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cdc/sorter: make unified sorter cgroup aware #3436

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merged 11 commits into from
Nov 12, 2021

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@overvenus overvenus commented Nov 12, 2021

What problem does this PR solve?

It fixes an OOM issue where memory limited by cgroup is smaller
than physical memory.

Note this patch only recognizes container cgroup, it may still
OOM when the cgroup is set by systemd or manually.

Cc https://github.com/pingcap/ticdc/issues/1798

Check List

Tests

  • Manual test (add detailed scripts or steps below)
  1. mysql -h TIDBIP -P 4000 -u root -E -e 'update mysql.tidb set VARIABLE_VALUE="2400h" where VARIABLE_NAME="tikv_gc_life_time";'
  2. tiup bench tpcc --host TIDBIP --port 4000 prepare -T 10 --warehouses 100
  3. tiup bench tpcc --host TIDBIP --port 4000 run -T 10 --warehouses 100
  4. run cdc in 8G memory docker container.
  5. ./cdc cli --pd="http://PDIP" changefeed create
    --sink-uri="mysql://xx:xx@MYSQLIP:3306/" -c "mysql37"
    --start-ts=$(( $(pd-ctl -u http://PDIP service-gc-safepoint | jq '.service_gc_safe_points[] | select(.service_id == "gc_worker") | .safe_point') + 1000 ))
    --no-confirm --sort-engine=unified
OOM log in demsg
[Fri Nov 12 17:23:50 2021] CPU: 6 PID: 2542 Comm: cdc Kdump: loaded Tainted: G               ------------ T 3.10.0-1127.13.1.el7.x86_64 #1
[Fri Nov 12 17:23:50 2021] Hardware name: Dell Inc. PowerEdge R630/02C2CP, BIOS 2.4.3 01/17/2017
[Fri Nov 12 17:23:50 2021] Call Trace:
[Fri Nov 12 17:23:50 2021]  [<ffffffffa197ffa5>] dump_stack+0x19/0x1b
[Fri Nov 12 17:23:50 2021]  [<ffffffffa197a8c3>] dump_header+0x90/0x229
[Fri Nov 12 17:23:50 2021]  [<ffffffffa1327aa4>] ? __css_tryget+0x24/0x50
[Fri Nov 12 17:23:50 2021]  [<ffffffffa13c24ce>] oom_kill_process+0x25e/0x3f0
[Fri Nov 12 17:23:50 2021]  [<ffffffffa1333a01>] ? cpuset_mems_allowed_intersects+0x21/0x30
[Fri Nov 12 17:23:50 2021]  [<ffffffffa1440c06>] mem_cgroup_oom_synchronize+0x546/0x570
[Fri Nov 12 17:23:50 2021]  [<ffffffffa1440080>] ? mem_cgroup_charge_common+0xc0/0xc0
[Fri Nov 12 17:23:50 2021]  [<ffffffffa13c2d74>] pagefault_out_of_memory+0x14/0x90
[Fri Nov 12 17:23:50 2021]  [<ffffffffa1978dd3>] mm_fault_error+0x6a/0x157
[Fri Nov 12 17:23:50 2021]  [<ffffffffa198d8d1>] __do_page_fault+0x491/0x500
[Fri Nov 12 17:23:50 2021]  [<ffffffffa198d975>] do_page_fault+0x35/0x90
[Fri Nov 12 17:23:50 2021]  [<ffffffffa1989778>] page_fault+0x28/0x30
[Fri Nov 12 17:23:50 2021] Task in /docker/2b34db4f57b5dff0b20a52ecbbdf1113450a5d19d86a68243bdd7814d4b743a6 killed as a result of limit of /docker/2b34db4f57b5dff0b20a52ecbbdf1113450a5d19d86a68243bdd7814d4b743a6
[Fri Nov 12 17:23:50 2021] memory: usage 8388608kB, limit 8388608kB, failcnt 41731
[Fri Nov 12 17:23:50 2021] memory+swap: usage 8388608kB, limit 16777216kB, failcnt 0
[Fri Nov 12 17:23:50 2021] kmem: usage 9100kB, limit 9007199254740988kB, failcnt 0
[Fri Nov 12 17:23:50 2021] Memory cgroup stats for /docker/2b34db4f57b5dff0b20a52ecbbdf1113450a5d19d86a68243bdd7814d4b743a6: cache:688KB rss:8378820KB rss_huge:0KB mapped_file:28KB swap:0KB inactive_anon:0KB active_anon:8378772KB inactive_file:152KB active_file:32KB unevictable:0KB
[Fri Nov 12 17:23:50 2021] [ pid ]   uid  tgid total_vm      rss nr_ptes swapents oom_score_adj name
[Fri Nov 12 17:23:50 2021] [33150]     0 33150      409       34       5        0             0 sh
[Fri Nov 12 17:23:50 2021] [35361]     0 35361      409       48       5        0             0 sh
[Fri Nov 12 17:23:50 2021] [36043]     0 36043      365       48       4        0             0 less
[Fri Nov 12 17:23:50 2021] [ 2532]     0  2532  2297379  2100625    4178        0             0 cdc
[Fri Nov 12 17:23:50 2021] Memory cgroup out of memory: Kill process 2621 (cdc) score 1003 or sacrifice child
[Fri Nov 12 17:23:50 2021] Killed process 2532 (cdc), UID 0, total-vm:9189516kB, anon-rss:8375780kB, file-rss:26720kB, shmem-rss:0kB

Left: master
Right: this PR

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Related changes

  • Need to cherry-pick to the release branch

Release note

Fix OOM in container environments.

It fixes an OOM issue where memory limited by cgroup is smaller
than physical memory.

Note this patch only recognizes container cgroup, it may still
OOM when the cgroup is set by systemd or manually.

Signed-off-by: Neil Shen <overvenus@gmail.com>
@overvenus overvenus added type/bugfix This PR fixes a bug. needs-cherry-pick-release-4.0 Should cherry pick this PR to release-4.0 branch. needs-cherry-pick-release-5.0 Should cherry pick this PR to release-5.0 branch. needs-cherry-pick-release-5.1 Should cherry pick this PR to release-5.1 branch. component/sorter Sorter component. needs-cherry-pick-release-5.2 Should cherry pick this PR to release-5.2 branch. needs-cherry-pick-release-5.3 Should cherry pick this PR to release-5.3 branch. labels Nov 12, 2021
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ti-chi-bot commented Nov 12, 2021

[REVIEW NOTIFICATION]

This pull request has been approved by:

  • 3AceShowHand
  • amyangfei

To complete the pull request process, please ask the reviewers in the list to review by filling /cc @reviewer in the comment.
After your PR has acquired the required number of LGTMs, you can assign this pull request to the committer in the list by filling /assign @committer in the comment to help you merge this pull request.

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@ti-chi-bot ti-chi-bot added release-note Denotes a PR that will be considered when it comes time to generate release notes. size/S Denotes a PR that changes 10-29 lines, ignoring generated files. labels Nov 12, 2021
Comment on lines 102 to 107
// TODO: The underlaying implementation only recognizes cgroups set by
// containers, we need to support cgroups set by systemd or manually.
totalMemory, err := memory.MemTotal()
if err != nil {
log.Panic("read memory stat failed", zap.Error(err))
}
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I notice there is no unit test for MemTotal and MemUsed in github.com/pingcap/tidb/util/memory, can we add a unit test in github action to verify it works.

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I think its hard to add unit tests, the best effort we can do is to verify if github.com/pingcap/tidb/util/memory parses cgroup info correctly, and it should be added in upstream not here.

Also, we plan to support cgroups set by systemd in a later PR, at that time, we can add unit tests.

@ti-chi-bot ti-chi-bot added the status/LGT1 Indicates that a PR has LGTM 1. label Nov 12, 2021
@ti-chi-bot ti-chi-bot added status/LGT2 Indicates that a PR has LGTM 2. and removed status/LGT1 Indicates that a PR has LGTM 1. labels Nov 12, 2021
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liuzix commented Nov 12, 2021

/run-integration-tests

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/merge

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This pull request has been accepted and is ready to merge.

Commit hash: cae5346

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/unhold

@ti-chi-bot ti-chi-bot removed the do-not-merge/hold Indicates that a PR should not merge because someone has issued a /hold command. label Nov 12, 2021
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/merge

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This pull request has been accepted and is ready to merge.

Commit hash: 27c3938

@ti-chi-bot ti-chi-bot added the status/can-merge Indicates a PR has been approved by a committer. label Nov 12, 2021
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/run-integration-tests

@ti-chi-bot ti-chi-bot merged commit 819615c into pingcap:master Nov 12, 2021
ti-chi-bot pushed a commit to ti-chi-bot/tiflow that referenced this pull request Nov 12, 2021
Signed-off-by: ti-chi-bot <ti-community-prow-bot@tidb.io>
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In response to a cherrypick label: new pull request created: #3437.

ti-chi-bot pushed a commit to ti-chi-bot/tiflow that referenced this pull request Nov 12, 2021
Signed-off-by: ti-chi-bot <ti-community-prow-bot@tidb.io>
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In response to a cherrypick label: new pull request created: #3438.

ti-chi-bot pushed a commit to ti-chi-bot/tiflow that referenced this pull request Nov 12, 2021
Signed-off-by: ti-chi-bot <ti-community-prow-bot@tidb.io>
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In response to a cherrypick label: new pull request created: #3439.

ti-chi-bot pushed a commit to ti-chi-bot/tiflow that referenced this pull request Nov 12, 2021
Signed-off-by: ti-chi-bot <ti-community-prow-bot@tidb.io>
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In response to a cherrypick label: new pull request created: #3440.

ti-chi-bot pushed a commit to ti-chi-bot/tiflow that referenced this pull request Nov 12, 2021
Signed-off-by: ti-chi-bot <ti-community-prow-bot@tidb.io>
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In response to a cherrypick label: new pull request created: #3441.

3AceShowHand pushed a commit to ti-chi-bot/tiflow that referenced this pull request Jan 13, 2022
overvenus pushed a commit that referenced this pull request Jan 18, 2022
* fix the txn_batch_size metric inaccuracy bug when the sink target is MQ

* address comments

* add comments for exported functions

* fix the compiling problem

* workerpool: limit the rate to output deadlock warning (#3775) (#3795)

* tests(ticdc): set up the sync diff output directory correctly (#3725) (#3741)

* relay(dm): use binlog name comparison (#3710) (#3712)

* dm/load: fix concurrent call Loader.Status (#3459) (#3468)

* cdc/sorter: make unified sorter cgroup aware (#3436) (#3439)

* tz (ticdc): fix timezone error (#3887) (#3906)

* pkg,cdc: do not use log package (#3902) (#3940)

* *: rename repo from pingcap/ticdc to pingcap/tiflow (#3959)

* http_*: add log for http api and refine the err handle logic (#2997) (#3307)

* etcd_worker: batch etcd patch (#3277) (#3389)

* http_api (ticdc): check --cert-allowed-cn before add server common name (#3628) (#3882)

* kvclient(ticdc): fix kvclient takes too long time to recover (#3612) (#3663)

* owner: fix owner tick block http request (#3490) (#3530)

* dm/syncer: use downstream PK/UK to generate DML (#3168) (#3256)

* dep(dm): update go-mysql (#3914) (#3934)

* dm/syncer: multiple rows use downstream schema (#3308) (#3953)

* errorutil,sink,syncer: add errorutil to handle ignorable error (#3264) (#3995)

* dm/worker: don't exit when failed to read checkpoint in relay (#3345) (#4005)

* syncer(dm): use an early location to reset binlog and open safemode (#3860)

* ticdc/owner: Fix ddl special comment syntax error (#3845) (#3978)

* dm/scheduler: fix inconsistent of relay status (#3474) (#4009)

* owner,scheduler(cdc): fix nil pointer panic in owner scheduler (#2980) (#4007) (#4016)

* config(ticdc): Fix old value configuration check for maxwell protocol (#3747) (#3783)

* sink(ticdc): cherry pick sink bug fix to release 5.3 (#4083)

* master(dm): clean and treat invalid load task (#4004) (#4145)

* loader: fix wrong progress in query-status for loader (#4093) (#4143)

close #3252

* ticdc/processor: Fix backoff base delay misconfiguration (#3992) (#4028)

* dm: load table structure from dump files (#3295) (#4163)

* compactor: fix duplicate entry in safemode (#3432) (#3434) (#4088)

* kv(ticdc): reduce eventfeed rate limited log (#4072) (#4111)

close #4006

* metrics(ticdc): add resolved ts and add changefeed to dataflow (#4038) (#4104)

* This is an automated cherry-pick of #4192

Signed-off-by: ti-chi-bot <ti-community-prow-bot@tidb.io>

* retry(dm): align with tidb latest error message (#4172) (#4254)

close #4159, close #4246

* owner(ticdc): Add bootstrap and try to fix the meta information in it (#3838) (#3865)

* redolog: add a precleanup process when s3 enable (#3525) (#3878)

* ddl(dm): make skipped ddl pass `SplitDDL()` (#4176) (#4227)

close #4173

* cdc/sink: remove Initialize method from the sink interface (#3682) (#3765)

Co-authored-by: Ling Jin <7138436+3AceShowHand@users.noreply.github.com>

* http_api (ticdc): fix http api 'get processor' panic. (#4117) (#4123)

close #3840

* sink (ticdc): fix a deadlock due to checkpointTs fall back in sinkNode (#4084) (#4099)

close #4055

* cdc/sink: adjust kafka initialization logic (#3192) (#4162)

* try fix conflicts.

* This is an automated cherry-pick of #4192

Signed-off-by: ti-chi-bot <ti-community-prow-bot@tidb.io>

* fix conflicts.

* fix conflicts.

Co-authored-by: zhaoxinyu <zhaoxinyu512@gmail.com>
Co-authored-by: amyangfei <yangfei@pingcap.com>
Co-authored-by: lance6716 <lance6716@gmail.com>
Co-authored-by: sdojjy <sdojjy@qq.com>
Co-authored-by: Ling Jin <7138436+3AceShowHand@users.noreply.github.com>
Co-authored-by: 3AceShowHand <jinl1037@hotmail.com>
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