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DNS intermittent delays of 5s #56903

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mikksoone opened this Issue Dec 6, 2017 · 113 comments

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mikksoone commented Dec 6, 2017

Is this a BUG REPORT or FEATURE REQUEST?:
/kind bug

What happened:
DNS lookup is sometimes taking 5 seconds.

What you expected to happen:
No delays in DNS.

How to reproduce it (as minimally and precisely as possible):

  1. Create a cluster in AWS using kops with cni networking:
kops create cluster     --node-count 3     --zones eu-west-1a,eu-west-1b,eu-west-1c     --master-zones eu-west-1a,eu-west-1b,eu-west-1c     --dns-zone kube.example.com   --node-size t2.medium     --master-size t2.medium  --topology private --networking cni   --cloud-labels "Env=Staging"  ${NAME}
  1. CNI plugin:
kubectl apply -f "https://cloud.weave.works/k8s/net?k8s-version=$(kubectl version | base64 | tr -d '\n')"
  1. Run this script in any pod with that has curl:
var=1
while true ; do
  res=$( { curl -o /dev/null -s -w %{time_namelookup}\\n  http://www.google.com; } 2>&1 )
  var=$((var+1))
  if [[ $res =~ ^[1-9] ]]; then
    now=$(date +"%T")
    echo "$var slow: $res $now"
    break
  fi
done

Anything else we need to know?:

  1. I am encountering this issue in both staging and production clusters, but for some reason staging cluster is having a lot more 5s delays.
  2. Delays happen both for external services (google.com) or internal, such as service.namespace.
  3. Happens on both 1.6 and 1.7 version of kubernetes, but did not encounter these issues in 1.5 (though the setup was a bit different - no CNI back then).
  4. Have not tested with 1.7 without CNI yet.

Environment:

  • Kubernetes version (use kubectl version):
Client Version: version.Info{Major:"1", Minor:"8", GitVersion:"v1.8.2", GitCommit:"bdaeafa71f6c7c04636251031f93464384d54963", GitTreeState:"clean", BuildDate:"2017-10-24T19:48:57Z", GoVersion:"go1.8.3", Compiler:"gc", Platform:"linux/amd64"}
Server Version: version.Info{Major:"1", Minor:"7", GitVersion:"v1.7.10", GitCommit:"bebdeb749f1fa3da9e1312c4b08e439c404b3136", GitTreeState:"clean", BuildDate:"2017-11-03T16:31:49Z", GoVersion:"go1.8.3", Compiler:"gc", Platform:"linux/amd64"}
  • Cloud provider or hardware configuration:
AWS
  • OS (e.g. from /etc/os-release):
PRETTY_NAME="Ubuntu 16.04.3 LTS"
  • Kernel (e.g. uname -a):
Linux ingress-nginx-3882489562-438sm 4.4.65-k8s #1 SMP Tue May 2 15:48:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

Similar issues

  1. kubernetes/dns#96 - closed but seems to be exactly the same
  2. #45976 - has some comments matching this issue, but is taking the direction of fixing kube-dns up/down scaling problem, and is not about the intermittent failures.

/sig network

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cmluciano commented Dec 8, 2017

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kgignatyev-inspur Dec 10, 2017

I have similar issue: consistently slow DNS resolution from pods, 20 seconds plus
from busybox:
time nslookup google.com
Server: 100.64.0.10
Address 1: 100.64.0.10

Name: google.com
Address 1: 2607:f8b0:400a:806::200e
Address 2: 172.217.3.206 sea15s12-in-f14.1e100.net
real 0m 50.03s
user 0m 0.00s
sys 0m 0.00s
/ #

I just created 1.8.5 cluster in AWS with kops, and only deviation from standard config is that I am using CentOS host machines (ami-e535c59d for us-west-2)

resolution from hosts is instanteneous, from pods: consistently slow

kgignatyev-inspur commented Dec 10, 2017

I have similar issue: consistently slow DNS resolution from pods, 20 seconds plus
from busybox:
time nslookup google.com
Server: 100.64.0.10
Address 1: 100.64.0.10

Name: google.com
Address 1: 2607:f8b0:400a:806::200e
Address 2: 172.217.3.206 sea15s12-in-f14.1e100.net
real 0m 50.03s
user 0m 0.00s
sys 0m 0.00s
/ #

I just created 1.8.5 cluster in AWS with kops, and only deviation from standard config is that I am using CentOS host machines (ami-e535c59d for us-west-2)

resolution from hosts is instanteneous, from pods: consistently slow

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ani82 Dec 23, 2017

we observe the same on GKE with version v1.8.4-gke0 and both Busybox (latest) or Debian9:

$ kubectl exec -ti busybox -- time nslookup storage.googleapis.com
Server: 10.39.240.10
Address 1: 10.39.240.10 kube-dns.kube-system.svc.cluster.local

Name: storage.googleapis.com
Address 1: 2607:f8b0:400c:c06::80 vl-in-x80.1e100.net
Address 2: 74.125.141.128 vl-in-f128.1e100.net
real 0m 10.02s
user 0m 0.00s
sys 0m 0.00s

DNS latency varies between 10 and 40s in multiples of 5s.

ani82 commented Dec 23, 2017

we observe the same on GKE with version v1.8.4-gke0 and both Busybox (latest) or Debian9:

$ kubectl exec -ti busybox -- time nslookup storage.googleapis.com
Server: 10.39.240.10
Address 1: 10.39.240.10 kube-dns.kube-system.svc.cluster.local

Name: storage.googleapis.com
Address 1: 2607:f8b0:400c:c06::80 vl-in-x80.1e100.net
Address 2: 74.125.141.128 vl-in-f128.1e100.net
real 0m 10.02s
user 0m 0.00s
sys 0m 0.00s

DNS latency varies between 10 and 40s in multiples of 5s.

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thockin Jan 6, 2018

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5s is pretty much ALWAYS indicating a DNS timeout, meaning some packet got dropped somewhere.

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thockin commented Jan 6, 2018

5s is pretty much ALWAYS indicating a DNS timeout, meaning some packet got dropped somewhere.

@thockin thockin added the area/dns label Jan 6, 2018

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ani82 Jan 9, 2018

Yes, it seems as if the local DNS servers timeout instead of answering :

[root@busybox /]# nslookup google.com
;; connection timed out; trying next origin
;; connection timed out; trying next origin
;; connection timed out; trying next origin
;; connection timed out; trying next origin
;; connection timed out; trying next origin
;; connection timed out; no servers could be reached

[root@busybox /]# tcpdump port 53
tcpdump: verbose output suppressed, use -v or -vv for full protocol decode
listening on eth0, link-type EN10MB (Ethernet), capture size 262144 bytes
15:38:10.423547 IP busybox.46239 > kube-dns.kube-system.svc.cluster.local.domain: 51779+ A? google.com.default.svc.cluster.local. (54)
15:38:10.424120 IP busybox.46757 > kube-dns.kube-system.svc.cluster.local.domain: 41018+ PTR? 10.240.39.10.in-addr.arpa. (43)
15:38:10.424595 IP kube-dns.kube-system.svc.cluster.local.domain > busybox.46757: 41018 1/0/0 PTR kube-dns.kube-system.svc.cluster.local. (95)
15:38:15.423611 IP busybox.46239 > kube-dns.kube-system.svc.cluster.local.domain: 51779+ A? google.com.default.svc.cluster.local. (54)
15:38:20.423809 IP busybox.46239 > kube-dns.kube-system.svc.cluster.local.domain: 51779+ A? google.com.default.svc.cluster.local. (54)
15:38:25.424247 IP busybox.44496 > kube-dns.kube-system.svc.cluster.local.domain: 63451+ A? google.com.svc.cluster.local. (46)
15:38:30.424508 IP busybox.39936 > kube-dns.kube-system.svc.cluster.local.domain: 14687+ A? google.com.cluster.local. (42)
15:38:35.424767 IP busybox.56675 > kube-dns.kube-system.svc.cluster.local.domain: 37241+ A? google.com.c.retailcatalyst-187519.internal. (61)
15:38:40.424992 IP busybox.35842 > kube-dns.kube-system.svc.cluster.local.domain: 22668+ A? google.com.google.internal. (44)
15:38:45.425295 IP busybox.52037 > kube-dns.kube-system.svc.cluster.local.domain: 6207+ A? google.com. (28)

ani82 commented Jan 9, 2018

Yes, it seems as if the local DNS servers timeout instead of answering :

[root@busybox /]# nslookup google.com
;; connection timed out; trying next origin
;; connection timed out; trying next origin
;; connection timed out; trying next origin
;; connection timed out; trying next origin
;; connection timed out; trying next origin
;; connection timed out; no servers could be reached

[root@busybox /]# tcpdump port 53
tcpdump: verbose output suppressed, use -v or -vv for full protocol decode
listening on eth0, link-type EN10MB (Ethernet), capture size 262144 bytes
15:38:10.423547 IP busybox.46239 > kube-dns.kube-system.svc.cluster.local.domain: 51779+ A? google.com.default.svc.cluster.local. (54)
15:38:10.424120 IP busybox.46757 > kube-dns.kube-system.svc.cluster.local.domain: 41018+ PTR? 10.240.39.10.in-addr.arpa. (43)
15:38:10.424595 IP kube-dns.kube-system.svc.cluster.local.domain > busybox.46757: 41018 1/0/0 PTR kube-dns.kube-system.svc.cluster.local. (95)
15:38:15.423611 IP busybox.46239 > kube-dns.kube-system.svc.cluster.local.domain: 51779+ A? google.com.default.svc.cluster.local. (54)
15:38:20.423809 IP busybox.46239 > kube-dns.kube-system.svc.cluster.local.domain: 51779+ A? google.com.default.svc.cluster.local. (54)
15:38:25.424247 IP busybox.44496 > kube-dns.kube-system.svc.cluster.local.domain: 63451+ A? google.com.svc.cluster.local. (46)
15:38:30.424508 IP busybox.39936 > kube-dns.kube-system.svc.cluster.local.domain: 14687+ A? google.com.cluster.local. (42)
15:38:35.424767 IP busybox.56675 > kube-dns.kube-system.svc.cluster.local.domain: 37241+ A? google.com.c.retailcatalyst-187519.internal. (61)
15:38:40.424992 IP busybox.35842 > kube-dns.kube-system.svc.cluster.local.domain: 22668+ A? google.com.google.internal. (44)
15:38:45.425295 IP busybox.52037 > kube-dns.kube-system.svc.cluster.local.domain: 6207+ A? google.com. (28)

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aguerra Jan 19, 2018

Just in case someone got here because of dns delays, in our case it was arp table overflow on the nodes (arp -n showing more than 1000 entries). Increasing the limits solved the problem.

aguerra commented Jan 19, 2018

Just in case someone got here because of dns delays, in our case it was arp table overflow on the nodes (arp -n showing more than 1000 entries). Increasing the limits solved the problem.

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lbrictson Jan 19, 2018

We have the same issue within all of our kops deployed aws clusters (5). We tried moving from weave to flannel to rule out the CNI but the issue is the same. Our kube-dns pods are healthy, one on every host and they have not crashed recently.

Our arp tables are no where near full (less than 100 entries usually)

lbrictson commented Jan 19, 2018

We have the same issue within all of our kops deployed aws clusters (5). We tried moving from weave to flannel to rule out the CNI but the issue is the same. Our kube-dns pods are healthy, one on every host and they have not crashed recently.

Our arp tables are no where near full (less than 100 entries usually)

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bowei Jan 19, 2018

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There are QPS limits on DNS at various places. I think in the past, people have hit AWS DNS server QPS limits in some cases, that may be worth checking.

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bowei commented Jan 19, 2018

There are QPS limits on DNS at various places. I think in the past, people have hit AWS DNS server QPS limits in some cases, that may be worth checking.

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lbrictson Jan 19, 2018

@bowei sadly this happens in very small clusters as well for us, ones that have so few containers that there is no feasible way we'd be hitting the QPS limit from AWS

lbrictson commented Jan 19, 2018

@bowei sadly this happens in very small clusters as well for us, ones that have so few containers that there is no feasible way we'd be hitting the QPS limit from AWS

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mikksoone Jan 19, 2018

Same here, small clusters, no arp nor QPS limits.
dnsPolicy: Default works without delays, but this unfortunately can not be used for all deployments.

mikksoone commented Jan 19, 2018

Same here, small clusters, no arp nor QPS limits.
dnsPolicy: Default works without delays, but this unfortunately can not be used for all deployments.

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lbrictson Jan 19, 2018

@mikksoone exact same situation as us then, dnsPolicy: Default fixes the problem entirely, but of course breaks accessing services internal to the cluster which is a no-go for most of ours.

lbrictson commented Jan 19, 2018

@mikksoone exact same situation as us then, dnsPolicy: Default fixes the problem entirely, but of course breaks accessing services internal to the cluster which is a no-go for most of ours.

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vasartori Jan 19, 2018

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@bowei We have the same problem here.
But we are not using AWS.

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vasartori commented Jan 19, 2018

@bowei We have the same problem here.
But we are not using AWS.

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Its seems a problem with glibc.
If you set a timeout on your /etc/resolv.conf this timeout will be respected.

On CoreOS Stable (glibc 2.23) this problem appears.

Setting with 0 in timeout on resolv.conf you will get a 1 secound delay....

I've try disable the IPv6, without success....

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vasartori commented Jan 22, 2018

Its seems a problem with glibc.
If you set a timeout on your /etc/resolv.conf this timeout will be respected.

On CoreOS Stable (glibc 2.23) this problem appears.

Setting with 0 in timeout on resolv.conf you will get a 1 secound delay....

I've try disable the IPv6, without success....

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vasartori Jan 23, 2018

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In my tests, using this option on /etc/resolv.conf
options single-request-reopen

Fixed the problem.
But I don't find a "clean" way to put it on pods in kubernetes 1.8.
What I do:

        lifecycle:
          postStart:
            exec:
              command:
              - /bin/sh
              - -c 
              - "/bin/echo 'options single-request-reopen' >> /etc/resolv.conf"

@mikksoone Could you try if it solve your problem too?

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vasartori commented Jan 23, 2018

In my tests, using this option on /etc/resolv.conf
options single-request-reopen

Fixed the problem.
But I don't find a "clean" way to put it on pods in kubernetes 1.8.
What I do:

        lifecycle:
          postStart:
            exec:
              command:
              - /bin/sh
              - -c 
              - "/bin/echo 'options single-request-reopen' >> /etc/resolv.conf"

@mikksoone Could you try if it solve your problem too?

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aca02djr Jan 24, 2018

Also experiencing this on 1.8.6-gke.0 - @vasartori suggested solution resolved the issue for us too 👍🏻

aca02djr commented Jan 24, 2018

Also experiencing this on 1.8.6-gke.0 - @vasartori suggested solution resolved the issue for us too 👍🏻

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mikksoone Jan 26, 2018

Doesn't solve the issue for me. Even with this option in resolv.conf I get timeouts of 5s, 2.5s and 3.5s - and they happen very often, twice per minute or so.

mikksoone commented Jan 26, 2018

Doesn't solve the issue for me. Even with this option in resolv.conf I get timeouts of 5s, 2.5s and 3.5s - and they happen very often, twice per minute or so.

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lauri-elevant Feb 5, 2018

We have the same symptoms on 1.8, intermittent DNS resolution stall of 5 seconds. The suggested workaround seems to be effective for us as well. Thank you @vasartori !

lauri-elevant commented Feb 5, 2018

We have the same symptoms on 1.8, intermittent DNS resolution stall of 5 seconds. The suggested workaround seems to be effective for us as well. Thank you @vasartori !

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sdtokkolabs Apr 3, 2018

I've been having this issue for some time on kubernetes 1.7 and 1.8. I was dropping dns queries from time to time
Yesterday I upgraded my cluster from 1.8.10 to 1.9.6 (kops from 1.8 to 1.9.0-alpha.3) and I started having this same issue ALL THE TIME. The workaround sugested in this issue has no effect and I can't find any way of stopping it. I've made a small workaround by assigning the most requested (and poblematic) DNS to fixed IPs in /etc/hosts.
Any idea on where the real problem is?
I'll test with a brand new cluster in the same versions and report back.

sdtokkolabs commented Apr 3, 2018

I've been having this issue for some time on kubernetes 1.7 and 1.8. I was dropping dns queries from time to time
Yesterday I upgraded my cluster from 1.8.10 to 1.9.6 (kops from 1.8 to 1.9.0-alpha.3) and I started having this same issue ALL THE TIME. The workaround sugested in this issue has no effect and I can't find any way of stopping it. I've made a small workaround by assigning the most requested (and poblematic) DNS to fixed IPs in /etc/hosts.
Any idea on where the real problem is?
I'll test with a brand new cluster in the same versions and report back.

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Same problem, but the most strange thing is that it appears on some nodes.

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xiaoxubeii commented Apr 12, 2018

Same problem, but the most strange thing is that it appears on some nodes.

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rajatjindal Apr 14, 2018

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@thockin @bowei

requesting your feedback therefore tagging you.

can this be of any interest here: https://tech.xing.com/a-reason-for-unexplained-connection-timeouts-on-kubernetes-docker-abd041cf7e02

there are multiple issues reported for this issue in kubernetes project, and will be great to have it resolved for everyone.

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rajatjindal commented Apr 14, 2018

@thockin @bowei

requesting your feedback therefore tagging you.

can this be of any interest here: https://tech.xing.com/a-reason-for-unexplained-connection-timeouts-on-kubernetes-docker-abd041cf7e02

there are multiple issues reported for this issue in kubernetes project, and will be great to have it resolved for everyone.

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sdtokkolabs Apr 17, 2018

tried with several versions of kubernetes on fresh clusters, all hae the same problem to some degree, dns lookups get lost on the way and retryes have to be made. I've also tested kubenet, flanel, canal and weave as network providers, having the lowest incidence in flanel. I've also tried overloading the nodes and splitting the nodes (dns on it's own machine) but it made no difference. On my production cluster the incidence of this issue is way higher than on a brand new cluster and i can't find the way to isolate the problem :(

sdtokkolabs commented Apr 17, 2018

tried with several versions of kubernetes on fresh clusters, all hae the same problem to some degree, dns lookups get lost on the way and retryes have to be made. I've also tested kubenet, flanel, canal and weave as network providers, having the lowest incidence in flanel. I've also tried overloading the nodes and splitting the nodes (dns on it's own machine) but it made no difference. On my production cluster the incidence of this issue is way higher than on a brand new cluster and i can't find the way to isolate the problem :(

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marshallford Aug 20, 2018

@Quentin-M Would you mind pushing the change to Docker Hub or does it make more sense for everyone to build their own image depending on the dns port used?

marshallford commented Aug 20, 2018

@Quentin-M Would you mind pushing the change to Docker Hub or does it make more sense for everyone to build their own image depending on the dns port used?

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@marshallford I just pushed a new image, as well as a very basic README. ^ I will not be able to test it tonight but the changes should be pretty minor (just adding env vars), please let me know.

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Quentin-M commented Aug 20, 2018

@marshallford I just pushed a new image, as well as a very basic README. ^ I will not be able to test it tonight but the changes should be pretty minor (just adding env vars), please let me know.

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szuecs Aug 20, 2018

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@Quentin-M we (@mikkeloscar and me) run dnsmasq on all nodes and point containers to the node ip without masquerading.
I think our issue is that coredns is the upstream for cluster.local with more than one instance behind service ip.
I am not sure if I am really right but we will probably test it.
If someone has a better understanding please let me know.

Update: our POD network to dnsmasq
Update2: MASQUERADING is involved in multiple stages

# container view
ip-172-31-8-219 ~ # docker exec -it 592b8debec23 /bin/sh
/ $ cat /etc/resolv.conf 
nameserver 172.31.8.219
nameserver 10.3.0.11
search kube-system.svc.cluster.local svc.cluster.local cluster.local eu-central-1.compute.internal
options ndots:5
/ $ ip r get 172.31.8.219
172.31.8.219 via 10.2.38.1 dev eth0  src 10.2.38.25 

# node interfaces
ip-172-31-8-219 ~ # ip a s | grep 10.2.38.    
    inet 10.2.38.0/32 scope global flannel.1
    inet 10.2.38.1/24 scope global cni0

# dnsmasq listening on eth0 node interface
/ # netstat -tlpen | grep :53
tcp        0      0 0.0.0.0:53              0.0.0.0:*               LISTEN      14/dnsmasq
tcp        0      0 :::53                   :::*                    LISTEN      14/dnsmasq
/ # ip-172-31-8-219 ~ # netstat -tlpen | grep :53
tcp        0      0 0.0.0.0:53              0.0.0.0:*               LISTEN      0          29166      1651/dnsmasq        
tcp6       0      0 :::53                   :::*                    LISTEN      0          29168      1651/dnsmasq       

So for us there is no masquerading in the path of container to dnsmasq.
Still we see problems and my best bet is the service IP issue mentioned by @brb. The conntrack table and the fail in the return path from CoreDNS pods running in POD network to dnsmasq is our issue.

Here this shows the masquerading from node to POD network:

# dnsmasq is running with upstream CoreDNS 10.3.0.11 serviceip for cluster.local and arpa IPv4 IPv6
ip-172-31-8-219 ~ # ps auxfww |grep dnsmas
root      1620  0.0  0.1  32760 18280 ?        Ssl  Aug14   0:28  |   \_ /dnsmasq-nanny -v=2 -logtostderr -configDir=/etc/k8s/dns/dnsmasq-nanny -restartDnsmasq=true -- -k --cache-size=10000 --no-negcache --server=/cluster.local/10.3.0.11#53 --server=/in-addr.arpa/10.3.0.11#53 --server=/ip6.arpa/10.3.0.11#53
root      1651  3.7  0.0   2188  1768 ?        S    Aug14 318:48  |       \_ /usr/sbin/dnsmasq -k --cache-size=10000 --no-negcache --server=/cluster.local/10.3.0.11#53 --server=/in-addr.arpa/10.3.0.11#53 --server=/ip6.arpa/10.3.0.11#53

# iptables for the service ip shows the POD IP lookup roundrobin from the list of endpoints
ip-172-31-8-219 ~ # iptables-save | grep  10.3.0.11
-A KUBE-SERVICES -d 10.3.0.11/32 -p tcp -m comment --comment "kube-system/coredns:dns-tcp cluster IP" -m tcp --dport 53 -j KUBE-SVC-FAITROITGXHS3QVF
-A KUBE-SERVICES -d 10.3.0.11/32 -p udp -m comment --comment "kube-system/coredns:dns cluster IP" -m udp --dport 53 -j KUBE-SVC-ZRLRAB2E5DTUX37C
ip-172-31-8-219 ~ # iptables-save | grep  KUBE-SVC-ZRLRAB2E5DTUX37C
:KUBE-SVC-ZRLRAB2E5DTUX37C - [0:0]
-A KUBE-SERVICES -d 10.3.0.11/32 -p udp -m comment --comment "kube-system/coredns:dns cluster IP" -m udp --dport 53 -j KUBE-SVC-ZRLRAB2E5DTUX37C
-A KUBE-SVC-ZRLRAB2E5DTUX37C -m comment --comment "kube-system/coredns:dns" -m statistic --mode random --probability 0.50000000000 -j KUBE-SEP-KFC565XMUCWSGLMT
-A KUBE-SVC-ZRLRAB2E5DTUX37C -m comment --comment "kube-system/coredns:dns" -j KUBE-SEP-SCXUEXHUCFW5K7VC
ip-172-31-8-219 ~ # iptables-save | grep  KUBE-SEP-KFC565XMUCWSGLMT
:KUBE-SEP-KFC565XMUCWSGLMT - [0:0]
-A KUBE-SEP-KFC565XMUCWSGLMT -s 10.2.37.18/32 -m comment --comment "kube-system/coredns:dns" -j KUBE-MARK-MASQ
-A KUBE-SEP-KFC565XMUCWSGLMT -p udp -m comment --comment "kube-system/coredns:dns" -m udp -j DNAT --to-destination 10.2.37.18:53
-A KUBE-SVC-ZRLRAB2E5DTUX37C -m comment --comment "kube-system/coredns:dns" -m statistic --mode random --probability 0.50000000000 -j KUBE-SEP-KFC565XMUCWSGLMT
ip-172-31-8-219 ~ # iptables-save | grep  KUBE-SEP-SCXUEXHUCFW5K7VC
:KUBE-SEP-SCXUEXHUCFW5K7VC - [0:0]
-A KUBE-SEP-SCXUEXHUCFW5K7VC -s 10.2.38.20/32 -m comment --comment "kube-system/coredns:dns" -j KUBE-MARK-MASQ
-A KUBE-SEP-SCXUEXHUCFW5K7VC -p udp -m comment --comment "kube-system/coredns:dns" -m udp -j DNAT --to-destination 10.2.38.20:53
-A KUBE-SVC-ZRLRAB2E5DTUX37C -m comment --comment "kube-system/coredns:dns" -j KUBE-SEP-SCXUEXHUCFW5K7VC

# Following the POD IPs for CoreDNS, we can find the masquerading as I said
ip-172-31-8-219 ~ # iptables-save | grep  MASQ
:KUBE-MARK-MASQ - [0:0]
-A POSTROUTING -s 172.17.0.0/16 ! -o docker0 -j MASQUERADE
-A POSTROUTING -s 10.2.0.0/16 ! -d 224.0.0.0/4 -j MASQUERADE
-A POSTROUTING ! -s 10.2.0.0/16 -d 10.2.0.0/16 -j MASQUERADE

Conntrack table shows that also external-dns and kube-service via route53 would be an issue without conntrack table fix in the kernel and disabling AAAA(?):

root@ip-172-31-8-219:/# conntrack  -L | grep dport=53 | head
udp      17 10 src=172.31.8.219 dst=172.31.0.2 sport=24667 dport=53 src=172.31.0.2 dst=172.31.8.219 sport=53 dport=24667 [ASSURED] mark=0 secctx=system_u:object_r:unlabeled_t:s0 use=1
udp      17 61 src=10.2.38.18 dst=172.31.8.219 sport=38782 dport=53 src=172.31.8.219 dst=10.2.38.18 sport=53 dport=38782 [ASSURED] mark=0 secctx=system_u:object_r:unlabeled_t:s0 use=1
udp      17 71 src=10.2.38.18 dst=172.31.8.219 sport=43361 dport=53 src=172.31.8.219 dst=10.2.38.18 sport=53 dport=43361 [ASSURED] mark=0 secctx=system_u:object_r:unlabeled_t:s0 use=1
...
root@ip-172-31-8-219:/# conntrack  -L | grep dport=53 | grep 10.3.0.11 | head
udp      17 7 src=172.31.8.219 dst=10.3.0.11 sport=54454 dport=53 src=10.2.37.18 dst=10.2.38.0 sport=53 dport=54454 mark=0 secctx=system_u:object_r:unlabeled_t:s0 use=1
udp      17 165 src=172.31.8.219 dst=10.3.0.11 sport=6249 dport=53 src=10.2.37.18 dst=10.2.38.0 sport=53 dport=6249 [ASSURED] mark=0 secctx=system_u:object_r:unlabeled_t:s0 use=1

Clearly if our issue is masquerading, the problem is in all of the paths from container to dnsmasq and dnsmasq to CoreDNS and if we would disallow the AAAA records in dnsmasq(?) and our base image we would have a fix.

Contributor

szuecs commented Aug 20, 2018

@Quentin-M we (@mikkeloscar and me) run dnsmasq on all nodes and point containers to the node ip without masquerading.
I think our issue is that coredns is the upstream for cluster.local with more than one instance behind service ip.
I am not sure if I am really right but we will probably test it.
If someone has a better understanding please let me know.

Update: our POD network to dnsmasq
Update2: MASQUERADING is involved in multiple stages

# container view
ip-172-31-8-219 ~ # docker exec -it 592b8debec23 /bin/sh
/ $ cat /etc/resolv.conf 
nameserver 172.31.8.219
nameserver 10.3.0.11
search kube-system.svc.cluster.local svc.cluster.local cluster.local eu-central-1.compute.internal
options ndots:5
/ $ ip r get 172.31.8.219
172.31.8.219 via 10.2.38.1 dev eth0  src 10.2.38.25 

# node interfaces
ip-172-31-8-219 ~ # ip a s | grep 10.2.38.    
    inet 10.2.38.0/32 scope global flannel.1
    inet 10.2.38.1/24 scope global cni0

# dnsmasq listening on eth0 node interface
/ # netstat -tlpen | grep :53
tcp        0      0 0.0.0.0:53              0.0.0.0:*               LISTEN      14/dnsmasq
tcp        0      0 :::53                   :::*                    LISTEN      14/dnsmasq
/ # ip-172-31-8-219 ~ # netstat -tlpen | grep :53
tcp        0      0 0.0.0.0:53              0.0.0.0:*               LISTEN      0          29166      1651/dnsmasq        
tcp6       0      0 :::53                   :::*                    LISTEN      0          29168      1651/dnsmasq       

So for us there is no masquerading in the path of container to dnsmasq.
Still we see problems and my best bet is the service IP issue mentioned by @brb. The conntrack table and the fail in the return path from CoreDNS pods running in POD network to dnsmasq is our issue.

Here this shows the masquerading from node to POD network:

# dnsmasq is running with upstream CoreDNS 10.3.0.11 serviceip for cluster.local and arpa IPv4 IPv6
ip-172-31-8-219 ~ # ps auxfww |grep dnsmas
root      1620  0.0  0.1  32760 18280 ?        Ssl  Aug14   0:28  |   \_ /dnsmasq-nanny -v=2 -logtostderr -configDir=/etc/k8s/dns/dnsmasq-nanny -restartDnsmasq=true -- -k --cache-size=10000 --no-negcache --server=/cluster.local/10.3.0.11#53 --server=/in-addr.arpa/10.3.0.11#53 --server=/ip6.arpa/10.3.0.11#53
root      1651  3.7  0.0   2188  1768 ?        S    Aug14 318:48  |       \_ /usr/sbin/dnsmasq -k --cache-size=10000 --no-negcache --server=/cluster.local/10.3.0.11#53 --server=/in-addr.arpa/10.3.0.11#53 --server=/ip6.arpa/10.3.0.11#53

# iptables for the service ip shows the POD IP lookup roundrobin from the list of endpoints
ip-172-31-8-219 ~ # iptables-save | grep  10.3.0.11
-A KUBE-SERVICES -d 10.3.0.11/32 -p tcp -m comment --comment "kube-system/coredns:dns-tcp cluster IP" -m tcp --dport 53 -j KUBE-SVC-FAITROITGXHS3QVF
-A KUBE-SERVICES -d 10.3.0.11/32 -p udp -m comment --comment "kube-system/coredns:dns cluster IP" -m udp --dport 53 -j KUBE-SVC-ZRLRAB2E5DTUX37C
ip-172-31-8-219 ~ # iptables-save | grep  KUBE-SVC-ZRLRAB2E5DTUX37C
:KUBE-SVC-ZRLRAB2E5DTUX37C - [0:0]
-A KUBE-SERVICES -d 10.3.0.11/32 -p udp -m comment --comment "kube-system/coredns:dns cluster IP" -m udp --dport 53 -j KUBE-SVC-ZRLRAB2E5DTUX37C
-A KUBE-SVC-ZRLRAB2E5DTUX37C -m comment --comment "kube-system/coredns:dns" -m statistic --mode random --probability 0.50000000000 -j KUBE-SEP-KFC565XMUCWSGLMT
-A KUBE-SVC-ZRLRAB2E5DTUX37C -m comment --comment "kube-system/coredns:dns" -j KUBE-SEP-SCXUEXHUCFW5K7VC
ip-172-31-8-219 ~ # iptables-save | grep  KUBE-SEP-KFC565XMUCWSGLMT
:KUBE-SEP-KFC565XMUCWSGLMT - [0:0]
-A KUBE-SEP-KFC565XMUCWSGLMT -s 10.2.37.18/32 -m comment --comment "kube-system/coredns:dns" -j KUBE-MARK-MASQ
-A KUBE-SEP-KFC565XMUCWSGLMT -p udp -m comment --comment "kube-system/coredns:dns" -m udp -j DNAT --to-destination 10.2.37.18:53
-A KUBE-SVC-ZRLRAB2E5DTUX37C -m comment --comment "kube-system/coredns:dns" -m statistic --mode random --probability 0.50000000000 -j KUBE-SEP-KFC565XMUCWSGLMT
ip-172-31-8-219 ~ # iptables-save | grep  KUBE-SEP-SCXUEXHUCFW5K7VC
:KUBE-SEP-SCXUEXHUCFW5K7VC - [0:0]
-A KUBE-SEP-SCXUEXHUCFW5K7VC -s 10.2.38.20/32 -m comment --comment "kube-system/coredns:dns" -j KUBE-MARK-MASQ
-A KUBE-SEP-SCXUEXHUCFW5K7VC -p udp -m comment --comment "kube-system/coredns:dns" -m udp -j DNAT --to-destination 10.2.38.20:53
-A KUBE-SVC-ZRLRAB2E5DTUX37C -m comment --comment "kube-system/coredns:dns" -j KUBE-SEP-SCXUEXHUCFW5K7VC

# Following the POD IPs for CoreDNS, we can find the masquerading as I said
ip-172-31-8-219 ~ # iptables-save | grep  MASQ
:KUBE-MARK-MASQ - [0:0]
-A POSTROUTING -s 172.17.0.0/16 ! -o docker0 -j MASQUERADE
-A POSTROUTING -s 10.2.0.0/16 ! -d 224.0.0.0/4 -j MASQUERADE
-A POSTROUTING ! -s 10.2.0.0/16 -d 10.2.0.0/16 -j MASQUERADE

Conntrack table shows that also external-dns and kube-service via route53 would be an issue without conntrack table fix in the kernel and disabling AAAA(?):

root@ip-172-31-8-219:/# conntrack  -L | grep dport=53 | head
udp      17 10 src=172.31.8.219 dst=172.31.0.2 sport=24667 dport=53 src=172.31.0.2 dst=172.31.8.219 sport=53 dport=24667 [ASSURED] mark=0 secctx=system_u:object_r:unlabeled_t:s0 use=1
udp      17 61 src=10.2.38.18 dst=172.31.8.219 sport=38782 dport=53 src=172.31.8.219 dst=10.2.38.18 sport=53 dport=38782 [ASSURED] mark=0 secctx=system_u:object_r:unlabeled_t:s0 use=1
udp      17 71 src=10.2.38.18 dst=172.31.8.219 sport=43361 dport=53 src=172.31.8.219 dst=10.2.38.18 sport=53 dport=43361 [ASSURED] mark=0 secctx=system_u:object_r:unlabeled_t:s0 use=1
...
root@ip-172-31-8-219:/# conntrack  -L | grep dport=53 | grep 10.3.0.11 | head
udp      17 7 src=172.31.8.219 dst=10.3.0.11 sport=54454 dport=53 src=10.2.37.18 dst=10.2.38.0 sport=53 dport=54454 mark=0 secctx=system_u:object_r:unlabeled_t:s0 use=1
udp      17 165 src=172.31.8.219 dst=10.3.0.11 sport=6249 dport=53 src=10.2.37.18 dst=10.2.38.0 sport=53 dport=6249 [ASSURED] mark=0 secctx=system_u:object_r:unlabeled_t:s0 use=1

Clearly if our issue is masquerading, the problem is in all of the paths from container to dnsmasq and dnsmasq to CoreDNS and if we would disallow the AAAA records in dnsmasq(?) and our base image we would have a fix.

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marshallford Aug 21, 2018

@Quentin-M Still no luck. Maybe my issue is unrelated to this. In a Jenkins job I am running on the cluster a docker:18.06.0 container in a jnlp pod can talk to Docker Hub just fine to pull down a Debian base image, but the build continues to fail due to Temporary failure resolving 'deb.debian.org' during an update step. Anything special about the dns records deb.debian.org or security.debian.org? I'm at a complete loss.

Update: The problem seemed to solve itself by blowing away the nodes.

marshallford commented Aug 21, 2018

@Quentin-M Still no luck. Maybe my issue is unrelated to this. In a Jenkins job I am running on the cluster a docker:18.06.0 container in a jnlp pod can talk to Docker Hub just fine to pull down a Debian base image, but the build continues to fail due to Temporary failure resolving 'deb.debian.org' during an update step. Anything special about the dns records deb.debian.org or security.debian.org? I'm at a complete loss.

Update: The problem seemed to solve itself by blowing away the nodes.

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sadok-f Aug 22, 2018

For alpine images, here an issue related to : gliderlabs/docker-alpine#255

sadok-f commented Aug 22, 2018

For alpine images, here an issue related to : gliderlabs/docker-alpine#255

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lenny87 Sep 3, 2018

Try to add

options use-vc

to your resolv.conf. It will force TCP for DNS lookups and will workaround this issue with ease

lenny87 commented Sep 3, 2018

Try to add

options use-vc

to your resolv.conf. It will force TCP for DNS lookups and will workaround this issue with ease

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dcowden Sep 3, 2018

@lenny87 nice idea, but not supported on all platforms (unfortunately including alpine, which is common)

dcowden commented Sep 3, 2018

@lenny87 nice idea, but not supported on all platforms (unfortunately including alpine, which is common)

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lenny87 Sep 3, 2018

Yap, it's supported only on glibc images (debian/ubuntu and so on), but I think it's still good workaround until it will get fixed in kernel conntrack

lenny87 commented Sep 3, 2018

Yap, it's supported only on glibc images (debian/ubuntu and so on), but I think it's still good workaround until it will get fixed in kernel conntrack

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memorais Sep 12, 2018

@marshallford What do you mean by "blowing away the nodes"? Can you be more clear about that? Did you restart your entire k8s node with "systemctl restart docker kubelet" or something like that?

Thanks.

memorais commented Sep 12, 2018

@marshallford What do you mean by "blowing away the nodes"? Can you be more clear about that? Did you restart your entire k8s node with "systemctl restart docker kubelet" or something like that?

Thanks.

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marshallford Sep 17, 2018

@memorais To clarify: I had a working cluster (for a while), DNS appeared to break, I tried the weave-tc image with no luck, I updated the AMI id of all my nodes and master which caused all of the instances in EC2 to be terminated and re-created and my issue with resolving deb.debian.org disappeared. It is almost like Weave wouldn't "patch" with weave-tc unless it was a first time install.

marshallford commented Sep 17, 2018

@memorais To clarify: I had a working cluster (for a while), DNS appeared to break, I tried the weave-tc image with no luck, I updated the AMI id of all my nodes and master which caused all of the instances in EC2 to be terminated and re-created and my issue with resolving deb.debian.org disappeared. It is almost like Weave wouldn't "patch" with weave-tc unless it was a first time install.

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Quentin-M commented Sep 17, 2018

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marshallford Sep 17, 2018

@Quentin-M Fair enough. That is how I interpreted your project readme as well. It is likely I am just stupid and either didn't add weave-tc correctly the first time, broke DNS myself in a different manner that the fresh VMs fixed, or I am misremembering the order that I troubleshooted the cluster. Regardless, my "advice" still stands -- @memorais if you are really desperate, get fresh VMs.

marshallford commented Sep 17, 2018

@Quentin-M Fair enough. That is how I interpreted your project readme as well. It is likely I am just stupid and either didn't add weave-tc correctly the first time, broke DNS myself in a different manner that the fresh VMs fixed, or I am misremembering the order that I troubleshooted the cluster. Regardless, my "advice" still stands -- @memorais if you are really desperate, get fresh VMs.

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kostyrev Sep 18, 2018

After applying this workaround I've got problems with cert-manager not being able to issue certificates.
Because after applying this workaround kube-dns cannot resolve external FQDNs (e.g. google.com and such).
Standalone dnsmasq on every node modifies /etc/resolv.conf and leaves only

nameserver 127.0.0.1
search ec2.internal

then when dnsmasq container in kube-dns pod starts it reads node's /etc/resolv.conf and use it as upstream nameservers. But as node's resolv.conf contains only 127.0.0.1 kube-dns (dnsmasq component more accurately) cannot resolve external dns names.

kostyrev commented Sep 18, 2018

After applying this workaround I've got problems with cert-manager not being able to issue certificates.
Because after applying this workaround kube-dns cannot resolve external FQDNs (e.g. google.com and such).
Standalone dnsmasq on every node modifies /etc/resolv.conf and leaves only

nameserver 127.0.0.1
search ec2.internal

then when dnsmasq container in kube-dns pod starts it reads node's /etc/resolv.conf and use it as upstream nameservers. But as node's resolv.conf contains only 127.0.0.1 kube-dns (dnsmasq component more accurately) cannot resolve external dns names.

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szuecs Sep 18, 2018

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@kostyrev no one said to configure 127.0.0.1 as upstream.
Use pod to nodeip to target dnsmasq localnode and use dnsmasq to split cluster.local (target coredns service endpoint) and public DNS (route53 in your case)

Contributor

szuecs commented Sep 18, 2018

@kostyrev no one said to configure 127.0.0.1 as upstream.
Use pod to nodeip to target dnsmasq localnode and use dnsmasq to split cluster.local (target coredns service endpoint) and public DNS (route53 in your case)

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kostyrev Sep 19, 2018

I didn't configure 127.0.0.1.
Dnsmasq by default does this.
UPD: this behaviour takes place only in Ubuntu or earlier Debian Jessie
So one has to have

sed -i '/IGNORE_RESOLVCONF/s/^#//g' /etc/default/dnsmasq
echo 'DNSMASQ_EXCEPT=lo' >> /etc/default/dnsmasq

these to force Ubuntu behave as Amazon Linux 2 or Debian Stretch

kostyrev commented Sep 19, 2018

I didn't configure 127.0.0.1.
Dnsmasq by default does this.
UPD: this behaviour takes place only in Ubuntu or earlier Debian Jessie
So one has to have

sed -i '/IGNORE_RESOLVCONF/s/^#//g' /etc/default/dnsmasq
echo 'DNSMASQ_EXCEPT=lo' >> /etc/default/dnsmasq

these to force Ubuntu behave as Amazon Linux 2 or Debian Stretch

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gaieges Sep 25, 2018

I think we found another fix for this - to use tcp mode on dns requests in a container by adding the following to the spec:

apiVersion: extensions/v1beta1
kind: Deployment
metadata:
  name: app
spec:
  template:
    spec:
      dnsConfig:
        options:
        - name: use-vc  # specifies to local dns resolver to use tcp over udp.  udp is flakey in containers
      containers:
...

gaieges commented Sep 25, 2018

I think we found another fix for this - to use tcp mode on dns requests in a container by adding the following to the spec:

apiVersion: extensions/v1beta1
kind: Deployment
metadata:
  name: app
spec:
  template:
    spec:
      dnsConfig:
        options:
        - name: use-vc  # specifies to local dns resolver to use tcp over udp.  udp is flakey in containers
      containers:
...
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timwebster9 Oct 4, 2018

use-vc didn't work for us (AKS). The queries were consistent, but they all took about 8.5 seconds. However single-request-reopen worked.

timwebster9 commented Oct 4, 2018

use-vc didn't work for us (AKS). The queries were consistent, but they all took about 8.5 seconds. However single-request-reopen worked.

dgrove-oss added a commit to dgrove-oss/openwhisk that referenced this issue Oct 4, 2018

Switch from alpine to jessie-slim for runner utility images
The Alpine based images have a nasty problem with DNS failures that
tends to surface when running them in Kubernetes.  After a fair amount
of poking around, it seems like the only reliable fix is to not use
Alpine images on Kubernetes until upstream bug fixes in various layers
of the software stack, including the Linux kernel propagate to the
Alpine releases.  For more context,
see:
  gliderlabs/docker-alpine#255
  kubernetes/kubernetes#56903
  https://www.weave.works/blog/racy-conntrack-and-dns-lookup-timeouts
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bbbmmmlll Oct 8, 2018

This worked for us:

net.ipv4.neigh.default.gc_thresh1 = 80000
net.ipv4.neigh.default.gc_thresh2 = 90000
net.ipv4.neigh.default.gc_thresh3 = 100000

The original values were 128, 512, and 1024. Our app and the Bash script from the first comment consistently showed intermittent DNS slowness. Changing the ARP cache settings resolved both issues immediately. I never saw any neighbor table overflow messages or any other indication of a problem with the ARP cache size.

Reference: Scaling Kubernetes to 2,500 Nodes

bbbmmmlll commented Oct 8, 2018

This worked for us:

net.ipv4.neigh.default.gc_thresh1 = 80000
net.ipv4.neigh.default.gc_thresh2 = 90000
net.ipv4.neigh.default.gc_thresh3 = 100000

The original values were 128, 512, and 1024. Our app and the Bash script from the first comment consistently showed intermittent DNS slowness. Changing the ARP cache settings resolved both issues immediately. I never saw any neighbor table overflow messages or any other indication of a problem with the ARP cache size.

Reference: Scaling Kubernetes to 2,500 Nodes

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kruczjak Oct 8, 2018

Hi, if you are searching for temporary solution which works really well (until conntrack will be patched), you can always setup local dns resolver and then route all DNS queries without iptables (so without DNAT) needed.
It's quite easy however you need the access to nodes and make rolling update afterwards.

We're running alpine containers and after adding DNS resolver on "local nodes" there are no more timeouts and delays on DNS queries.

Here you can find a quick description what to do to achieve it: #45363 (comment)
I can expand the topic if someone would need that :)

kruczjak commented Oct 8, 2018

Hi, if you are searching for temporary solution which works really well (until conntrack will be patched), you can always setup local dns resolver and then route all DNS queries without iptables (so without DNAT) needed.
It's quite easy however you need the access to nodes and make rolling update afterwards.

We're running alpine containers and after adding DNS resolver on "local nodes" there are no more timeouts and delays on DNS queries.

Here you can find a quick description what to do to achieve it: #45363 (comment)
I can expand the topic if someone would need that :)

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