2020-10-19 Operating System automated update, caused wide-scale instability

Date	19 Oct 2020
Authors	Andy Nash (Unlicensed) Joseph (Pepe) Kelly John Simmons (Deactivated) Andy Dingley Simon Meredith (Unlicensed) Paul Hoang (Unlicensed) Sachin Mehta (Unlicensed)
Status	LiveDefect resolved. Actions being ticketed up (Andy Nash (Unlicensed))
Summary	On Friday evening we noticed the server used to build our applications and run scheduled jobs was struggling. It then crashed, subsequently causing ETL (scheduled data flows between systems) and data related issues. Systems used to search, transfer and display data in TIS along with data stores then also froze between Friday and Saturday
Impact	No Stage or Production environments. No data synchronisation between systems

Technical Detail

Summary

On Friday evening we saw Jenkins struggling, and then fell over, subsequently causing ETL and data related issues. Elasticsearch, RabbitMQ and MongoDB then also fell over between Friday and Saturday

Timeline (collation and interpretation from across all Slack monitoring channels)

First trigger
c. 6am 2020-10-16 06:33 2020-10-16 06:36 2020-10-16 06:42 2020-10-16 06:??	Friday	Patch comes out for the kernel ESR Data exporter triggered a build of outstanding PRs (resulting from Dependabot - upgrade at Git repo level) one ES cluster node failed amazon-ssm-agent kicked off an `apt` upgrade (at OS level): which included `xxd`, `python 2.7`, `vim`, `python 2.6`, `linux AWS 5.4 headers`. old versions of `xxd`, `python 2.7`, `vim`, `python 2.6`, `linux AWS 5.4 headers` were removed - the upgrades were auto-applied without a restart via LivePatch.
Starting Friday and continuing over the weekend
2020-10-16 07:18 2020-10-16 07:38 2020-10-16 07:38 2020-10-16 07:58 2020-10-16 08:43 2020-10-16 12:03 2020-10-16 16:38	Friday	Staging RabbitMQ node 2 down (PH) Prod ES node 3 down (PH) Prod ES node 1 & 2 down - additional alert of too few nodes running - at this point, prod person search should not be working Staging ES node 2 down (PH) Phil W asks what this all means, Phil J summaries (PH) Old concerns on green&blue stage goes down (PH) Jenkins goes down (PH)	because of sharding, users may have been seeing only partial results at this point) (PH) 👈 need to look into and confirm this assumption…
Then
6am 2020-10-17 01:13 2020-10-17 01:28 2020-10-17 06:00 2020-10-17 06:00 2020-10-17 06:02 2020-10-17 07:08 2020-10-17 07:18 2020-10-17 07:33 2020-10-17 07:43	Saturday	Patch comes out for the kernel High messages in RabbitMQ Prod (PH) High messages in RabbitMQ Staging (PH) ESR n-d-l cron job didn’t start - manually kicked by Paul at 10:08, exited at 10:09 ESR ETL ES Docker container failure (see Sachin’s snippet on Slack channel) Staging ES node 2 down, Prod RabbitMQ node 3 down (PH) Staging ES node 1 & 3 down (PH) Staging RabbitMQ node 1 & 3 down (PH) Prod Mongo goes down (PH)
…at this point ☝ pretty much everything is being effected by the combination of issues
👇 shall I remove this section of the timeline completely from this incident log? Seems overkill, given pretty much everything was down at this point
2020-10-17 08:48 2020-10-17 09:27 2020-10-17 10:23 2020-10-17 10:23 2020-10-18 02:42 2020-10-18 07:37 2020-10-18 10:23 2020-10-18 10:25 2020-10-18 07:37 2020-10-19 01:29 2020-10-19 07:46 2020-10-19 08:59 2020-10-19 07:54 2020-10-19 08:17 2020-10-19 10:35 2020-10-17	Saturday Sunday Monday Tuesday	(see Prometheus graph below) (see Prometheus graph below) D/B Prod/Stage sync started but never completed NDW ETL: Stage (PaaS) failed ESR Sentry errors x 7 (reappearance of the same issue across all services) TCS ES sync job failed to run/complete on either blue or green servers NDW ETL: Stage (PaaS) failed NDW ETL: Stage (current) failed TCS ES sync job failed to run/complete on either blue or green servers TCS ES Person sync job failed (None of the configured nodes were available) Users started reporting problems using Search on Prod Users reporting problems using Search on Prod had been resolved (see Prometheus graph below) (see Prometheus graph below) (see Prometheus graph below) Massive Sentry hit, on ESR, using up our entire monthly allocation

Root Cause(s)

OS apt patch running every morning used the LivePatch function to apply the patch without needing to restart everything.
This caused conflict with Docker - Note, however, that this conflict has not been seen before since TIS’s inception. So the working theory is that this was a one-off conflict that is not likely to reoccur.
The index of trainees for the searchpage (elasticsearch) was unreachable and couldn’t start up.
The conflict then compromised everything else in a domino effect, compounded by the backed up Dependabot PRs and builds which, in the case of the ESR area, creates multiple concurrent containers which trips Jenkins up (not enough RAM)
Many downstream processes rely on Jenkins being up
We haven’t configured the monthly Dependabot sweep to stagger the hit of PRs / builds

Trigger

6am OS patch process auto-applied the patches via LivePatch, causing a conflict with Docker which needed to be restarted
Failure of Docker restarting following the OS patch puts strain on ElasticSearch and Jenkins (and everything else)
ElasticSearch issues compromised the search function for users of the app
Dependencies of many timed jobs on Jenkins being available
Not enough configuration of retries

Resolution

Restarted Jenkins
Restarted NDW ETLs on Stage (current and PaaS)
Restarted Docker on ES nodes
Restarted Neo4J container (rather than the service)
Spun up CDC (Paul) - looking at the HUGE backlog of messages from changes to TIS data (which started coming down rapidly. Phew!)
Removed all the dangling volumes from Mongo (several times) (old images that are taking up space)

Detection

Good news is that there were lots of monitoring alerts in various channels in Slack and from the graphs, below, there was probably enough evidence there to have alerted us to a problem needing resolution
Users pointed out the issue with search not functioning correctly on TIS
Bad news is we didn’t act on the initial Friday indicators (they didn’t appear to be as serious an indicator as they were)

Action Items

Confirmed action Items	Owner	Status	Comments
0. Spike the creation an Ansible config to do a full restart (John Simmons (Deactivated) to complete the description of this) - in case we come across this situation happening again.	Ops	To do
1. bump up the Jenkins RAM to 32Gb (short term ONLY). Add a reminder to revisit this in 1 month / 2 months?	Ops	Done
2. disable integration tests on ESR projects for PR pipeline (they’d still run on merge to master, rather than each PR). These are what fire up the local stack and test containers (hold back on…'if we’re not planning to do any further ESR work once Leeerrroooy leave, we could just disable the integration tests in ESR') ESR guys not keen at all on this. Risk of breaking the pipeline and blocking anything thereafter. When you need them the most… don’t have tests switched off! 2. Code in AWS S3 creds to save firing up local stack. Need to be careful setting this up. Shared bucket for integration tests across Reval, TISSS as well. With archiving rules deleting everything >5 days old. See ‘diet’ ticket below - lots of work, but an investment that will have its uses across all products within the TIS portfolio	ESR & others	To do
3. Close outstanding ESR major version change PRs - how many is ‘critical mass’? But without being blazé about approving PRs. Ignore minor versions.	Sachin	To do	Consider ways to reduce system resources instead? Discussed with Doris and ESR team last week…
4. Restrict the number of PRs Dependabot opens on each ESR project to 1 and to major versions only (given they’re microservices, we still might get significant numbers). There are dependencies between PRs. So restricting to one might have a chain reaction. No getting round that things like this will need manual intervention. So let’s see how restricting to major versions affects things and decide on further action if needed at that point.	AndyD	To do
5. Use Jenkins pipeline rather than node - to make things sequential rather than concurrent disableConcurrentBuilds Disallow concurrent executions of the Pipeline. Can be useful for preventing simultaneous accesses to shared resources, etc. For example: `options { disableConcurrentBuilds() }`	AndyD / Pepe	To do	Pipelines not written to take advantage of extra nodes - is the time investment required greater than the benefit
6. Address https://hee-tis.atlassian.net/browse/TISNEW-5613 quickly (removing local stack from the Data exporter process). Needs refining and sub-tasking with ESR and perm team, before ESR disappear.	ESR & perm team	To do	Spike ticket completed this Sprint. This ticket is the result of that Spike.
7. The ElasticSearch nightly sync shouldn’t be necessary. Verify that ElasticSearch is being updated properly during the day.	Pepe	To do	TBC

Lessons Learned (Good and Bad)

Check monitoring channels in Slack, check Prometheus, check Grafana as a matter of professional pride, daily.
Act* on anything unusual (* resolve yourself if you can, alert others immediately if you think it’s serious, raise on stand ups otherwise).
Incident has encouraged us to do the most thorough route cause analysis we have ever done, and subsequently identify some inefficiencies in related areas, and to map out a range of actions short and longer term to address them all.

Techy Stuff

5 whys

Everything fell over

Comments following catch up 2020-10-21

Jenkins
ESR containers taking up all the resource
Too many (Dependabot) PRs outstanding, builds, rebasing
ESR did not have time to action them because of the launch of new world code

Underlying OS upgrade occurred and was applied (LivePatch)
Probably something to do with that very specific update (it’s never happened before and has been running since the Apps were built
Did Docker struggle with the patch, rather than Amazon making a mistake with applying the patch (no complaints on Amazon forums, so looks quite specific to us)
Version of Docker is linked to whatever’s available in apt
Not worth changing our set up for the sake of a ‘freak’ occurrence that probably will only happen once every 3 years? Or scheduling the OS upgrades to a better time / day, so we can actively check that they’ve done what they were expected to do, and not caused conflicts. We can then determine whether a full restart immediately afterwards would be sensible too.

Jenkins could to with some TLC. ES went down too (before Jenkins). However, there is an underlying OS update issue that we believe triggered everything.

It destabilised the system, stopping Docker. When Docker was manually restarted on Monday morning, everything started coming back up again. And stability was restored.

Initial discussion, along with short and longer term actions

What can we do about Dependabot creating and building simultaneously?

Dependabot does run sequentially, but much faster than Jenkins can process things so everything appears concurrent.

~~We could get Dependabot to add a GitHub label to the PR - add something to the Jenkins file to read the label and mark as “Don’t run”. But this stops Dependabot being useful.~~

ESR preoccupied with launching New World, understandably!

Can perm team keep on top of ESR stuff when they leave?

Even when keeping on top of things, will it eventually be too much anyway?
Or is it simply a case of the team not controlling the overall number of open PRs?

Original Jenkins build was never designed to handle this much load - underlying architecture isn’t there for the level of automation we now have. It is designed for a single node, not load-balancing

Is Jenkins the right tool for everything it’s being asked to do? No:

bump up the Jenkins RAM to 32Gb (short term ONLY). Add a reminder to revisit this in 1 month / 2 months?
disable integration tests on ESR projects for PR pipeline (they’d still run on merge to master, rather than each PR). These are what fire up the local stack and test containers (hold back on…'if we’re not planning to do any further ESR work once Leeerrroooy leave, we could just disable the integration tests in ESR')
Close outstanding ESR PRs - how many is ‘critical mass’? But without being blazé about approving PRs
Restrict the number of PRs Dependabot opens on each ESR project to 1 (but given they’re microservices, it still might be a big number). Not much of a concern if we do 2. above.
The ElasticSearch nightly sync shouldn’t be necessary. Verify that ElasticSearch is being updated properly during the day.
move ETLs over to ECS tasks (serverless ‘run container' instructions to AWS - not reliant on our infrastructure).
This would remove the dependency on Jenkins - so if it went down, the jobs could continue. N.B. This doesn’t apply to the ElasticSearch job.
Don’t do scheduled jobs / anything with a timer - use Cron server instead for this stuff.
Just use Jenkins as a build server (~~Metabase also runs on Jenkins, but doesn’t use much~~)
ticket up addressing our infrastructure so that the set up ESR have created does run - it’s been done right!
get ourselves a dedicated Jenkins server (what size )
move to ElasticSearch SaaS

Checklist of actions should take in future

One-off task: Look at the way updates are applied - AWS system manager - tell it when you want to do the patching. Schedule to patch Stage first, check and then apply to Prod / Then set up a simple Slack reminder to check all is well

Manage user expectations - alert them AS SOON AS we know something’s amiss. AND keep updates flowing as we resolve things. UNDERSTAND what of our remedial actions will have what affect on users. UPDATE status alert on TIS (ensure it’s not just Phil KOTN who has access / does this
When an ES node fails, generate an auto-restart
Check logs
Platform-wide restart - ensure everything is brought back up ‘clean’
Recheck