Troubleshooting Apache Kudu

Issues Starting or Restarting the Master or Tablet Server

Error During Hole Punch Test

Kudu requires hole punching capabilities in order to be efficient. Support for hole punching depends on your operating system kernel version and local filesystem. On Linux, hole punching is the use of the fallocate() system call with the FALLOC_FL_PUNCH_HOLE option set.
  • RHEL or CentOS 6.4 or later, patched to kernel version of 2.6.32-358 or later. Unpatched RHEL or CentOS 6.4 does not include a kernel with support for hole punching.
  • Ubuntu 14.04 includes version 3.13 of the Linux kernel, which supports hole punching.
  • Newer versions of the EXT4 or XFS filesystems support hole punching, but EXT3 does not. Older versions of XFS that do not support hole punching return a EOPNOTSUPP (operation not supported) error. Older versions of either EXT4 or XFS that do not support hole punching cause Kudu to emit an error message such as the following and to fail to start:
    Error during hole punch test. The log block manager requires a
    filesystem with hole punching support such as ext4 or xfs. On el6,
    kernel version 2.6.32-358 or newer is required. To run without hole
    punching (at the cost of some efficiency and scalability), reconfigure
    Kudu with --block_manager=file. Refer to the Kudu documentation for more
    details. Raw error message follows.
  • Without hole punching support, the log block manager will never delete blocks and progressively occupy even more space on disk, which makes it unsafe to use.
  • Workaround - If you can’t use hole punching in your environment, you can still try Kudu. Enable the file block manager instead of the log block manager by adding the --block_manager=file flag to the commands you use to start the master and tablet servers. Note that the file block manager does not scale as well as the log block manager, and should only be used for small-scale deployments.

NTP Clock Synchronization

For the master and tablet server daemons, the server’s clock must be synchronized using NTP. In addition, the maximum clock error(not to be mistaken with the estimated error) must be below a configurable threshold. The default value is 10 seconds, but it can be set with the flag --max_clock_sync_error_usec.

If NTP is not installed, or if the clock is reported as unsynchronized, Kudu will not start, and will emit a message such as:

F0924 20:24:36.336809 14550 hybrid_clock.cc:191 Couldn't get the current time: Clock unsynchronized. Status: Service unavailable: Error reading clock. Clock considered unsynchronized.

If NTP is installed and synchronized, but the maximum clock error is too high, the user will see a message such as:

Sep 17, 8:13:09.873 PM FATAL hybrid_clock.cc:196 Couldn't get the current time: Clock synchronized, but error: 11130000, is past the maximum allowable error: 10000000

or

Sep 17, 8:32:31.135 PM FATAL tablet_server_main.cc:38 Check failed: _s.ok() Bad status: Service unavailable: Cannot initialize clock: Cannot initialize HybridClock. Clock synchronized but error was too high (11711000 us).

Installing NTP

To install NTP, use the command appropriate for your operating system:

OS Command

Debian/Ubuntu

sudo apt-get install ntp

RHEL/CentOS

sudo yum install ntp

If NTP is installed but not running, start it using one of these commands:

OS Command

Debian/Ubuntu

sudo service ntp restart

RHEL/CentOS

sudo /etc/init.d/ntpd restart

Monitoring NTP Status

When NTP is installed, you can monitor the synchronization status by running ntptime. For example, a healthy system may report:

ntp_gettime() returns code 0 (OK)
  time de24c0cf.8d5da274  Tue, Feb  6 2018 16:03:27.552, (.552210980),
  maximum error 224455 us, estimated error 383 us, TAI offset 0
ntp_adjtime() returns code 0 (OK)
  modes 0x0 (),
  offset 1279.543 us, frequency 2.500 ppm, interval 1 s,
  maximum error 224455 us, estimated error 383 us,
  status 0x2001 (PLL,NANO),
  time constant 10, precision 0.001 us, tolerance 500 ppm,

In particular, note the following most important parts of output:

  • maximum error 22455 us: This value is well under the 10-second maximum error required by Kudu.

  • status 0x2001 (PLL,NANO): This indicates a healthy synchronization status.

In contrast, a system without NTP properly configured and running will output something like the following:

ntp_gettime() returns code 5 (ERROR)
  time de24c240.0c006000  Tue, Feb  6 2018 16:09:36.046, (.046881),
  maximum error 16000000 us, estimated error 16000000 us, TAI offset 0
ntp_adjtime() returns code 5 (ERROR)
  modes 0x0 (),
  offset 0.000 us, frequency 2.500 ppm, interval 1 s,
  maximum error 16000000 us, estimated error 16000000 us,
  status 0x40 (UNSYNC),
  time constant 10, precision 1.000 us, tolerance 500 ppm,

Note the UNSYNC status and the 16-second maximum error.

If more detailed information is needed, the ntpq or ntpdc tools can be used to dump further information about which network time servers are currently acting as sources:

$ ntpq -nc lpeers
     remote           refid      st t when poll reach   delay   offset  jitter
------------------------------------------------------------------------------
-108.59.2.24     130.133.1.10     2 u   13   64    1   71.743    0.373   0.016
+192.96.202.120  129.6.15.28      2 u   12   64    1   72.583   -0.426   0.028
-69.10.161.7     204.26.59.157    3 u   11   64    1   15.741    2.641   0.021
-173.255.206.154 45.56.123.24     3 u   10   64    1   43.502    0.199   0.029
-69.195.159.158  128.138.140.44   2 u    9   64    1   53.885   -0.016   0.013
*216.218.254.202 .CDMA.           1 u    6   64    1    1.475   -0.400   0.012
+129.250.35.250  249.224.99.213   2 u    7   64    1    1.342   -0.640   0.018
 45.76.244.193   216.239.35.4     2 u    6   64    1   17.380   -0.754   0.051
 69.89.207.199   212.215.1.157    2 u    5   64    1   57.796   -3.411   0.059
 171.66.97.126   .GPSs.           1 u    4   64    1    1.024   -0.374   0.018
 66.228.42.59    211.172.242.174  3 u    3   64    1   72.409    0.895   0.964
 91.189.89.198   17.253.34.125    2 u    2   64    1  135.195   -0.329   0.171
 162.210.111.4   216.218.254.202  2 u    1   64    1   28.570    0.693   0.306
 199.102.46.80   .GPS.            1 u    2   64    1   55.652   -0.039   0.019
 91.189.89.199   17.253.34.125    2 u    1   64    1  135.265   -0.413   0.037

$ ntpq -nc opeers
     remote           local      st t when poll reach   delay   offset    disp
------------------------------------------------------------------------------
-108.59.2.24     10.17.100.238    2 u   17   64    1   71.743    0.373 187.573
+192.96.202.120  10.17.100.238    2 u   16   64    1   72.583   -0.426 187.594
-69.10.161.7     10.17.100.238    3 u   15   64    1   15.741    2.641 187.569
-173.255.206.154 10.17.100.238    3 u   14   64    1   43.502    0.199 187.580
-69.195.159.158  10.17.100.238    2 u   13   64    1   53.885   -0.016 187.561
*216.218.254.202 10.17.100.238    1 u   10   64    1    1.475   -0.400 187.543
+129.250.35.250  10.17.100.238    2 u   11   64    1    1.342   -0.640 187.588
 45.76.244.193   10.17.100.238    2 u   10   64    1   17.380   -0.754 187.596
 69.89.207.199   10.17.100.238    2 u    9   64    1   57.796   -3.411 187.541
 171.66.97.126   10.17.100.238    1 u    8   64    1    1.024   -0.374 187.578
 66.228.42.59    10.17.100.238    3 u    7   64    1   72.409    0.895 187.589
 91.189.89.198   10.17.100.238    2 u    6   64    1  135.195   -0.329 187.584
 162.210.111.4   10.17.100.238    2 u    5   64    1   28.570    0.693 187.606
 199.102.46.80   10.17.100.238    1 u    4   64    1   55.652   -0.039 187.587
 91.189.89.199   10.17.100.238    2 u    3   64    1  135.265   -0.413 187.621
Using chrony for time synchronization

Some operating systems offer chrony as an alternative to ntpd for network time synchronization. Kudu has been tested most thoroughly using ntpd and use of chrony is considered experimental.

In order to use chrony for synchronization, chrony.conf must be configured with the rtcsync option.

NTP Configuration Best Practices

In order to provide stable time synchronization with low maximum error, follow these best NTP configuration best practices.

Always configure at least four time sources for NTP. In addition to providing redundancy in case one or more time sources becomes unavailable, The NTP protocol is designed to increase its accuracy with a diversity of sources. Even if your organization provides one or more local time servers, configuring additional remote servers is highly recommended for a robust setup.

Pick servers in your server’s local geography. For example, if your servers are located in Europe, pick servers from the European NTP pool. If your servers are running in a public cloud environment, consult the cloud provider’s documentation for a recommended NTP setup. Many cloud providers offer highly accurate clock synchronization as a service.

Use the iburst option for faster synchronization at startup. The iburst option instructs ntpd to send an initial "burst" of time queries at startup. This typically results in a faster time synchronization when a machine restarts.

An example NTP server list may appear as follows:

# Use my organization's internal NTP servers.
server ntp1.myorg.internal iburst
server ntp2.myorg.internal iburst
# Provide several public pool servers from the US pool for
# redundancy and robustness.
server 0.pool.us.ntp.org iburst
server 1.pool.us.ntp.org iburst
server 2.pool.us.ntp.org iburst
server 3.pool.us.ntp.org iburst

Troubleshooting NTP Stability Problems

As of Kudu 1.6.0, Kudu daemons are able to continue to operate during a brief loss of NTP synchronization. If NTP synchronization is lost for several hours, however, daemons may crash. If a daemon crashes due to NTP synchronization issues, consult the ERROR log for a dump of related information which may help to diagnose the issue.

Reporting Kudu Crashes Using Breakpad

Kudu uses the Google Breakpad library to generate a minidump whenever Kudu experiences a crash. A minidump file contains important debugging information about the process that crashed, including shared libraries loaded and their versions, a list of threads running at the time of the crash, the state of the processor registers and a copy of the stack memory for each thread, and CPU and operating system version information. These minidumps are typically only a few MB in size and are generated even if core dump generation is disabled. Currently, generating minidumps is only possible on Linux deployments.

By default, Kudu stores its minidumps in a subdirectory of the configured glog directory called minidumps. This location can be customized by setting the --minidump_path flag. Kudu will retain only a certain number of minidumps before deleting the older ones, in an effort to avoid filling up the disk with minidump files. The maximum number of minidumps that will be retained can be controlled by setting the --max_minidumps gflag.

Minidumps contain information specific to the binary that created them and are therefore not useful without access to the exact binary that crashed, or a very similar binary.

Kudu developers can access the minidump tools in their development environment because they are installed as part of the Kudu thirdparty build. They can be found in the Kudu development environment under uninstrumented/bin. For example, thirdparty/installed/uninstrumented/bin/minidump-2-core.

If minidumps are enabled, it is possible to force Kudu to create a minidump without killing the process. To do that, send a USR1 signal to the kudu-tserver or kudu-master process. For example:

sudo pkill -USR1 kudu-tserver

Viewing the minidump Stack Trace with the GNU Debugger

Although a minidump contains no heap information, it does contain thread and stack information. You can convert a minidump to a core file to view it with GDB.

To convert the minidump (.dmp file) to a core file:

minidump-2-core -o 02cb4a97-ee37-6454-73a9d9cb-590c7dde.core \
02cb4a97-ee37-6454-73a9d9cb-590c7dde.dmp

To view the core file with GDB (on a parcel deployment):

gdb /opt/cloudera/parcels/KUDU/lib/kudu/sbin-release/kudu-master \
-s /opt/cloudera/parcels/KUDU/lib/debug/usr/lib/kudu/sbin-release/kudu-master.debug \
02cb4a97-ee37-6454-73a9d9cb-590c7dde.core

For more information, see Getting started with Breakpad and Chrome developer tips for minidump file debugging.

Troubleshooting Performance Issues

Kudu Tracing

The Kudu master and tablet server daemons include built-in support for tracing based on the open source Chromium Tracing framework. You can use tracing to diagnose latency issues or other problems on Kudu servers.

Accessing the Tracing Web Interface

The tracing interface is part of the embedded web server in each of the Kudu daemons, and can be accessed using a web browser. Note that while the interface has been known to work in recent versions of Google Chrome, other browsers may not work as expected.

Daemon URL

Tablet Server

<tablet-server-1.example.com>:8050/tracing.html

Master

<master-1.example.com>:8051/tracing.html

Saving Traces

After you have collected traces, you can save these traces as JSON files by clicking Save. To load and analyze a saved JSON file, click Load and choose the file.

RPC Timeout Traces

If client applications are experiencing RPC timeouts, the Kudu tablet server WARNING level logs should contain a log entry which includes an RPC-level trace. For example:

W0922 00:56:52.313848 10858 inbound_call.cc:193] Call kudu.consensus.ConsensusService.UpdateConsensus
from 192.168.1.102:43499 (request call id 3555909) took 1464ms (client timeout 1000).
W0922 00:56:52.314888 10858 inbound_call.cc:197] Trace:
0922 00:56:50.849505 (+     0us) service_pool.cc:97] Inserting onto call queue
0922 00:56:50.849527 (+    22us) service_pool.cc:158] Handling call
0922 00:56:50.849574 (+    47us) raft_consensus.cc:1008] Updating replica for 2 ops
0922 00:56:50.849628 (+    54us) raft_consensus.cc:1050] Early marking committed up to term: 8 index: 880241
0922 00:56:50.849968 (+   340us) raft_consensus.cc:1056] Triggering prepare for 2 ops
0922 00:56:50.850119 (+   151us) log.cc:420] Serialized 1555 byte log entry
0922 00:56:50.850213 (+    94us) raft_consensus.cc:1131] Marking committed up to term: 8 index: 880241
0922 00:56:50.850218 (+     5us) raft_consensus.cc:1148] Updating last received op as term: 8 index: 880243
0922 00:56:50.850219 (+     1us) raft_consensus.cc:1195] Filling consensus response to leader.
0922 00:56:50.850221 (+     2us) raft_consensus.cc:1169] Waiting on the replicates to finish logging
0922 00:56:52.313763 (+1463542us) raft_consensus.cc:1182] finished
0922 00:56:52.313764 (+     1us) raft_consensus.cc:1190] UpdateReplicas() finished
0922 00:56:52.313788 (+    24us) inbound_call.cc:114] Queueing success response

These traces can indicate which part of the request was slow. Make sure you include them when filing bug reports related to RPC latency outliers.

Kernel Stack Watchdog Traces

Each Kudu server process has a background thread called the Stack Watchdog, which monitors other threads in the server in case they are blocked for longer-than-expected periods of time. These traces can indicate operating system issues or bottle-necked storage.

When the watchdog thread identifies a case of thread blockage, it logs an entry in the WARNING log as follows:

W0921 23:51:54.306350 10912 kernel_stack_watchdog.cc:111] Thread 10937 stuck at /data/kudu/consensus/log.cc:505 for 537ms:
Kernel stack:
[<ffffffffa00b209d>] do_get_write_access+0x29d/0x520 [jbd2]
[<ffffffffa00b2471>] jbd2_journal_get_write_access+0x31/0x50 [jbd2]
[<ffffffffa00fe6d8>] __ext4_journal_get_write_access+0x38/0x80 [ext4]
[<ffffffffa00d9b23>] ext4_reserve_inode_write+0x73/0xa0 [ext4]
[<ffffffffa00d9b9c>] ext4_mark_inode_dirty+0x4c/0x1d0 [ext4]
[<ffffffffa00d9e90>] ext4_dirty_inode+0x40/0x60 [ext4]
[<ffffffff811ac48b>] __mark_inode_dirty+0x3b/0x160
[<ffffffff8119c742>] file_update_time+0xf2/0x170
[<ffffffff8111c1e0>] __generic_file_aio_write+0x230/0x490
[<ffffffff8111c4c8>] generic_file_aio_write+0x88/0x100
[<ffffffffa00d3fb1>] ext4_file_write+0x61/0x1e0 [ext4]
[<ffffffff81180f5b>] do_sync_readv_writev+0xfb/0x140
[<ffffffff81181ee6>] do_readv_writev+0xd6/0x1f0
[<ffffffff81182046>] vfs_writev+0x46/0x60
[<ffffffff81182102>] sys_pwritev+0xa2/0xc0
[<ffffffff8100b072>] system_call_fastpath+0x16/0x1b
[<ffffffffffffffff>] 0xffffffffffffffff

User stack:
    @       0x3a1ace10c4  (unknown)
    @          0x1262103  (unknown)
    @          0x12622d4  (unknown)
    @          0x12603df  (unknown)
    @           0x8e7bfb  (unknown)
    @           0x8f478b  (unknown)
    @           0x8f55db  (unknown)
    @          0x12a7b6f  (unknown)
    @       0x3a1b007851  (unknown)
    @       0x3a1ace894d  (unknown)
    @              (nil)  (unknown)

These traces can be useful for diagnosing root-cause latency issues in Kudu especially when they are caused by underlying systems such as disk controllers or file systems.

Memory Limits

Kudu has a hard and soft memory limit. The hard memory limit is the maximum amount a Kudu process is allowed to use, and is controlled by the --memory_limit_hard_bytes flag. The soft memory limit is a percentage of the hard memory limit, controlled by the flag memory_limit_soft_percentage and with a default value of 80%, that determines the amount of memory a process may use before it will start rejecting some write operations.

If the logs or RPC traces contain messages such as the following example, then Kudu is rejecting writes due to memory back pressure. This may result in write timeouts.

Service unavailable: Soft memory limit exceeded (at 96.35% of capacity)

There are several ways to relieve the memory pressure on Kudu:

  • If the host has more memory available for Kudu, increase --memory_limit_hard_bytes.

  • Increase the rate at which Kudu can flush writes from memory to disk by increasing the number of disks or increasing the number of maintenance manager threads --maintenance_manager_num_threads. Generally, the recommended ratio of maintenance manager threads to data directories is 1:3.

  • Reduce the volume of writes flowing to Kudu on the application side.

Finally, check the value of the --block_cache_capacity_mb setting. This setting determines the maximum size of Kudu's block cache. While a higher value can help with read and write performance, setting it too high as a percentage of the --memory_limit_hard_bytes setting is harmful. Do not raise --block_cache_capacity_mb above --memory_pressure_percentage (default 60%) of --memory_limit_hard_bytes, as this will cause Kudu to flush aggressively even if write throughput is low. The recommended value for --block_cache_capacity_mb is below the following:

(50% * --memory_pressure_percentage) * --memory_limit_hard_bytes

With the defaults, this means the --block_cache_capacity_mb should not exceed 30% of --memory_limit_hard_bytes.

Heap Sampling

For advanced debugging of memory usage, administrators may enable heap sampling on Kudu daemons. This allows Kudu developers to associate memory usage with the specific lines of code and data structures responsible. When reporting a bug related to memory usage or an apparent memory leak, heap profiling can give quantitative data to pinpoint the issue.

CAUTION:
Heap sampling is an advanced troubleshooting technique and may cause performance degradation or instability of the Kudu service. Currently it is not recommended to enable this in a production environment unless specifically requested by the Kudu development team.

To enable heap sampling on a Kudu daemon, pass the flag --heap-sample-every-n-bytes=524588. If heap sampling is enabled, the current sampled heap occupancy can be retrieved over HTTP by visiting http://tablet-server.example.com:8050/pprof/heap or http://master.example.com:8051/pprof/heap. The output is a machine-readable dump of the stack traces with their associated heap usage.

Rather than visiting the heap profile page directly in a web browser, it is typically more useful to use the pprof tool that is distributed as part of the gperftools open source project. For example, a developer with a local build tree can use the following command to collect the sampled heap usage and output an SVG diagram:

thirdparty/installed/uninstrumented/bin/pprof -svg  'http://localhost:8051/pprof/heap' > /tmp/heap.svg

The resulting SVG may be visualized in a web browser or sent to the Kudu community to help troubleshoot memory occupancy issues.

Disk Issues

When Kudu starts, it checks each configured data directory, expecting either for all to be initialized or for all to be empty. If a server fails to start with a log message such as the following, then this precondition check has failed.

Check failed: _s.ok() Bad status: Already present: FS layout already exists; not overwriting existing layout: FSManager roots already exist: /data0/kudu/data

This could be because Kudu was configured with non-empty data directories on first startup, or because a previously-running, healthy Kudu process was restarted and at least one data directory was deleted or is somehow corrupted, perhaps because of a disk error. If it is the latter, refer Changing Directory Configuration.

Slow DNS Lookups and nscd

If the logs contain messages about slow name resolution like below, it may help to run nscd, the name server cache daemon.

W0926 11:19:01.339553 27231 net_util.cc:129] Time spent resolving address for kudu-tserver.example.com: real 4.647s user 0.000s sys 0.000s

Consult your operating system's documentation for how to install and enable nscd.

Usability Issues

ClassNotFoundException: com.cloudera.kudu.hive.KuduStorageHandler

You will encounter this exception when you try to access a Kudu table using Hive. This is not a case of a missing jar, but simply that Impala stores Kudu metadata in Hive in a format that is unreadable to other tools, including Hive itself. and Spark. Currently, there is no workaround for Hive users. Spark users can work around this by creating temporary tables.

Runtime error: Could not create thread: Resource temporarily unavailable (error 11)

You will encounter this error when Kudu is unable to create more threads, usually on versions older than CDH 5.15 / Kudu 1.7. It happens on tablet servers, and is a sign that the tablet server hosts too many tablet replicas.

To fix the issue, you can raise the nproc ulimit as detailed in the documentation for your operating system or distribution.

However, the better solution is to reduce the number of replicas on the tablet server. This may involve rethinking the table's partitioning schema. For the recommended limits on number of replicas per tablet server, see the known issues and scaling limitations documentation.

Tombstoned or STOPPED tablet replicas

You may notice some replicas on a tablet server are in a STOPPED state and remain on the server indefinitely. These replicas are tombstones. A tombstone indicates that the tablet server once held a bona fide replica of its tablet. For example, in case a tablet server goes down and its replicas are re-replicated elsewhere, if the tablet server rejoins the cluster, its replicas will become tombstones. A tombstone will remain until the table it belongs to is deleted, or a new replica of the same tablet is placed on the tablet server. A count of tombstoned replicas and details of each one are available on the /tablets page of the tablet server web UI. The Raft consensus algorithm that Kudu uses for replication requires tombstones for correctness in certain rare situations. They consume minimal resources and hold no data. They must not be deleted.