Can't start clickhouse on baremetal + sysbox

[ssdscreator]

I borrowed an Debian 11, xeon amd64 baremetal server. I am trying to start clickhouse service in gitlab ci with sys box, but I can't. Also I can't start it manually with sys box. It start correctly Postgres or dind containers. Also clickhouse started correctly in default runc runner or in Virtual Machine with sysbox.
Strace of clickhouse:

futex(0x7fb05f822ae8, FUTEX_WAKE_PRIVATE, 12025.08.29 06:32:57.617101 [ 2857 ] {} <Trace> AsynchronousMetrics: Scanning /sys/class/thermal
) = 1
stat("/sys/class/thermal/thermal_zone0/temp", {st_mode=S_IFREG|0644, st_size=6, ...}) = 0
openat(AT_FDCWD, "/sys/class/thermal/thermal_zone0/temp", O_RDONLY|O_CLOEXEC) = 32
pread64(32, "45000\n", 4096, 0)         = 6
stat("/sys/class/thermal/thermal_zone1/temp", {st_mode=S_IFREG|0444, st_size=4096, ...}) = 0
openat(AT_FDCWD, "/sys/class/thermal/thermal_zone1/temp", O_RDONLY|O_CLOEXEC) = 33
pread64(33, "", 4096, 0)                = 0
close(33)                               = 0
close(32)                               = 0
close(31)                               = 0
close(30)                               = 0
close(29)                               = 0
close(27)                               = 0
close(28)                               = 0
close(22)                               = 0
close(21)                               = 0
close(20)                               = 0
close(25)                               = 0
close(19)                               = 0
close(18)                               = 0
close(24)                               = 0
close(23)                               = 0
close(26)                               = 0
close(17)                               = 0
close(16)                               = 0
getpid()                                = 2857
futex(0x7fb05f493e70, FUTEX_WAKE_PRIVATE, 1) = 1
futex(0x7fb05f493e80, FUTEX_WAKE_PRIVATE, 1) = 1
futex(0x7fb05f822c18, FUTEX_WAKE_PRIVATE, 1) = 1
futex(0x7fb05f822c28, FUTEX_WAKE_PRIVATE, 1) = 1
futex(0x7fb05f822b7c, FUTEX_WAKE_PRIVATE, 1) = 1
futex(0x7fb05f822b88, FUTEX_WAKE_PRIVATE, 1) = 1
futex(0x7fb05f822ad8, FUTEX_WAKE_PRIVATE, 1) = 1
futex(0x7fb05f822ae8, FUTEX_WAKE_PRIVATE, 12025.08.29 06:32:57.620140 [ 2857 ] {} <Information> Application: Waiting for background threads
) = 1
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---
futex(0x7fb02d200910, FUTEX_WAIT_BITSET|FUTEX_CLOCK_REALTIME, 2940, NULL, FUTEX_BITSET_MATCH_ANY) = ? ERESTARTSYS (To be restarted if SA_RESTART is set)
--- SIGWINCH {si_signo=SIGWINCH, si_code=SI_KERNEL} ---

In this part clickhouse stuck.
Logs of sys box:

Aug 29 07:53:37 systemd[1]: var-lib-sysboxfs-48080c882ed194ce37b35e954c96350359d4021ae04379d58289af88e17b6655.mount: Deactivated successfully.

Aug 29 07:53:38 sysbox-mgr[89293]: time="2025-08-29 07:53:38" level=info msg="unregistered container 48080c882ed1"

Aug 29 07:54:10 sysbox-mgr[89293]: time="2025-08-29 07:54:10" level=info msg="registered new container bff59f76bbf1"

Aug 29 07:54:10 sysbox-fs[89312]: time="2025-08-29 07:54:10" level=info msg="Container pre-registration completed: id = bff59f76bbf1"

Aug 29 07:54:10 sysbox-fs[89312]: time="2025-08-29 07:54:10" level=info msg="Container registration completed: id = bff59f76bbf1, initPid = 618625, uid:gid = 165536:165536"

Aug 29 07:55:35 sysbox-fs[89312]: time="2025-08-29 07:55:35" level=info msg="Container unregistration completed: id = bff59f76bbf1"

Aug 29 07:55:35 sysbox-mgr[89293]: time="2025-08-29 07:55:35" level=info msg="unregister bff59f76bbf1: chown rootfs overlayfs upper layer at /data/docker/overlay2/622027f0f5caead87951f664932d250e0e0f8e5248d120291f0b3e02b1812765/diff (165536 -> 0)"

Aug 29 07:55:35 systemd[1]: var-lib-sysboxfs-bff59f76bbf1d9a60bf847e0f0c80eb3981e98d090763e064442957a30a1baff.mount: Deactivated successfully.

Aug 29 07:55:36 sysbox-mgr[89293]: time="2025-08-29 07:55:36" level=info msg="unregistered container bff59f76bbf1"

Aug 29 07:55:55 sysbox-mgr[89293]: time="2025-08-29 07:55:55" level=info msg="registered new container 1a2e52bdc33c"

Aug 29 07:55:55 sysbox-fs[89312]: time="2025-08-29 07:55:55" level=info msg="Container pre-registration completed: id = 1a2e52bdc33c"

Aug 29 07:55:55 sysbox-fs[89312]: time="2025-08-29 07:55:55" level=info msg="Container registration completed: id = 1a2e52bdc33c, initPid = 620059, uid:gid = 165536:165536"

Aug 29 08:33:54 sysbox-mgr[89293]: time="2025-08-29 08:33:54" level=info msg="registered new container 090cde04e637"

Aug 29 08:33:54 sysbox-fs[89312]: time="2025-08-29 08:33:54" level=info msg="Container pre-registration completed: id = 090cde04e637"

Aug 29 08:33:54 sysbox-fs[89312]: time="2025-08-29 08:33:54" level=info msg="Container registration completed: id = 090cde04e637, initPid = 635229, uid:gid = 165536:165536"

Aug 29 08:40:25 systemd[1]: var-lib-sysboxfs-090cde04e63769ce8d068eccaf5078f6846909ffd40fb1a8513febcc8ce133be.mount: Deactivated successfully.

Aug 29 08:40:25 sysbox-fs[89312]: time="2025-08-29 08:40:25" level=info msg="Container unregistration completed: id = 090cde04e637"

Aug 29 08:40:25 sysbox-mgr[89293]: time="2025-08-29 08:40:25" level=info msg="unregister 090cde04e637: chown rootfs overlayfs upper layer at /data/docker/overlay2/8c33845fa43d78048962f9308710d5f94555e264569a32779ca5f0f74a140017/diff (165536 -> 0)"

Aug 29 08:40:25 sysbox-mgr[89293]: time="2025-08-29 08:40:25" level=info msg="unregistered container 090cde04e637"

[ctalledo]

Hi @ssdscreator, thanks for giving Sysbox a try.

I am trying to start clickhouse service in gitlab ci with sys box, but I can't. Also I can't start it manually with sys box. It start correctly Postgres or dind containers. Also clickhouse started correctly in default runc runner or in Virtual Machine with sysbox.

I am not familiar with clickhouse.

Can you provide some simple steps to reproduce the problem?

Thanks!

[ssdscreator]

Hi, sure. If you start docker container like this docker run -it docker.io/library/clickhouse:25.6.5-jammy, than you will see

entrypoint.sh: neither CLICKHOUSE_USER nor CLICKHOUSE_PASSWORD is set, disabling network access for user 'default'
Processing configuration file '/etc/clickhouse-server/config.xml'.
Merging configuration file '/etc/clickhouse-server/config.d/docker_related_config.xml'.
Logging trace to /var/log/clickhouse-server/clickhouse-server.log
Logging errors to /var/log/clickhouse-server/clickhouse-server.err.log
2025.09.01 04:46:09.421081 [ 1 ] {} <Debug> CrashWriter: Sending crash reports is initialized with https://crash.clickhouse.com/ endpoint (anonymized)
2025.09.01 04:46:09.421465 [ 1 ] {} <Debug> Application: Sending logical errors is enabled
2025.09.01 04:46:09.470341 [ 1 ] {} <Information> Application: Starting ClickHouse 25.6.5.41 (revision: 54503, git hash: 533d68057fc87ec46238313c7b0219957cc50e67, build id: 09F3A83647B70A0529F134DB415D5D156D53B204), PID 1
2025.09.01 04:46:09.470471 [ 1 ] {} <Information> Application: starting up
2025.09.01 04:46:09.470495 [ 1 ] {} <Information> Application: OS name: Linux, version: 6.7.12+bpo-amd64, architecture: x86_64
2025.09.01 04:46:09.471313 [ 1 ] {} <Information> Jemalloc: Value for background_thread set to true (from true)
2025.09.01 04:46:09.478617 [ 1 ] {} <Information> Application: Available RAM: 503.53 GiB; logical cores: 128; used cores: 64.
2025.09.01 04:46:09.478654 [ 1 ] {} <Information> Application: Available CPU instruction sets: SSE, SSE2, SSE3, SSSE3, SSE41, SSE42, F16C, POPCNT, BMI1, BMI2, PCLMUL, AES, AVX, FMA, AVX2, AVX512F, AVX512DQ, AVX512IFMA, AVX512CD, AVX512BW, AVX512VL, AVX512VBMI, AVX512VBMI2, SHA, ADX, RDRAND, RDSEED, RDTSCP, CLFLUSHOPT, CLWB, XSAVE, OSXSAVE
2025.09.01 04:46:09.478697 [ 1 ] {} <Trace> Pipe: Pipe capacity is 1.00 MiB
2025.09.01 04:46:09.482025 [ 1 ] {} <Information> CgroupsReader: Will create cgroup reader from '/sys/fs/cgroup/init.scope' (cgroups version: v2)
2025.09.01 04:46:09.519282 [ 1 ] {} <Trace> AsynchronousMetrics: Scanning /sys/class/thermal
2025.09.01 04:46:09.520789 [ 1 ] {} <Information> Application: Waiting for background threads

It stuck in this place. In common work it should be like that:

/entrypoint.sh: neither CLICKHOUSE_USER nor CLICKHOUSE_PASSWORD is set, disabling network access for user 'default'
Processing configuration file '/etc/clickhouse-server/config.xml'.
Merging configuration file '/etc/clickhouse-server/config.d/docker_related_config.xml'.
Logging trace to /var/log/clickhouse-server/clickhouse-server.log
Logging errors to /var/log/clickhouse-server/clickhouse-server.err.log
2025.09.01 04:47:27.594867 [ 1 ] {} <Debug> CrashWriter: Sending crash reports is initialized with https://crash.clickhouse.com/ endpoint (anonymized)
2025.09.01 04:47:27.595196 [ 1 ] {} <Debug> Application: Sending logical errors is enabled
2025.09.01 04:47:27.647428 [ 1 ] {} <Information> Application: Starting ClickHouse 25.6.5.41 (revision: 54503, git hash: 533d68057fc87ec46238313c7b0219957cc50e67, build id: 1B4F00CC91E5FE8AEB391CAC6AF4FE6B6ED2516F), PID 1
2025.09.01 04:47:27.647506 [ 1 ] {} <Information> Application: starting up
2025.09.01 04:47:27.647529 [ 1 ] {} <Information> Application: OS name: Linux, version: 6.10.14-linuxkit, architecture: aarch64
2025.09.01 04:47:27.647897 [ 1 ] {} <Information> Jemalloc: Value for background_thread set to true (from true)
2025.09.01 04:47:27.666806 [ 1 ] {} <Information> Application: Available RAM: 7.65 GiB; logical cores: 14; used cores: 14.
2025.09.01 04:47:27.666845 [ 1 ] {} <Trace> Pipe: Pipe capacity is 1.00 MiB
2025.09.01 04:47:27.667660 [ 1 ] {} <Information> CgroupsReader: Will create cgroup reader from '/sys/fs/cgroup/' (cgroups version: v2)
2025.09.01 04:47:27.667743 [ 1 ] {} <Trace> AsynchronousMetrics: Scanning /sys/class/thermal
2025.09.01 04:47:27.667760 [ 1 ] {} <Trace> AsynchronousMetrics: Scanning /sys/block
2025.09.01 04:47:27.667959 [ 1 ] {} <Trace> AsynchronousMetrics: Scanning /sys/devices/system/edac
2025.09.01 04:47:27.667972 [ 1 ] {} <Trace> AsynchronousMetrics: Scanning /sys/class/hwmon
2025.09.01 04:47:27.672158 [ 1 ] {} <Warning> Application: Integrity check of the executable skipped because the reference checksum could not be read.
2025.09.01 04:47:27.672183 [ 1 ] {} <Information> Application: It looks like the process has no CAP_IPC_LOCK capability, binary mlock will be disabled. It could happen due to incorrect ClickHouse package installation. You could resolve the problem manually with 'sudo setcap cap_ipc_lock=+ep /usr/bin/clickhouse'. Note that it will not work on 'nosuid' mounted filesystems.
2025.09.01 04:47:27.672205 [ 1 ] {} <Information> MemoryWorker: Starting background memory thread with period of 50ms, using Cgroups as source
2025.09.01 04:47:27.672305 [ 1 ] {} <Information> BackgroundSchedulePool/BgSchPool: Create BackgroundSchedulePool with 512 threads
2025.09.01 04:47:27.694041 [ 1 ] {} <Debug> Application: rlimit on number of file descriptors is 1048576
2025.09.01 04:47:27.694056 [ 101 ] {BgSchPool::9c829d24-0f73-4aa9-aa3b-3595df347535} <Trace> CancellationChecker: Started worker function
2025.09.01 04:47:27.694091 [ 1 ] {} <Debug> Application: rlimit on number of threads is 18446744073709551615
2025.09.01 04:47:27.694113 [ 1 ] {} <Debug> Application: Initializing DateLUT.
2025.09.01 04:47:27.694152 [ 1 ] {} <Trace> Application: Initialized DateLUT with time zone 'UTC'.
2025.09.01 04:47:27.695304 [ 1 ] {} <Debug> Context: Setting up /var/lib/clickhouse/tmp/ to store temporary data in it
2025.09.01 04:47:27.697038 [ 1 ] {} <Debug> Application: Configuration parameter 'interserver_http_host' doesn't exist or exists and empty. Will use '7d1b8f68a5f5' as replica host.
2025.09.01 04:47:27.697057 [ 1 ] {} <Debug> Application: Initializing interserver credentials.
2025.09.01 04:47:27.697136 [ 1 ] {} <Information> Application: Lowered uncompressed cache size to 3.83 GiB because the system has limited RAM
2025.09.01 04:47:27.697167 [ 1 ] {} <Information> Application: Lowered mark cache size to 3.83 GiB because the system has limited RAM
2025.09.01 04:47:27.697179 [ 1 ] {} <Information> Application: Lowered primary index cache size to 3.83 GiB because the system has limited RAM
2025.09.01 04:47:27.697184 [ 1 ] {} <Information> Application: Lowered index mark cache size to 3.83 GiB because the system has limited RAM
2025.09.01 04:47:27.697192 [ 1 ] {} <Information> Application: Lowered vector similarity index cache size to 3.83 GiB because the system has limited RAM
2025.09.01 04:47:27.697870 [ 1 ] {} <Trace> NamedCollectionsMetadataStorage: Using local storage for named collections at path: /var/lib/clickhouse/named_collections
2025.09.01 04:47:27.697935 [ 1 ] {} <Debug> FileCacheFactory: Will load 0 caches from default cache config
2025.09.01 04:47:27.703840 [ 1 ] {} <Debug> ConfigReloader: Loading config '/etc/clickhouse-server/config.xml'
2025.09.01 04:47:27.703865 [ 1 ] {} <Debug> ConfigProcessor: Processing configuration file '/etc/clickhouse-server/config.xml'.
2025.09.01 04:47:27.704472 [ 1 ] {} <Debug> ConfigProcessor: Merging configuration file '/etc/clickhouse-server/config.d/docker_related_config.xml'.
2025.09.01 04:47:27.706416 [ 1 ] {} <Debug> ConfigProcessor: Saved preprocessed configuration to '/var/lib/clickhouse/preprocessed_configs/config.xml'.
2025.09.01 04:47:27.706488 [ 1 ] {} <Debug> ConfigReloader: Loaded config '/etc/clickhouse-server/config.xml', performing update on configuration
2025.09.01 04:47:27.708882 [ 1 ] {} <Information> Application: Changed setting 'max_server_memory_usage' to 6.89 GiB (7.65 GiB available memory * 0.90 max_server_memory_usage_to_ram_ratio)
2025.09.01 04:47:27.708898 [ 1 ] {} <Information> Application: Setting merges_mutations_memory_usage_soft_limit was set to 3.83 GiB (7.65 GiB available * 0.50 merges_mutations_memory_usage_to_ram_ratio)
2025.09.01 04:47:27.708909 [ 1 ] {} <Information> Application: Merges and mutations memory limit is set to 3.83 GiB
2025.09.01 04:47:27.709849 [ 1 ] {} <Information> Application: Setting max_remote_read_network_bandwidth_for_server was set to 0
2025.09.01 04:47:27.709859 [ 1 ] {} <Information> Application: Setting max_remote_write_network_bandwidth_for_server was set to 0
2025.09.01 04:47:27.709862 [ 1 ] {} <Information> Application: Setting max_local_read_bandwidth_for_server was set to 0
2025.09.01 04:47:27.709870 [ 1 ] {} <Information> Application: Setting max_local_write_bandwidth_for_server was set to 0
2025.09.01 04:47:27.709875 [ 1 ] {} <Information> Application: ConcurrencyControl limit is set to 28 CPU slots with 'fair_round_robin' scheduler
2025.09.01 04:47:27.709900 [ 1 ] {} <Information> BackgroundSchedulePool/BgBufSchPool: Create BackgroundSchedulePool with 16 threads
2025.09.01 04:47:27.710505 [ 1 ] {} <Information> BackgroundSchedulePool/BgMBSchPool: Create BackgroundSchedulePool with 16 threads
2025.09.01 04:47:27.711135 [ 1 ] {} <Information> BackgroundSchedulePool/BgDistSchPool: Create BackgroundSchedulePool with 16 threads
2025.09.01 04:47:27.713071 [ 1 ] {} <Debug> ConfigReloader: Loaded config '/etc/clickhouse-server/config.xml', performed update on configuration
2025.09.01 04:47:27.713101 [ 1 ] {} <Trace> ConfigReloader: Config reload interval set to 2000ms
2025.09.01 04:47:27.715321 [ 1 ] {} <Warning> Application: Listen [::]:9009 failed: Poco::Exception. Code: 1000, e.code() = 0, DNS error: EAI: Address family for hostname not supported (version 25.6.5.41 (official build)). If it is an IPv6 or IPv4 address and your host has disabled IPv6 or IPv4, then consider to specify not disabled IPv4 or IPv6 address to listen in <listen_host> element of configuration file. Example for disabled IPv6: <listen_host>0.0.0.0</listen_host> . Example for disabled IPv4: <listen_host>::</listen_host>
2025.09.01 04:47:27.715764 [ 1 ] {} <Information> Application: Listening for replica communication (interserver): http://0.0.0.0:9009
2025.09.01 04:47:27.716900 [ 1 ] {} <Debug> ConfigReloader: Loading config '/etc/clickhouse-server/users.xml'
2025.09.01 04:47:27.716912 [ 1 ] {} <Debug> ConfigProcessor: Processing configuration file '/etc/clickhouse-server/users.xml'.
2025.09.01 04:47:27.716980 [ 1 ] {} <Debug> ConfigProcessor: Merging configuration file '/etc/clickhouse-server/users.d/default-user.xml'.
2025.09.01 04:47:27.717462 [ 1 ] {} <Debug> ConfigProcessor: Saved preprocessed configuration to '/var/lib/clickhouse/preprocessed_configs/users.xml'.
2025.09.01 04:47:27.717477 [ 1 ] {} <Debug> ConfigReloader: Loaded config '/etc/clickhouse-server/users.xml', performing update on configuration
2025.09.01 04:47:27.717755 [ 1 ] {} <Debug> ConfigReloader: Loaded config '/etc/clickhouse-server/users.xml', performed update on configuration
2025.09.01 04:47:27.717765 [ 1 ] {} <Trace> ConfigReloader: Config reload interval set to 2000ms
2025.09.01 04:47:27.718148 [ 1 ] {} <Debug> Access(user directories): Added users_xml access storage 'users_xml', path: /etc/clickhouse-server/users.xml
2025.09.01 04:47:27.718254 [ 1 ] {} <Warning> Access(local_directory): File /var/lib/clickhouse/access/users.list doesn't exist
2025.09.01 04:47:27.718271 [ 1 ] {} <Warning> Access(local_directory): Recovering lists in directory /var/lib/clickhouse/access/
2025.09.01 04:47:27.718332 [ 1 ] {} <Debug> Access(user directories): Added local_directory access storage 'local_directory', path: /var/lib/clickhouse/access/
2025.09.01 04:47:27.718416 [ 1 ] {} <Information> CgroupsMemoryUsageObserver: Started cgroup current memory usage observer thread
2025.09.01 04:47:27.718738 [ 657 ] {} <Information> CgroupsMemoryUsageObserver: Memory amount initially available to the process is 7.65 GiB
2025.09.01 04:47:27.719824 [ 1 ] {} <Information> Context: Initialized background executor for merges and mutations with num_threads=16, num_tasks=32, scheduling_policy=round_robin
2025.09.01 04:47:27.720213 [ 1 ] {} <Information> Context: Initialized background executor for move operations with num_threads=8, num_tasks=8
2025.09.01 04:47:27.720720 [ 1 ] {} <Information> Context: Initialized background executor for fetches with num_threads=16, num_tasks=16
2025.09.01 04:47:27.721036 [ 1 ] {} <Information> Context: Initialized background executor for common operations (e.g. clearing old parts) with num_threads=8, num_tasks=8
2025.09.01 04:47:27.722072 [ 1 ] {} <Warning> Context: Linux transparent hugepages are set to "always". Check /sys/kernel/mm/transparent_hugepage/enabled
2025.09.01 04:47:27.722135 [ 1 ] {} <Warning> Context: Delay accounting is not enabled, OSIOWaitMicroseconds will not be gathered. You can enable it using `echo 1 > /proc/sys/kernel/task_delayacct` or by using sysctl.
2025.09.01 04:47:27.722460 [ 1 ] {} <Information> DNSCacheUpdater: Update period 15 seconds
2025.09.01 04:47:27.722481 [ 1 ] {} <Information> Application: Loading metadata from /var/lib/clickhouse/
2025.09.01 04:47:27.722495 [ 102 ] {BgSchPool::2dd1b3f5-58a4-4171-aa62-398f41416363} <Debug> DNSResolver: Updating DNS cache
2025.09.01 04:47:27.722531 [ 1 ] {} <Information> Context: Database disk name: default
2025.09.01 04:47:27.722578 [ 102 ] {BgSchPool::2dd1b3f5-58a4-4171-aa62-398f41416363} <Debug> DNSResolver: Updated DNS cache
2025.09.01 04:47:27.722736 [ 1 ] {} <Information> Context: Database disk name: default, path: /var/lib/clickhouse/
2025.09.01 04:47:27.722840 [ 1 ] {} <Debug> loadSystemDatabase: metadata_file_path metadata/system.sql, existsFile false
2025.09.01 04:47:27.723032 [ 91 ] {} <Information> MemoryTracker: Correcting the value of global memory tracker from 17.36 MiB to 456.51 MiB
2025.09.01 04:47:27.723837 [ 1 ] {} <Information> DatabaseAtomic (system): Metadata disk default, path /var/lib/clickhouse/
2025.09.01 04:47:27.725037 [ 1 ] {} <Debug> loadSystemDatabase: metadata_file_path metadata/information_schema.sql, existsFile false
2025.09.01 04:47:27.725508 [ 1 ] {} <Debug> loadSystemDatabase: metadata_file_path metadata/INFORMATION_SCHEMA.sql, existsFile false
2025.09.01 04:47:27.726044 [ 1 ] {} <Information> DatabaseAtomic (system): Metadata processed, database system has 0 tables, 0 dictionaries and 0 materialized views in total.
2025.09.01 04:47:27.726058 [ 1 ] {} <Information> TablesLoader: Parsed metadata of 0 tables in 1 databases in 2.9916e-05 sec
2025.09.01 04:47:27.726065 [ 1 ] {} <Trace> ReferentialDeps: No tables
2025.09.01 04:47:27.726090 [ 1 ] {} <Trace> LoadingDeps: No tables
2025.09.01 04:47:27.726093 [ 1 ] {} <Trace> MaterializedViewFromDeps: No tables
2025.09.01 04:47:27.726096 [ 1 ] {} <Trace> MaterializedViewToDeps: No tables
2025.09.01 04:47:27.726372 [ 1 ] {} <Debug> AsyncLoader: Prioritize load job 'startup Atomic database system': BackgrndStartup -> ForegroundLoad
2025.09.01 04:47:27.726382 [ 1 ] {} <Debug> AsyncLoader: Prioritize load job 'startup Ordinary database system': BackgrndStartup -> ForegroundLoad
2025.09.01 04:47:27.726388 [ 1 ] {} <Debug> AsyncLoader: Schedule load job 'startup Ordinary database system' into ForegroundLoad
2025.09.01 04:47:27.726400 [ 1 ] {} <Debug> AsyncLoader: Schedule load job 'startup Atomic database system' into ForegroundLoad
2025.09.01 04:47:27.726419 [ 1 ] {} <Debug> AsyncLoader: Change current priority: none -> 0
2025.09.01 04:47:27.726427 [ 1 ] {} <Debug> AsyncLoader: Spawn loader worker #1 in ForegroundLoad
2025.09.01 04:47:27.726471 [ 1 ] {} <Debug> AsyncLoader: Wait load job 'startup Atomic database system' in ForegroundLoad
2025.09.01 04:47:27.726724 [ 722 ] {} <Debug> AsyncLoader: Execute load job 'startup Ordinary database system' in ForegroundLoad
2025.09.01 04:47:27.726983 [ 722 ] {} <Debug> AsyncLoader: Finish load job 'startup Ordinary database system' with status OK
2025.09.01 04:47:27.726993 [ 722 ] {} <Debug> AsyncLoader: Spawn loader worker #2 in ForegroundLoad
2025.09.01 04:47:27.727062 [ 722 ] {} <Debug> AsyncLoader: Execute load job 'startup Atomic database system' in ForegroundLoad
2025.09.01 04:47:27.727082 [ 723 ] {} <Debug> AsyncLoader: Stop worker in ForegroundLoad
2025.09.01 04:47:27.727534 [ 722 ] {} <Debug> AsyncLoader: Finish load job 'startup Atomic database system' with status OK
2025.09.01 04:47:27.727545 [ 722 ] {} <Debug> AsyncLoader: Stop worker in ForegroundLoad
2025.09.01 04:47:27.727549 [ 722 ] {} <Debug> AsyncLoader: Change current priority: 0 -> none
2025.09.01 04:47:27.727806 [ 1 ] {} <Debug> SystemLog: Creating system.query_log from query_log
2025.09.01 04:47:27.730769 [ 1 ] {} <Debug> SystemLog: Creating system.query_thread_log from query_thread_log
2025.09.01 04:47:27.731088 [ 1 ] {} <Debug> SystemLog: Creating system.part_log from part_log
2025.09.01 04:47:27.731482 [ 1 ] {} <Debug> SystemLog: Creating system.trace_log from trace_log
2025.09.01 04:47:27.732208 [ 1 ] {} <Debug> SystemLog: Creating system.crash_log from crash_log
2025.09.01 04:47:27.732282 [ 1 ] {} <Debug> SystemLog: Creating system.text_log from text_log
2025.09.01 04:47:27.732764 [ 1 ] {} <Debug> SystemLog: Creating system.metric_log from metric_log
2025.09.01 04:47:27.737106 [ 1 ] {} <Debug> SystemLog: Not creating system.transposed_metric_log since corresponding section 'transposed_metric_log' is missing from config
2025.09.01 04:47:27.737121 [ 1 ] {} <Debug> SystemLog: Creating system.latency_log from latency_log
2025.09.01 04:47:27.737276 [ 1 ] {} <Debug> SystemLog: Creating system.error_log from error_log
2025.09.01 04:47:27.737432 [ 1 ] {} <Debug> SystemLog: Not creating system.filesystem_cache_log since corresponding section 'filesystem_cache_log' is missing from config
2025.09.01 04:47:27.737455 [ 1 ] {} <Debug> SystemLog: Not creating system.filesystem_read_prefetches_log since corresponding section 'filesystem_read_prefetches_log' is missing from config
2025.09.01 04:47:27.737472 [ 1 ] {} <Debug> SystemLog: Creating system.s3queue_log from s3queue_log
2025.09.01 04:47:27.737638 [ 1 ] {} <Debug> SystemLog: Not creating system.azure_queue_log since corresponding section 'azure_queue_log' is missing from config
2025.09.01 04:47:27.737650 [ 1 ] {} <Debug> SystemLog: Creating system.asynchronous_metric_log from asynchronous_metric_log
2025.09.01 04:47:27.737771 [ 1 ] {} <Debug> SystemLog: Creating system.opentelemetry_span_log from opentelemetry_span_log
2025.09.01 04:47:27.737914 [ 1 ] {} <Debug> SystemLog: Creating system.query_views_log from query_views_log
2025.09.01 04:47:27.738055 [ 1 ] {} <Debug> SystemLog: Not creating system.zookeeper_log since corresponding section 'zookeeper_log' is missing from config
2025.09.01 04:47:27.738067 [ 1 ] {} <Debug> SystemLog: Not creating system.session_log since corresponding section 'session_log' is missing from config
2025.09.01 04:47:27.738108 [ 1 ] {} <Debug> SystemLog: Not creating system.transactions_info_log since corresponding section 'transactions_info_log' is missing from config
2025.09.01 04:47:27.738140 [ 1 ] {} <Debug> SystemLog: Creating system.processors_profile_log from processors_profile_log
2025.09.01 04:47:27.738370 [ 1 ] {} <Debug> SystemLog: Creating system.asynchronous_insert_log from asynchronous_insert_log
2025.09.01 04:47:27.738571 [ 1 ] {} <Debug> SystemLog: Creating system.backup_log from backup_log
2025.09.01 04:47:27.738733 [ 1 ] {} <Debug> SystemLog: Creating system.blob_storage_log from blob_storage_log
2025.09.01 04:47:27.739068 [ 1 ] {} <Debug> SystemLog: Creating system.query_metric_log from query_metric_log
2025.09.01 04:47:27.742758 [ 1 ] {} <Debug> DatabaseAtomic (system): Creating directory symlink, path_to_metadata_symlink: metadata/system, metadata_path: store/09a/09a7ee77-643e-4507-b63c-6dbf4f4378d7/
2025.09.01 04:47:27.749813 [ 1 ] {} <Information> DatabaseAtomic (default): Metadata disk default, path /var/lib/clickhouse/
2025.09.01 04:47:27.750405 [ 1 ] {} <Information> DatabaseAtomic (default): Metadata processed, database default has 0 tables, 0 dictionaries and 0 materialized views in total.
2025.09.01 04:47:27.750418 [ 1 ] {} <Information> TablesLoader: Parsed metadata of 0 tables in 1 databases in 1.9792e-05 sec
2025.09.01 04:47:27.750425 [ 1 ] {} <Trace> ReferentialDeps: No tables
2025.09.01 04:47:27.750431 [ 1 ] {} <Trace> LoadingDeps: No tables
2025.09.01 04:47:27.750433 [ 1 ] {} <Trace> MaterializedViewFromDeps: No tables
2025.09.01 04:47:27.750445 [ 1 ] {} <Trace> MaterializedViewToDeps: No tables
2025.09.01 04:47:27.750464 [ 1 ] {} <Information> loadMetadata: Start asynchronous loading of databases
2025.09.01 04:47:27.750474 [ 1 ] {} <Debug> AsyncLoader: Schedule load job 'startup Ordinary database default' into BackgrndStartup
2025.09.01 04:47:27.750477 [ 1 ] {} <Debug> AsyncLoader: Schedule load job 'startup Atomic database default' into BackgrndStartup
2025.09.01 04:47:27.750490 [ 1 ] {} <Debug> AsyncLoader: Change current priority: none -> 2
2025.09.01 04:47:27.750495 [ 1 ] {} <Debug> AsyncLoader: Spawn loader worker #1 in BackgrndStartup
2025.09.01 04:47:27.750563 [ 744 ] {} <Debug> AsyncLoader: Execute load job 'startup Ordinary database default' in BackgrndStartup
2025.09.01 04:47:27.750579 [ 1 ] {} <Information> UserDefinedSQLObjectsLoaderFromDisk: Loading user defined objects from /var/lib/clickhouse/user_defined/
2025.09.01 04:47:27.750581 [ 744 ] {} <Debug> AsyncLoader: Finish load job 'startup Ordinary database default' with status OK
2025.09.01 04:47:27.750584 [ 1 ] {} <Debug> UserDefinedSQLObjectsLoaderFromDisk: The directory for user defined objects (/var/lib/clickhouse/user_defined/) does not exist: nothing to load
2025.09.01 04:47:27.750585 [ 744 ] {} <Debug> AsyncLoader: Spawn loader worker #2 in BackgrndStartup
2025.09.01 04:47:27.750771 [ 1 ] {} <Information> WorkloadEntityDiskStorage: Loading workload entities from /var/lib/clickhouse/workload/
2025.09.01 04:47:27.750782 [ 1 ] {} <Debug> WorkloadEntityDiskStorage: The directory for workload entities (/var/lib/clickhouse/workload/) does not exist: nothing to load
2025.09.01 04:47:27.750786 [ 1 ] {} <Debug> Application: Loaded metadata.
2025.09.01 04:47:27.750807 [ 1 ] {} <Information> Application: Tasks stats provider: procfs
2025.09.01 04:47:27.750838 [ 1 ] {} <Information> Application: It looks like the process has no CAP_SYS_NICE capability, the setting 'os_thread_priority' will have no effect. It could happen due to incorrect ClickHouse package installation. You could resolve the problem manually with 'sudo setcap cap_sys_nice=+ep /usr/bin/clickhouse'. Note that it will not work on 'nosuid' mounted filesystems.
2025.09.01 04:47:27.751044 [ 1 ] {} <Warning> Application: Listen [::]:8123 failed: Poco::Exception. Code: 1000, e.code() = 0, DNS error: EAI: Address family for hostname not supported (version 25.6.5.41 (official build)). If it is an IPv6 or IPv4 address and your host has disabled IPv6 or IPv4, then consider to specify not disabled IPv4 or IPv6 address to listen in <listen_host> element of configuration file. Example for disabled IPv6: <listen_host>0.0.0.0</listen_host> . Example for disabled IPv4: <listen_host>::</listen_host>
2025.09.01 04:47:27.751094 [ 744 ] {} <Debug> AsyncLoader: Execute load job 'startup Atomic database default' in BackgrndStartup
2025.09.01 04:47:27.751101 [ 1 ] {} <Warning> Application: Listen [::]:9000 failed: Poco::Exception. Code: 1000, e.code() = 0, DNS error: EAI: Address family for hostname not supported (version 25.6.5.41 (official build)). If it is an IPv6 or IPv4 address and your host has disabled IPv6 or IPv4, then consider to specify not disabled IPv4 or IPv6 address to listen in <listen_host> element of configuration file. Example for disabled IPv6: <listen_host>0.0.0.0</listen_host> . Example for disabled IPv4: <listen_host>::</listen_host>
2025.09.01 04:47:27.751195 [ 744 ] {} <Debug> AsyncLoader: Finish load job 'startup Atomic database default' with status OK
2025.09.01 04:47:27.751205 [ 744 ] {} <Debug> AsyncLoader: Stop worker in BackgrndStartup
2025.09.01 04:47:27.751266 [ 1 ] {} <Warning> Application: Listen [::]:9004 failed: Poco::Exception. Code: 1000, e.code() = 0, DNS error: EAI: Address family for hostname not supported (version 25.6.5.41 (official build)). If it is an IPv6 or IPv4 address and your host has disabled IPv6 or IPv4, then consider to specify not disabled IPv4 or IPv6 address to listen in <listen_host> element of configuration file. Example for disabled IPv6: <listen_host>0.0.0.0</listen_host> . Example for disabled IPv4: <listen_host>::</listen_host>
2025.09.01 04:47:27.751310 [ 1 ] {} <Warning> Application: Listen [::]:9005 failed: Poco::Exception. Code: 1000, e.code() = 0, DNS error: EAI: Address family for hostname not supported (version 25.6.5.41 (official build)). If it is an IPv6 or IPv4 address and your host has disabled IPv6 or IPv4, then consider to specify not disabled IPv4 or IPv6 address to listen in <listen_host> element of configuration file. Example for disabled IPv6: <listen_host>0.0.0.0</listen_host> . Example for disabled IPv4: <listen_host>::</listen_host>
2025.09.01 04:47:27.751230 [ 745 ] {} <Debug> AsyncLoader: Stop worker in BackgrndStartup
2025.09.01 04:47:27.751487 [ 745 ] {} <Debug> AsyncLoader: Change current priority: 2 -> none
2025.09.01 04:47:27.778459 [ 1 ] {} <Trace> MySQLHandlerFactory: Failed to create SSL context. SSL will be disabled. Error: Poco::Exception. Code: 1000, e.code() = 0, SSL Exception: Configuration error: no certificate file has been specified (version 25.6.5.41 (official build))
2025.09.01 04:47:27.778500 [ 1 ] {} <Trace> MySQLHandlerFactory: Failed to read RSA key pair from server certificate. Error: Poco::Exception. Code: 1000, e.code() = 0, Not found: openSSL.server.privateKeyFile (version 25.6.5.41 (official build))
2025.09.01 04:47:27.778507 [ 1 ] {} <Trace> MySQLHandlerFactory: Generating new RSA key pair.
2025.09.01 04:47:27.801295 [ 1 ] {} <Information> CertificateReloader: One of paths is empty. Cannot apply new configuration for certificates. Fill all paths and try again.
2025.09.01 04:47:27.801310 [ 1 ] {} <Information> CertificateReloader: One of paths is empty. Cannot apply new configuration for certificates. Fill all paths and try again.
2025.09.01 04:47:27.803176 [ 1 ] {} <Debug> ExternalDictionariesLoader: Periodic updates enabled
2025.09.01 04:47:27.803254 [ 747 ] {} <Debug> ExternalDictionariesLoader: Starting periodic updates
2025.09.01 04:47:27.803406 [ 1 ] {} <Debug> ExternalUserDefinedExecutableFunctionsLoader: Periodic updates enabled
2025.09.01 04:47:27.803645 [ 1 ] {} <Information> Application: Listening for http://0.0.0.0:8123
2025.09.01 04:47:27.803716 [ 1 ] {} <Information> Application: Listening for native protocol (tcp): 0.0.0.0:9000
2025.09.01 04:47:27.803525 [ 746 ] {} <Debug> ExternalUserDefinedExecutableFunctionsLoader: Starting periodic updates
2025.09.01 04:47:27.803803 [ 1 ] {} <Information> Application: Listening for MySQL compatibility protocol: 0.0.0.0:9004
2025.09.01 04:47:27.803931 [ 1 ] {} <Information> Application: Listening for PostgreSQL compatibility protocol: 0.0.0.0:9005
2025.09.01 04:47:27.803949 [ 1 ] {} <Information> Application: Ready for connections.

Later we found, that it can start with docker run -it --tmpfs /sys/class/thermal:rw --tmpfs /sys/class/hwmon:rw --rm -d --name test-clickhouse -e CLICKHOUSE_USER=ci_user -e CLICKHOUSE_PASSWORD=123456 -e CLICKHOUSE_DB=testdb docker.io/clickhouse/clickhouse-server:25.5-alpine, but we not sure, it will be working in gitlab ci service. Maybe you have more simple and useful solution?

[ssdscreator]

Some upd. We can work in case disabling hardware monitoring. But we don't want to do this, because we have to disable nvme. Can you add implementation of paths like this https://github.com/nestybox/sysbox-fs/blob/master/handler/implementations/root.go for /sys/class/thermal and /sys/class/hwmon or make them empty by a flag?