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If a Linux timestamp repeats, moves backward by one second, or differs from another host around a leap second, first separate two problems: wall-clock behavior and elapsed-time measurement. Keep CLOCK_REALTIME for civil timestamps, but use CLOCK_MONOTONIC (or, for specialized cases, CLOCK_MONOTONIC_RAW) for durations, deadlines, retries, and event ordering. Then ensure exactly one time daemon controls the host and choose one chrony leap policy: system, step, slew, or ignore.
The one-second anomaly is usually not repaired by editing stored timestamps. It is fixed by selecting the right clock in the application, removing competing time services, keeping leap-second data current, and verifying synchronization after the change.
What the one-second error actually means
Linux exposes several clock domains with different guarantees. CLOCK_REALTIME represents UTC-style civil time used for filesystem times, audit records, logs, expiry dates, and timestamps that must remain meaningful after a reboot. It is not an elapsed-time clock. The kernel documentation specifically warns that realtime can jump backward because of a leap-second update, an NTP adjustment, or a userspace settimeofday() operation.
For an inserted leap second, chrony documents the sequence as a one-second backward step when the kernel clock reaches 00:00:00 UTC. A deleted leap second is handled with a forward step at 23:59:59 UTC. Because the normal Linux realtime interface follows POSIX-style civil-time numbering and does not expose a regular numeric 23:59:60 value, two events can receive the same wall-clock second or appear out of order.
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An NTP correction can produce the same symptom even when no leap second is involved. If the daemon discovers that the host is ahead or behind, it may step the wall clock or gradually change its rate. A log that uses realtime for both event labels and duration arithmetic therefore cannot assume that successive numeric timestamps strictly increase.
The important distinction is between a timestamp’s meaning and its ordering. Realtime tells a reader approximately when an event occurred according to civil time, but it is allowed to be corrected. A monotonic reading has no calendar meaning, yet it is suitable for measuring the interval between two events. Treating either clock as if it supplied both guarantees is the usual cause of “negative duration” and “timeout fired early” bugs.
Choose the correct clock for each job
| Clock | Meaning | Can move backward? | NTP frequency adjustment | Use it for | Do not use it for |
|---|---|---|---|---|---|
CLOCK_REALTIME |
System wall clock and civil UTC timestamps | Yes, during leap handling or a clock step | Yes; its rate can be corrected | User-visible time, expiry dates, audit and persisted timestamps | Timeouts, latency, retry intervals, or ordering assumptions |
CLOCK_MONOTONIC |
Elapsed time since an unspecified starting point | No, under normal Linux clock semantics | Its rate may be adjusted to keep elapsed time aligned with system time | Deadlines, durations, watchdogs, retries, latency and event ordering | Persisted timestamps or dates shown to users |
CLOCK_MONOTONIC_RAW |
Raw hardware-derived elapsed time | No, under normal operation | Excludes NTP frequency adjustments | Measurements that specifically require the hardware rate | Long-term civil-time correlation or wall-clock display |
CLOCK_TAI |
Continuous atomic-time reference with leap-second semantics | Does not jump on leap-second updates | Depends on synchronization of the host’s TAI offset | Applications that need an atomic, leap-aware timeline and understand its semantics | Ordinary user-facing UTC dates unless conversion is deliberate |
The practical rule is simple: record both a wall-clock value and a monotonic start or deadline when an operation needs human-readable timestamps and reliable duration measurement. The wall-clock value answers “when,” while the monotonic value answers “how long.” Never subtract two CLOCK_REALTIME readings to decide whether a timeout has expired.
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One free scan finds every outdated or missing driver and matches the right update for your exact hardware.Free scan · exact hardware matchCLOCK_TAI is different from merely adding a fixed offset to UTC. Its value depends on the host’s current TAI-UTC information, so consumers must document how values are converted and exchanged. It is appropriate only when downstream code understands atomic-time semantics. For ordinary logs, UTC realtime remains easier to interpret, provided that ordering and duration fields are not derived from it.
Why a leap second can duplicate a displayed second
At an insertion, the announced leap is represented by a correction at the UTC boundary. The kernel can reach the beginning of the next day and then step the realtime value backward by one second. A service that sampled the clock immediately before and after that operation may therefore see the same second twice. A deletion removes a second from the transition and produces the opposite, forward adjustment. Neither behavior means that the hardware timer stopped; it means the civil-time representation was corrected.
The Linux clock_settime(2) documentation also makes clear that CLOCK_REALTIME ignores leap seconds as a regular numeric timeline. Code that expects a literal 23:59:60 value, or assumes every integer second exists exactly once, is not portable across the standard realtime interface. If an application needs to preserve the leap event itself, store an explicit event marker or use a time representation whose leap semantics are documented rather than inferring it from adjacent realtime values.
Diagnose the host before changing leap policy
Changing chrony while another daemon is still active can create repeated steps, unstable offsets, and misleading leap status. Establish which service owns the system clock first.
- Check the common time services:
systemctl status chronyd systemd-timesyncd. - Inspect the overall clock state with
timedatectl statusandtimedatectl show. - Identify distribution-specific configuration files and enabled units. A package may use
chronyd,chrony, or an included configuration directory. - Stop or disable every competing synchronizer. Exactly one service should be allowed to discipline
CLOCK_REALTIME. - Capture a baseline with
date -u. If chrony is active, also runchronyc trackingandchronyc sources -v.
chronyc tracking provides the daemon’s synchronization state and selected-source information; chronyc sources -v shows whether configured sources are reachable and usable. Save this baseline before editing the configuration so that a later change can be correlated with a change in offset or leap status.
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Do not assume that a container has an independent system clock. Containers commonly observe the host’s realtime clock, so a host-level policy change can affect every container at once. Conversely, a containerized process that attempts to set time can make diagnosis harder if it has the required privilege. Check host units, container supervisors, and any hardware-management agent that might issue a manual time change.
Find whether the upstream service smears or announces the leap
NTP providers can handle a leap second in two fundamentally different ways. An announcing service tells clients that an insertion or deletion is pending, allowing the client and kernel to apply a discrete correction. A leap-smearing service changes the clock rate over an interval so that clients experience a gradual offset rather than a one-second step.
Do not combine an independent leap correction with a smearing provider. In particular, a client using a smear must not be configured with chrony’s leapsectz right/UTC directive, because that directive supplies a conventional leap schedule and TAI-UTC data rather than the provider’s smear policy. Mixing the two approaches can make the host differ from the service and from other machines that use the same provider.
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Document the policy for every upstream source and keep a consistent policy within a cluster. A database node, application node, and logging node that use different smear or insertion behavior can disagree by nearly one second even when each reports that it is synchronized. During an incident, compare the selected source and leap status on each host instead of comparing only their formatted dates.
Select a chrony leap-second mode
In /etc/chrony/chrony.conf, or in the distribution’s included chrony configuration, set leapsecmode deliberately. The four modes have different owners for the correction and different effects on applications.
| Mode | Who performs the correction? | Effect on CLOCK_REALTIME |
When it fits | Important limitation |
|---|---|---|---|---|
system |
The kernel | The kernel applies the leap step | The normal choice when the kernel and system time driver correctly support leap seconds | Relies on kernel leap-second behavior; applications using realtime can see the step |
step |
chronyd |
chronyd steps the wall clock |
Systems where avoiding a kernel leap-second code path is preferable | The wall clock still jumps; realtime-based duration calculations remain unsafe |
slew |
chronyd, by changing the clock rate |
No abrupt one-second jump; the clock remains temporarily offset | Applications that cannot tolerate an instantaneous discontinuity | On Linux with chrony’s default maxslewrate, the one-second correction is spread over 12 seconds |
ignore |
No dedicated correction by that chrony instance | Depends on another authority or the surrounding architecture | Only when another instance controls the system clock or the design intentionally handles the leap elsewhere | Unsafe if it leaves the host without a valid leap policy |
system is chrony’s documented default when the system driver supports leap seconds. Choose step when kernel behavior is known to be problematic but an explicit wall-clock step is acceptable. Choose slew when a temporary one-second offset is safer than a jump. Use ignore only with a clearly identified alternate authority; it is not a general workaround for an unsynchronized host.
The choice is an application contract, not merely a daemon preference. A scheduler that compares realtime deadlines can still fail under slew, because the clock remains offset while the correction is distributed. A log viewer may prefer slew to avoid a visible discontinuity, while a system that must match an external UTC event may require an announced step. Make the tolerance explicit in the service design and test it before a scheduled leap.
Configure and apply the chrony change
- Open the active chrony configuration and add one policy, for example
leapsecmode system,leapsecmode step,leapsecmode slew, orleapsecmode ignore. - Confirm that the selected NTP sources use the same insertion, deletion, or smear convention as the host policy.
- If the reference does not reliably announce leap seconds, add
leapsectz right/UTCand ensure the system timezone data is current. - Reload or restart the single active time service using the method required by the distribution.
- Run
chronyc trackingandchronyc sources -vagain. Inspect the service log for the selected source, synchronization state, and leap status. - If the initial offset is large, use a configured
makesteppolicy for the initial correction rather than manually rewriting application timestamps. The policy should be limited to the startup or initial-synchronization conditions appropriate for the system.
A restart is not required merely because timezone data has been updated for the right/UTC data path, although restarting or reloading the time service is still appropriate after changing its configuration.
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Keep a copy of the effective configuration and the pre-change tracking output. This makes rollback possible and helps distinguish a leap-policy change from a source outage. Do not edit multiple chrony files without checking which file the service actually includes; a correct directive in an unused file has no effect.
Verify the right/UTC data path when it is intentional
The right/UTC zone includes leap-second information. Chrony’s documented check is:
TZ=right/UTC date -d 'Dec 31 2008 23:59:60'
When the data path is correctly installed, the command accepts the leap-second notation instead of treating it as an invalid ordinary civil-time second. This test is meaningful only when the host is intentionally using announced leap-second data. It is not a test to run as a substitute for understanding a provider’s smear policy.
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Keep the timezone database updated through the operating system’s normal update mechanism. A stale database can leave a host without current future leap information even when chrony itself is configured correctly.
Fix the application that produced the bad timestamp
Changing the daemon does not make CLOCK_REALTIME suitable for elapsed-time arithmetic. Update code that measures a timeout, retry interval, request latency, lease duration, or event order.
C and POSIX code
Read a monotonic clock for the deadline and compute the difference using its seconds and nanoseconds. Store the realtime reading separately if the record needs a human-readable timestamp.
#include <time.h>
struct timespec start, now;
clock_gettime(CLOCK_MONOTONIC, &start);
/* perform work */
clock_gettime(CLOCK_MONOTONIC, &now);
long long elapsed_ns =
(long long)(now.tv_sec - start.tv_sec) * 1000000000LL +
(now.tv_nsec - start.tv_nsec);
For a timeout, calculate one monotonic deadline and compare every later reading with that deadline. Do not recalculate the deadline from the current wall clock after each retry. If raw hardware-rate measurements are required, substitute CLOCK_MONOTONIC_RAW, understanding that it intentionally excludes NTP frequency adjustments.
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When converting a timespec difference, normalize seconds and nanoseconds or use a duration type that handles the borrow when now.tv_nsec is smaller than start.tv_nsec. The key property is that both readings come from the same clock domain. Mixing a realtime start with a monotonic end produces a number with no defined meaning.
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When CLOCK_TAI is appropriate
Use CLOCK_TAI only when the application needs a continuous atomic-time reference and can handle the difference between TAI and civil UTC. It is useful for systems that must maintain a leap-aware timeline without the backward leap update seen by realtime. It is not a drop-in replacement for displaying UTC dates, and persisted TAI values require a documented conversion policy for readers and downstream systems.
Persist wall time and elapsed time as different fields
An audit record can contain a realtime UTC timestamp for legal or human interpretation and a monotonic interval measured from the operation’s start. The monotonic value has no meaningful cross-reboot or cross-host epoch, so it should not replace the persisted wall-clock field. Conversely, the wall-clock field should not be used to infer ordering when a leap or NTP step is possible.
For distributed events, include the host identity, the UTC wall-clock value, and an elapsed or sequence value generated by the application. That gives operators a readable date while preserving a local ordering signal when two records share the same displayed second.
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- Exactly one enabled service controls
CLOCK_REALTIME. timedatectlreports synchronization, or chrony reports a reachable source and a bounded offset.chronyc trackingshows the expected leap status and a valid selected source.- The
right/UTCcommand accepts23:59:60only when that data path is intentionally configured. - Application tests use monotonic deadlines and do not require realtime timestamps to increase strictly.
- Logs and persisted records distinguish UTC wall-clock timestamps from elapsed-duration measurements.
- The host is compared with an independent trusted time source after synchronization.
- Monitoring remains active long enough to detect repeated one-second steps or a return to an unsynchronized state.
Run the checks after a service restart and again after the host has remained synchronized. A single successful query proves only that the daemon answered at that moment; it does not prove that the source remains reachable or that another service will not step the clock later.
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The clock still jumps after selecting slew
Check for a second daemon or a manual time-setting process. The selected chrony instance cannot prevent another service, container supervisor, hardware-management agent, or administrator command from stepping the clock. Re-run the service checks and inspect logs for settimeofday()-style changes.
Hosts disagree by roughly one second
Compare their upstream policies. One host may be following an announced leap while another follows a smear. Standardize the provider and chrony configuration, then verify each host’s source and leap status.
The leap-second test rejects 23:59:60
Confirm that right/UTC is actually selected, timezone data is current, and the command is being run with the exact TZ=right/UTC environment. If the host is a smear client, do not add the directive merely to make the test pass; use the provider’s documented smear behavior instead.
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Search the application for time(), gettimeofday(), or CLOCK_REALTIME used in subtraction or deadline calculations. Replace those reads with CLOCK_MONOTONIC. Leave realtime reads in place where the value is genuinely a civil timestamp.
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The host is far from the correct time after boot
Use the daemon’s configured makestep policy for the permitted initial correction and verify the source afterward. Do not “repair” the situation by changing historical timestamps in the database or log files; those records describe what the system previously recorded and should remain auditable.
A restart appears to fix the problem temporarily
A restart can force a fresh synchronization but does not correct an architectural conflict. Check whether a competing service returns at boot, whether the selected source is unstable, and whether application code still subtracts realtime readings. The durable fix is one clock authority plus clock-appropriate application logic.
A safe operational sequence
- Record the current UTC time, synchronization state, active services, and chrony source list.
- Stop competing time daemons and confirm that only one authority remains.
- Classify the upstream as leap-announcing or leap-smearing.
- Choose
system,step,slew, orignoreto match that architecture and the application’s tolerance for a wall-clock jump. - Configure
right/UTConly for an announcing reference that needs local leap data, never for a smear client. - Reload or restart the active service, then inspect tracking, sources, and logs.
- Deploy the application fix: monotonic clocks for elapsed time, realtime for civil timestamps, and TAI only where its atomic-time semantics are required.
- Compare the corrected host with an independent source and monitor for renewed steps or loss of synchronization.
Frequently Asked Questions
Why did my Linux timestamp move backward by one second?
CLOCK_REALTIME can step backward when the kernel handles an inserted leap second, and it can also step during an NTP correction or a userspace time-setting operation. That behavior is valid for a civil wall clock but unsafe for elapsed-time calculations.
How do I fix a one-second timestamp error after a leap second?
Do not rewrite historical records first. Ensure one time daemon controls the host, match chrony’s leap mode to the upstream policy, keep leap-second data current, and change duration and timeout code to use CLOCK_MONOTONIC.
Should I use CLOCK_MONOTONIC instead of CLOCK_REALTIME?
Use monotonic time for durations, deadlines, retries, latency, and event ordering. Keep realtime for user-visible UTC timestamps, expiry dates, audit records, and values that must retain civil-time meaning after a reboot.
When should I use CLOCK_MONOTONIC_RAW?
Use it for specialized measurements that need the raw hardware-derived rate and should exclude NTP frequency adjustments. It is not appropriate for displaying dates or correlating long-term events to UTC.
When is CLOCK_TAI a better choice?
Use CLOCK_TAI when an application needs a continuous atomic-time timeline and can document conversion between TAI and civil UTC. It is not a general replacement for UTC display fields.
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Set one deliberate leapsecmode: system, step, slew, or ignore. Use system when kernel handling is trusted, step to let chronyd perform the step, slew to spread the correction, and ignore only when another authority handles it.
Can I use leapsectz right/UTC with a leap-smearing NTP provider?
No. The directive supplies conventional leap scheduling and TAI-UTC data. A smear client must follow the provider’s smear policy instead of independently applying that leap data.
Why does chrony’s slewed correction take time to settle?
With Linux’s default maxslewrate, chrony documents that a one-second leap correction is spread over 12 seconds. The clock avoids an abrupt jump but remains temporarily offset while the rate correction is applied.
The Bottom Line
A leap-second timestamp error is usually a clock-selection and synchronization-policy problem, not damaged data. Use CLOCK_REALTIME for civil timestamps, CLOCK_MONOTONIC for elapsed time, and CLOCK_TAI only for applications designed around atomic time. Run one synchronizer, match chrony’s leap mode to the provider’s announce-or-smear behavior, keep right/UTC data current when appropriate, and verify the host and application after the change.
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