves stopping the instance, cleaning the bad data, and restarting. Follow these steps carefully to avoid data loss beyond the corrupted segments.
- Stop the Prometheus Service: Prevent further writes to the disk. Use your system's service manager, such as systemd, to halt the process. Running
systemctl stop prometheusensures no new data is appended while you manipulate the files. - Backup the Data Directory: Before deleting anything, copy the entire
--storage.tsdb.pathdirectory to a safe location. This is critical because once deleted, the data cannot be recovered unless you have remote replication or long-term storage configured. - Identify Corrupted Blocks: Navigate to the TSDB directory. You will see folders named with timestamp hashes (e.g.,
01H2J3K4L5M6N7P8Q9R0S1T2U3). Use thepromtool tsdb checkcommand against specific block directories to verify their integrity. For example:
If the command returns an error, that block is corrupted.promtool tsdb check /path/to/prometheus/data/01H2J3K4L5M6N7P8Q9R0S1T2U3 - Delete Corrupted Blocks: Remove the directories identified in the previous step. Do not delete the current head block unless absolutely necessary, as this results in the loss of recent data points. Removing older, corrupted blocks allows Prometheus to skip them during startup.
- Restart Prometheus: Start the service again. Prometheus will scan the remaining blocks, skip the missing ones, and begin writing new data. Check the logs for warnings about skipped blocks to confirm the issue is resolved.
Preventing Future Corruption
Recovery is reactive; prevention is proactive. Ensure your underlying filesystem is mounted with appropriate flags, such as noatime, to reduce I/O overhead. Regularly monitor disk space usage, as running out of space during compaction is a primary cause of corruption. Additionally, configure remote storage backends like Thanos or Cortex to ensure that even if local disks fail, you retain historical data. This approach minimizes the impact of local repairs, as you can often restore data from remote repositories rather than relying solely on local blocks.
If you are experiencing issues with metric scraping despite healthy storage, consider reviewing related troubleshooting guides. For problems involving cluster applications not being scraped, see Prometheus Stack Operator Not Scraping Metrics of Cluster Application. While unrelated to direct storage repair, network and configuration issues often mimic storage failures. Another common scenario involves DNS resolution errors that prevent targets from being reached, detailed in Troubleshooting Host Name Lookup and DNS Resolution on Tech Support Sites.
Frequently Asked Questions
Can I use promtool to fix a corrupted WAL?
No, promtool cannot repair Write-Ahead Log (WAL) files directly. The WAL is used for crash recovery before data is committed to blocks. If the WAL is corrupted, you must delete the entire TSDB data directory and allow Prometheus to re-scrape all data from the beginning, provided you have long-term retention elsewhere.
Will deleting a block cause data gaps?
Yes, deleting a block creates a gap in your time series for that specific two-hour window. However, if the block is corrupted, queries over that period would already return errors or incomplete data. Deleting it restores system stability, allowing you to visualize other healthy periods.
How do I know if my disk is failing?
Check your system logs (/var/log/syslog or dmesg) for I/O errors. Prometheus logs will also show frequent "compaction failed" or "block load failed" messages. If these errors persist after cleaning up corrupted blocks, your hardware storage may be physically degraded.
Is there a way to repair without losing data?
Not natively. Prometheus relies on idempotent writes and compaction. There is no tool to patch a broken index file. Your best option is to rely on remote storage backups to fill the gaps left by deleted local blocks.
What happens if I delete the head block?
Deleting the head block forces Prometheus to create a new one upon restart. You will lose all metrics collected since the last successful compaction, which could be minutes or hours of data. Always try to isolate and delete only older, corrupted blocks first.