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How to Fix NTP Sync Problems on a Linux VPS

A practical, evidence-based guide to fixing “System clock synchronized: no” on a Linux VPS, from identifying competing daemons to validating chrony sources, firewalls and provider-specific time services.
Length9 min Posted Quest giverVGSources Team
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If timedatectl reports System clock synchronized: no, first identify which time service owns the clock, then verify that it can exchange NTP packets over UDP port 123. On most VPSs, a single, correctly configured chrony instance is the most practical solution. A running service is not proof of synchronization: you must confirm a selected source and valid replies.

This guide takes you from diagnosis to a persistent fix, including competing daemons, firewalls, large clock offsets, virtual-machine time sources, and the choice between chrony and systemd-timesyncd.

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What “not synchronized” actually means

timedatectl exposes two different facts. NTP service: active means a supported time service is enabled or running. System clock synchronized: yes means the system has obtained and accepted time from a valid source. The first can be true while the second remains false because DNS, UDP traffic, source selection, or a competing daemon is broken.

For chrony, use its own evidence as well as timedatectl:

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  • chronyc tracking shows the selected source, reference state, offset, frequency, and other clock parameters.
  • chronyc sources -v lists configured sources, their reachability, and selection state. A ^* marker identifies the current source; ^+ identifies a usable candidate.
  • A Reach value of 0 means chrony has received no valid responses from that source. Treat it as a network, DNS, server, or policy problem before changing poll intervals.

A correct clock matters to TLS certificates, package repositories, log ordering, scheduled jobs, authentication, monitoring, and game-server events. It does not require the guest clock to be perfect to the microsecond; it does require a stable, trusted source and a daemon that can recover after drift or a virtual-machine pause.

Identify the active time manager before changing anything

Do not install or enable another daemon until you know what is already controlling the clock. Run these commands as an administrator:

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date -u
timedatectl
systemctl list-units --type=service | grep -E 'chrony|chronyd|timesyncd|ntp'

Then inspect each service that appears:

systemctl status chrony --no-pager
systemctl status chronyd --no-pager
systemctl status systemd-timesyncd --no-pager
systemctl status ntp --no-pager

Some distributions call the unit chrony; others use chronyd. Package and unit names therefore need to match your distribution. Ubuntu’s documentation also warns that timedatectl steps back when chrony is installed. Leave only one network time manager adjusting the guest clock: chrony, systemd-timesyncd, or ntpd, not several at once.

timedatectl set-ntp true asks the distribution to enable its supported network-time service. It does not repair a blocked network path, select a valid chrony source, or prove that synchronization has completed, so inspect the service and its logs afterward.

Use a repeatable diagnostic sequence

1. Record the current state

Capture the UTC clock, synchronization flag, active units, and recent messages before editing configuration:

date -u
timedatectl
systemctl list-units --type=service | grep -E 'chrony|chronyd|timesyncd|ntp'
journalctl -b -p warning..err --no-pager

Save this output if you need to involve your VPS provider. The timestamps in the logs help distinguish a persistent configuration fault from a clock jump after suspension or host maintenance.

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2. Check chrony’s view of the sources

If chrony is active, run:

chronyc tracking
chronyc sources -v
chronyc sourcestats -v
journalctl -u chrony -b --no-pager

Use journalctl -u chronyd instead when that is the unit name. In the sources output, look for a selected ^* source, one or more ^+ candidates, a non-zero Reach, and current sample data. If every source has Reach 0, changing the preferred server or poll interval is unlikely to help until replies can reach the VPS.

3. Check the simpler systemd client

For systemd-timesyncd, inspect both service state and its status command:

systemctl status systemd-timesyncd --no-pager
timedatectl timesync-status
timedatectl show-timesync --all

The exact fields vary by systemd release. You are looking for a configured server, a recent successful exchange, and a state that is not merely “service running.” Do not run this client alongside chrony or ntpd.

Choose one client for the VPS

Chrony is generally the better default when a VPS needs more than a minimal client: it handles changing network conditions, learns local clock drift, offers detailed source diagnostics, and is designed for systems that may be disconnected or resumed. The chrony project recommends it over timesyncd when a full-featured client is desired.

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systemd-timesyncd implements SNTP only. It is intentionally small and suits a simple systemd-managed machine with reliable, trusted sources. It steps large offsets and slews smaller ones, but it exposes fewer source-selection and troubleshooting controls than chrony.

Aspect chrony systemd-timesyncd
Protocol and features Full NTP client with richer source selection and diagnostics Minimal SNTP service; large offsets are stepped and smaller offsets are slewed
Practical fit VPSs with measurable drift, multiple sources, intermittent connectivity, or detailed troubleshooting needs Simple systemd-managed clients with dependable sources
Diagnostics chronyc tracking, sources, and sourcestats timedatectl timesync-status and systemctl status systemd-timesyncd
Conflict rule Must not run concurrently with systemd-timesyncd or ntpd Must not run concurrently with chrony or ntpd

Chrony’s current FAQ recommends at least three NTP servers for reliable operation. Use several trustworthy sources or the source documented by your VPS provider rather than relying on one public server.

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Install and activate chrony without leaving a competing daemon running

On Debian- and Ubuntu-family systems, a typical migration is:

sudo apt update
sudo apt install chrony
sudo systemctl disable --now systemd-timesyncd 2>/dev/null || true
sudo systemctl enable --now chrony
systemctl status chrony --no-pager

If your distribution installs a chronyd unit, substitute that name in the final commands. Before enabling it, stop and disable any active ntpd service as well. Do not mask a service blindly on a distribution that uses it as the supported default; confirm the replacement is installed and starts successfully first.

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On Ubuntu 25.10, Canonical’s current server documentation makes chrony the default instead of systemd-timesyncd. Older Ubuntu releases and other distributions can still use different defaults, so inspect the units rather than assuming the release’s behavior.

Apply a conservative chrony configuration

A minimal Internet-client configuration from the chrony project is:

pool pool.ntp.org iburst
driftfile /var/lib/chrony/drift
makestep 1 3
rtcsync

Use the drift-file path supplied by your distribution; it can differ from the example. The directives have distinct jobs:

  • pool lets chrony obtain several addresses from a pool. You can instead use several explicit server lines, preferably from a provider-approved source or a set of trustworthy servers.
  • iburst sends a short burst at startup so the initial measurement completes faster. It does not bypass a firewall.
  • driftfile stores chrony’s estimate of the guest clock’s natural rate of gain or loss, improving behavior after restart.
  • makestep 1 3 permits a large correction during the first three updates when the offset exceeds one second. Without a step allowance, chrony normally slews the clock gradually.
  • rtcsync allows the kernel to copy the synchronized system time to a real-time clock where that mechanism exists. Many VPSs have no meaningful emulated RTC, so its effect depends on the platform.

Edit the configuration file named by your distribution, then restart and immediately inspect the result:

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sudo systemctl restart chrony   # or chronyd
chronyc tracking
chronyc sources -v

Do not add a large list of unrelated servers to hide a fault. A smaller set of known, reachable sources makes source selection and packet captures easier to interpret.

Prove that DNS and UDP 123 work

NTP requests and replies normally use UDP port 123. A successful ICMP ping proves only that some ICMP traffic works; it does not prove that NTP packets leave the VPS or that replies are allowed back.

Resolve the configured names

Check every hostname shown by chronyc sources -v or in the timesyncd configuration:

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getent ahosts pool.ntp.org
resolvectl query pool.ntp.org

If resolution fails, fix the VPS resolver, local DNS policy, or provider DNS settings first. If names resolve to addresses that are unreachable from the VPS network, use a provider-documented source or another valid server.

Inspect outbound and return policy

  • Review cloud security-group or network ACL egress rules for UDP/123.
  • Review the VPS host firewall, such as nftables, iptables, or a distribution firewall.
  • For a stateless firewall, allow the return traffic as well as the outbound request.
  • Check provider-level restrictions on public NTP and any policy that requires a local time endpoint.

When Reach remains zero, use logs and a packet capture rather than repeatedly editing the configuration. Chrony’s troubleshooting guidance recommends packet inspection with tools such as tcpdump or Wireshark when a firewall is suspected.

sudo tcpdump -ni any udp port 123

Start the capture, wait through a polling attempt, and compare outbound requests with inbound replies. Requests without replies point to a route, security rule, server, or return-path problem. Replies visible on the interface but not reflected in chrony suggest local filtering or a daemon/configuration issue.

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Correct a large offset safely

Chrony normally slews a small error so applications see a continuous rate of change. A very large error may take too long to correct by slewing, which is why the baseline includes makestep. systemd-timesyncd similarly steps large offsets and slews smaller ones.

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Avoid repeatedly running date -s or another manual clock-setting command while a daemon is active. Manual jumps can make source selection and logs confusing and can disturb applications that depend on ordered timestamps or a stable monotonic timeline. If the initial offset is severe, stop the competing manager, ensure chrony has a reachable source, allow the configured startup step, and then verify chronyc tracking.

After a step, check services that are sensitive to time changes: authentication, TLS, schedulers, databases, and game servers that persist event timestamps. A one-time correction is different from a clock that repeatedly jumps; recurring jumps usually require investigation of the virtualization host or suspension behavior.

Use the VPS provider’s time source when appropriate

A virtual machine may receive time from a host clock or a provider-operated link-local service. Provider guidance can be more reliable than sending traffic to public Internet servers, especially when public UDP/123 is filtered.

Azure virtual machines

Azure documents host synchronization and, for supported Linux VM configurations, the /dev/ptp_hyperv device. Follow the current image and kernel requirements for your VM type. A host or PTP source is not interchangeable with another provider’s endpoint; use only the mechanism documented for the Azure environment.

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AWS EC2

AWS documents the local Amazon Time Sync Service at 169.254.169.123 and recommends it as the direct EC2 source. Because it is link-local, do not test it as though it were a normal Internet address, and do not copy it to a VPS hosted elsewhere.

If your provider publishes a time-source hostname, PTP device, or special route, prefer that documentation over a generic public pool. Provider images and kernels can change their supported method, so verify the instructions for the exact image and region.

Verify the fix after restart and under normal load

Synchronization that works once but fails after a reboot, host migration, or busy period is not fixed. Recheck the state at several points:

  1. Immediately after enabling or restarting the chosen service, run timedatectl, chronyc tracking, and chronyc sources -v (or timedatectl timesync-status for timesyncd).
  2. After the first few polls, confirm that a source is selected, Reach is non-zero for chrony, and the offset and frequency are settling.
  3. Reboot the VPS and repeat the checks. Confirm that the same single manager starts and that its configuration and drift file are readable.
  4. Observe the VPS during normal CPU and network load. A stable service should continue receiving valid samples rather than losing every source when the machine is busy.
  5. If the clock jumps after host maintenance, suspension, or migration, collect service logs with their timestamps and open a provider ticket. Include the observed jump, the selected source, and whether the guest was paused.

Common symptoms and the next action

Symptom Most useful next check
System clock synchronized: no while a service is active Inspect the manager’s own status: chronyc tracking and sources -v, or timedatectl timesync-status.
Every chrony source shows Reach 0 Verify DNS, UDP/123 egress, return traffic, security groups, host firewall rules, and packet capture results.
Both chrony and timesyncd (or ntpd) are running Choose one manager, stop and disable the others, then restart the selected service.
Clock is far wrong immediately after boot Confirm a reachable source and a startup makestep policy; avoid repeated manual clock changes.
Synchronization disappears after a VM pause or host event Check provider-specific host, PTP, or link-local time guidance and provide logs to the provider if the behavior repeats.

Final checklist

  • One and only one guest time manager is enabled.
  • The selected service is active and its logs show no persistent errors.
  • DNS resolves every configured source.
  • UDP/123 requests and replies are permitted, including return traffic through stateless firewalls.
  • Chrony has a non-zero Reach and a selected ^* source, or timesyncd reports a successful exchange.
  • The configuration uses several trustworthy sources or the VPS provider’s documented endpoint.
  • Large initial offsets are handled by an intentional step policy rather than repeated manual changes.
  • Synchronization survives reboot, normal load, and expected virtual-machine lifecycle events.

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