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Add the prometheus-longterm-metrics and thanos optional components #461

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37 changes: 36 additions & 1 deletion CHANGES.md
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Expand Up @@ -15,7 +15,42 @@
[Unreleased](https://github.com/bird-house/birdhouse-deploy/tree/master) (latest)
------------------------------------------------------------------------------------------------------------------

[//]: # (list changes here, using '-' for each new entry, remove this when items are added)
## Changes

- Add the `prometheus-longterm-metrics` and `thanos` optional components

The `prometheus-longterm-metrics` component collects longterm monitoring metrics from the original prometheus instance
(the one created by the ``components/monitoring`` component).

Longterm metrics are any prometheus rule that have the label ``group: longterm-metrics`` or in other words are
selectable using prometheus's ``'{group="longterm-metrics"}'`` query filter. To see which longterm metric rules are
added by default see the
``optional-components/prometheus-longterm-metrics/config/monitoring/prometheus.rules.template`` file.

If you do not want the default longterm-metric rules included, set the ``PROMETHEUS_LONGTERM_RULES_FILE`` to anything
other than ``True`` in your ``env.local`` file.
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To configure this component:

* update the ``PROMETHEUS_LONGTERM_RETENTION_TIME`` variable to set how long the data will be kept by prometheus

Enabling the `prometheus-longterm-metrics` component creates the additional endpoint ``/prometheus-longterm-metrics``.

The `thanos` component enables better storage of longterm metrics collected by the
``optional-components/prometheus-longterm-metrics`` component. Data will be collected from the
``prometheus-longterm-metrics`` and stored in an S3 object store indefinitely.

When enabling this component, please change the default values for the ``THANOS_MINIO_ROOT_USER`` and ``THANOS_MINIO_ROOT_PASSWORD``
by updating the ``env.local`` file. These set the login credentials for the root user that runs the
[minio](https://min.io/) object store.

Enabling the `thanos` component creates the additional endpoints:
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* ``/thanos-query``: a prometheus-like query interface to inspect the data stored by thanos
* ``/thanos-minio``: a minio web console to inspect the data stored by minio.
Comment on lines +46 to +47
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Should those be configurable?

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Which bits would be useful to configure? The endpoints, paths, images, other?

I agree that we could always add more configuration options, I'm just wondering which are a priority for you?

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The endpoints would be the priority, to allow serving them from some other location, though still a low priority relative to the feature as a whole. Worst case, redirects can be defined in the nginx configuration, so don't block the PR just for this.


This also includes an update to the prometheus version from `v2.19.0` to the current latest `v2.52.0`. This is to
required to support the interaction between prometheus and thanos.
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[2.4.0](https://github.com/bird-house/birdhouse-deploy/tree/2.4.0) (2024-06-04)
------------------------------------------------------------------------------------------------------------------
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2 changes: 1 addition & 1 deletion birdhouse/components/monitoring/default.env
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Expand Up @@ -8,7 +8,7 @@ export GRAFANA_VERSION="7.0.3"
export GRAFANA_DOCKER=grafana/grafana
export GRAFANA_IMAGE='${GRAFANA_DOCKER}:${GRAFANA_VERSION}'

export PROMETHEUS_VERSION="v2.19.0"
export PROMETHEUS_VERSION="v2.52.0"
export PROMETHEUS_DOCKER=prom/prometheus
export PROMETHEUS_IMAGE='${PROMETHEUS_DOCKER}:${PROMETHEUS_VERSION}'

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8 changes: 8 additions & 0 deletions birdhouse/env.local.example
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Expand Up @@ -574,6 +574,14 @@ export THREDDS_ADDITIONAL_CATALOG=""
#export ALERTMANAGER_EXTRA_INHIBITION=""
#export ALERTMANAGER_EXTRA_RECEIVERS=""

# Below are for the prometheus-longterm-metrics optional component
#export PROMETHEUS_LONGTERM_RETENTION_TIME=1y

# Below are for the thanos optional component
# Change these from the default for added security
#export THANOS_MINIO_ROOT_USER="${__DEFAULT__THANOS_MINIO_ROOT_USER}"
#export THANOS_MINIO_ROOT_PASSWORD="${__DEFAULT__THANOS_MINIO_ROOT_PASSWORD}"

#############################################################################
# Emu optional vars
#############################################################################
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45 changes: 45 additions & 0 deletions birdhouse/optional-components/README.rst
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Expand Up @@ -443,3 +443,48 @@ How to enable X-Robots-Tag Header in ``env.local`` (a copy from `env.local.examp

.. seealso::
See the `env.local.example`_ file for more details about this ``BIRDHOUSE_PROXY_ROOT_LOCATION`` behaviour.

Prometheus Long-term Metrics
----------------------------

This is a second prometheus instance that collects longterm monitoring metrics from the original prometheus instance
(the one created by the ``components/monitoring`` component).

Longterm metrics are any prometheus rule that have the label ``group: longterm-metrics`` or in other words are
selectable using prometheus' ``'{group="longterm-metrics"}'`` query filter. To add some default longterm metrics rules
also enable the ``prometheus-longterm-rules`` component.

You may also choose to create your own set of rules in another component that you would like to use instead of the
default ones.

To configure this component:

* update the ``PROMETHEUS_LONGTERM_RETENTION_TIME`` variable to set how long the data will be kept by prometheus

Enabling this component creates the additional endpoint ``/prometheus-longterm-metrics``.

Prometheus Long-term Rules
--------------------------

This adds some default longterm metrics rules to the `prometheus` component for use by the `prometheus-longterm-metrics`
component. These rules all have the label ``group: longterm-metrics``.

To see which rules are added, check out the
`optional-components/prometheus-longterm-rules/config/monitoring/prometheus.rules` file.

Thanos
------

This enables better storage of longterm metrics collected by the ``optional-components/prometheus-longterm-metrics``
component. Data will be collected from the ``prometheus-longterm-metrics`` and stored in an S3 object store
indefinitely.
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Indefinitely ! Do we actually want this? Can we set an expiry after like 10 years?

Grafana will be able to display data from Thanos go to back to 10 years? With this kind of extreme long term stats, what is the UI to visualize it?

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You can choose to change this if you wish. Thanos suggests keeping data indefinitely by default. If you do not need to keep data forever, I suggest just using the prometheus-longterm-monitoring component without thanos and setting the PROMETHEUS_LONGTERM_RETENTION_TIME to whatever you'd like.

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Oh I see, is there a switch to disable Thanos?

Same question, in the case we want to use Thanos, how to visualize the data stored on Thanos? I assume if Thanos is enabled, the retention duration on the Prometheus side will be very short to avoid doubling the storage so without data being stored in Prometheus, how to visualize that data stored on Thanos.

Just a question. If another component is required, we can do it in a follow up Pr.

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Oh I see, is there a switch to disable Thanos?

To answer my own question, Thanos is actually a separate component so it does not have to be enabled together with the Prometheus-long-term component? The Prometheus-long-term component can function standalone of Thanos?

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Thanos is actually a separate component so it does not have to be enabled together with the Prometheus-long-term component

Yes that's right. prometheus-longterm-metrics collects and stores specific metrics that we want to keep for longer from prometheus. If you want to also enable thanos, then thanos will store those same metrics in a much more compact/efficient way so that you can store more data over a longer time period.

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I'm happy with forever storage for long-term-metrics. The point is to keep an archive of key metrics. If those are daily or hourly, archiving a few dozen metrics won't be a problem.

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Let's see how much space that will take in practice and we will adjust. And eventually we need a way to visualize those older metrics. Otherwise, what's the point to keep them forever if we can not visualize?


When enabling this component, please change the default values for the ``THANOS_MINIO_ROOT_USER`` and
``THANOS_MINIO_ROOT_PASSWORD`` by updating the ``env.local`` file. These set the login credentials for the root user
that runs the minio_ object store.

Enabling this component creates the additional endpoints:
* ``/thanos-query``: a prometheus-like query interface to inspect the data stored by thanos
* ``/thanos-minio``: a minio_ web console to inspect the data stored by minio_.

.. _minio: https://min.io/
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prometheus.yml
config/magpie/config.yml
config/proxy/conf.extra-service.d/monitoring.conf
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providers:
prometheus-longterm-metrics:
# below URL is only used to fill in the required location in Magpie
# actual auth validation is performed with Twitcher 'verify' endpoint without accessing this proxied URL
url: http://proxy:80
title: PrometheusLongtermMetrics
public: true
c4i: false
type: api
sync_type: api

permissions:
- service: prometheus-longterm-metrics
permission: read
group: administrators
action: create
- service: prometheus-longterm-metrics
permission: write
group: administrators
action: create
- service: prometheus-longterm-metrics
permission: read
group: monitoring
action: create
- service: prometheus-longterm-metrics
permission: write
group: monitoring
action: create
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version: "3.4"

services:
magpie:
volumes:
- ./optional-components/prometheus-longterm-metrics/config/magpie/config.yml:${MAGPIE_PERMISSIONS_CONFIG_PATH}/prometheus-longterm-metrics.yml:ro
- ./optional-components/prometheus-longterm-metrics/config/magpie/config.yml:${MAGPIE_PROVIDERS_CONFIG_PATH}/prometheus-longterm-metrics.yml:ro
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location /prometheus-longterm-metrics {
auth_request /secure-prometheus-longterm-metrics-auth;
auth_request_set $auth_status $upstream_status;
proxy_pass http://prometheus-longterm-metrics:9090;
proxy_set_header Host $host;
}

location = /secure-prometheus-longterm-metrics-auth {
internal;
proxy_pass https://${BIRDHOUSE_FQDN_PUBLIC}${TWITCHER_VERIFY_PATH}/prometheus-longterm-metrics$request_uri;
proxy_pass_request_body off;
proxy_set_header Host $host;
proxy_set_header Content-Length "";
proxy_set_header X-Original-URI $request_uri;
proxy_set_header X-Forwarded-Proto $real_scheme;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header X-Forwarded-Host $host:$server_port;
}
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version: "3.4"

services:
proxy:
volumes:
- ./optional-components/prometheus-longterm-metrics/config/proxy/conf.extra-service.d:/etc/nginx/conf.extra-service.d/prometheus-longterm-metrics:ro
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export PROMETHEUS_LONGTERM_VERSION='${PROMETHEUS_VERSION:-"v2.52.0"}'
export PROMETHEUS_LONGTERM_DOCKER='${PROMETHEUS_DOCKER:-prom/prometheus}'
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export PROMETHEUS_LONGTERM_IMAGE='${PROMETHEUS_LONGTERM_DOCKER}:${PROMETHEUS_LONGTERM_VERSION}'

export PROMETHEUS_LONGTERM_RETENTION_TIME=1y
export PROMETHEUS_LONGTERM_SCRAPE_INTERVAL=1h

# These are the prometheus defaults
export PROMETHEUS_LONGTERM_TSDB_MIN_BLOCK_DURATION=2h
export PROMETHEUS_LONGTERM_TSDB_MAX_BLOCK_DURATION=1d12h

# These are the targets that
export PROMETHEUS_LONGTERM_TARGETS='["prometheus:9090"]' # yaml list syntax

OPTIONAL_VARS="
$OPTIONAL_VARS
\$PROMETHEUS_LONGTERM_SCRAPE_INTERVAL
\$PROMETHEUS_LONGTERM_TARGETS
"

export DELAYED_EVAL="
$DELAYED_EVAL
PROMETHEUS_LONGTERM_VERSION
PROMETHEUS_LONGTERM_DOCKER
PROMETHEUS_LONGTERM_IMAGE
PROMETHEUS_LONGTERM_RULES_FILE
"

# Note that this component does not depend explicitly on the `components/monitoring` component so that this can
# theoretically be deployed on a different machine than the `prometheus` service. This is currently untested.
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Curious how that would work out?
It seems to depend on prometheus:9090 and extends the volumes of prometheus service.
I think it is more confusing to omit the dependency.

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It's actually a completely separate service with no shared volumes. It does depend on prometheus:9090 by default but that default can be updated by setting the PROMETHEUS_LONGTERM_TARGETS variable.

PROMETHEUS_LONGTERM_TARGETS can point to any prometheus endpoints at all.

See the discussion about this here: #461 (comment)

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What I meant is that the rules are mounted under prometheus service here:
https://github.com/bird-house/birdhouse-deploy/blob/longterm-monitoring/birdhouse/optional-components/prometheus-longterm-rules/config/monitoring/docker-compose-extra.yml

So, whether PROMETHEUS_LONGTERM_TARGETS refers to the same instance or a custom remote one, the local instance needs to have the long-term rules defined. Therefore, doesn't that mean that prometheus service (i.e.: using components/monitoring) becomes mandatory regardless, since it is needed to mount the rules?

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Yes, prometheus must be running on the same host as the rest of the birdhouse stack.

That first prometheus instance must have at least one rule that has the longterm-metrics group label in order for a second prometheus instance (either running on the same machine or elsewhere) to know which metrics it should monitor and store from the first prometheus instance.

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I've taken a second look at the directory structure, and starting to see why components/monitoring is not a dependency. Is it only because components/monitoring combines cardvisor, grafana, alertmanager, prometheus, etc. all together?

Therefore, if someone wants "only" longterm-metrics, they need to define their own prometheus service with a definition similar to this?

prometheus:
image: ${PROMETHEUS_IMAGE}
container_name: prometheus
volumes:
- ./components/monitoring/prometheus.yml:/etc/prometheus/prometheus.yml:ro
- ./components/monitoring/prometheus.rules:/etc/prometheus/prometheus.rules:ro
- prometheus_persistence:/prometheus:rw
command:
# restore original CMD from image
- --config.file=/etc/prometheus/prometheus.yml
- --storage.tsdb.path=/prometheus
- --web.console.libraries=/usr/share/prometheus/console_libraries
- --web.console.templates=/usr/share/prometheus/consoles
# https://prometheus.io/docs/prometheus/latest/storage/
- --storage.tsdb.retention.time=90d
# wrong default was http://container-hash:9090/
- --web.external-url=https://${BIRDHOUSE_FQDN_PUBLIC}/prometheus/
restart: always

I think part of what makes all of this confusing is that there are 2 different, though related, component definitions (and I still do not understand why):

From a user's perspective, this all seems really convoluted.
Isn't there are way to simplify this hierarchy? For example, what if there was a distinct optional-components/prometheus definition, and components/monitoring depends on it. Then, optional-components/prometheus-longterm-metrics could also depend only on optional-components/prometheus?

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@fmigneault

Therefore, if someone wants "only" longterm-metrics, they need to define their own prometheus service with a definition similar to this?

If someone only wants longterm metrics then they can have a single prometheus service that sets --storage.tsdb.retention.time to something longer than 90 days.

However, if you want some metrics to be stored for longer than others, you need a second prometheus instance. This is because the --storage.tsdb.retention.time value is set for an entire prometheus instance (see discussion here: #277 (comment) and here: #461 (comment)).

I think part of what makes all of this confusing is that there are 2 different, though related, component definitions (and I still do not understand why)

These are separate in order to accommodate @tlvu's request to be able to deploy the prometheus-longterm-metrics component on a different server. prometheus-longterm-rules are just suggested default rules to be added to the prometheus server. As described in the README file:

This adds some default longterm metrics rules to the `prometheus` component 

These rules are added to the prometheus component on the same machine that is running the rest of the stack because that is where all the relevant metrics are collected by the rest of the monitoring components (cadvisor, nodeexporter). These rules are not necessary, they are recommended defaults but you can customize them however you like. It is easier to customize and add your own if the rules are separate. Users can choose to include the defaults, or not.

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Agree with Misha's explanations. I just want to add that each organization needs are different so we should not force a certain "configuration".

Specifically to this PR, we should not force the 2 Prometheus to be on the same machine. So optional-components/prometheus-longterm-metrics should not depend on components/monitoring. We should also not be forced to use optional-components/prometheus-longterm-rules because each org will probably have different metrics they deemed useful to keep for longterm.

During Misha's leave, a sysadmin from PCIC actually had a question about how to pull existing metrics from our PAVICS Prometheus into his own centralized Prometheus for a centralized view of all his servers in one place. I point him to this PR for inspiration.

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My bad. I was not clear in my explanation. What I intended to say was:
"if someone wants only prometheus monitoring with both long-term and short term metrics, they need to define their own prometheus service" [...], because they cannot activate prometheus on its own (i.e.: they must use the full package components/monitoring that includes all other services).

Having short/long-term separate, and having them configurable on different servers is perfectly fine by me. I'm all for that flexibility, and never mentioned otherwise.

It just seems from the configuration files that, in order for long-term metrics to be sent to the remote server, the rules must be mounted into the short-term local prometheus (as shown below), and since that prometheus must exist, then it should be a dependency. I understand long-term-prometheus NOT being a dependency to toggle it independently of the short-term one. This is good. Here I am referring to https://github.com/bird-house/birdhouse-deploy/tree/3f75d496b932ab4d90857206003d0225cd20c435/birdhouse/optional-components/prometheus-longterm-rules having component/monitoring dependency, NOT https://github.com/bird-house/birdhouse-deploy/tree/3f75d496b932ab4d90857206003d0225cd20c435/birdhouse/optional-components/prometheus-longterm-metrics. In other words, if one adds optional-components/prometheus-longterm-rules ONLY without also thinking to add components/monitoring, docker-compose will complain that service: prometheus is not defined.

services:
prometheus:
volumes:
- ./optional-components/prometheus-longterm-rules/config/monitoring/prometheus.rules:/etc/prometheus/prometheus-longterm-metrics.rules:ro

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Ok I understand your concern now.

In other words, if one adds optional-components/prometheus-longterm-rules ONLY without also thinking to add components/monitoring, docker-compose will complain that service: prometheus is not defined.

Docker compose won't actually complain in this case. Additional settings defined under the config/ folder in components are only applied if the component that it references is also enabled. So in this case, if you add prometheus-longterm-rules as a component but not monitoring, then nothing will happen (since the additional docker-compose settings are in prometheus-longterm-rules/config/monitoring.

If we do make the prometheus-longterm-rules component dependent on the monitoring components then if someone adds the prometheus-longterm-rules but not the monitoring rule to the BIRDHOUSE_EXTRA_CONF_DIRS configuration variable, then monitoring will be added in automatically. This is also a surprising behaviour that users may not expect.

My opinion is that we should leave it as is, so that users must specify both components if they want both components. I'm open to other opinions on this subject though.

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Thanks for validating how this resolves.
I'm fine with either approach if the README indicates clearly what is supposed to happen and what to do if the one or the other situation is desired.

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version: "3.4"

x-logging:
&default-logging
driver: "json-file"
options:
max-size: "50m"
max-file: "10"

services:
prometheus-longterm-metrics:
image: ${PROMETHEUS_LONGTERM_IMAGE}
container_name: prometheus-longterm-metrics
volumes:
- ./optional-components/prometheus-longterm-metrics/prometheus.yml:/etc/prometheus/prometheus.yml:ro
- prometheus_longterm_persistence:/prometheus:rw
command:
- --config.file=/etc/prometheus/prometheus.yml
- --storage.tsdb.path=/prometheus
- --web.console.libraries=/usr/share/prometheus/console_libraries
- --web.console.templates=/usr/share/prometheus/consoles
- --storage.tsdb.retention.time=${PROMETHEUS_LONGTERM_RETENTION_TIME}
- --web.external-url=https://${BIRDHOUSE_FQDN_PUBLIC}/prometheus-longterm-metrics/
- --storage.tsdb.min-block-duration=${PROMETHEUS_LONGTERM_TSDB_MIN_BLOCK_DURATION}
- --storage.tsdb.max-block-duration=${PROMETHEUS_LONGTERM_TSDB_MAX_BLOCK_DURATION}
restart: always
logging: *default-logging

volumes:
prometheus_longterm_persistence:
external:
name: prometheus_longterm_persistence
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#!/bin/sh -x

docker volume create prometheus_longterm_persistence # metrics db
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global:
external_labels:
instance_name: prometheus-longterm-metrics

scrape_configs:
- job_name: 'federate'
scrape_interval: ${PROMETHEUS_LONGTERM_SCRAPE_INTERVAL}

honor_labels: true
metrics_path: '/prometheus/federate'

params:
'match[]':
- '{group="longterm-metrics"}'

static_configs:
- targets: ${PROMETHEUS_LONGTERM_TARGETS}
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version: "3.4"

services:
prometheus:
volumes:
- ./optional-components/prometheus-longterm-rules/config/monitoring/prometheus.rules:/etc/prometheus/prometheus-longterm-metrics.rules:ro
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groups:
- name: longterm-metrics-hourly
interval: 1h
rules:
# percentage of the time, over the last hour, that all CPUs were working
# 1 means all CPUs were working all the time, 0 means they were all idle all the time
- record: instance:cpu_load:avg_rate1h
expr: avg by(instance) (rate(node_cpu_seconds_total{mode!="idle"}[1h]))
labels:
group: longterm-metrics
# total number of bytes that were sent or received over the network in the last hour
- record: instance:network_bytes_transmitted:sum_rate1h
expr: sum by(instance) (rate(node_network_transmit_bytes_total[1h]) + rate(node_network_receive_bytes_total[1h]))
labels:
group: longterm-metrics
2 changes: 2 additions & 0 deletions birdhouse/optional-components/thanos/.gitignore
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config/magpie/config.yml
config/proxy/conf.extra-service.d/monitoring.conf
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providers:
thanos:
# below URL is only used to fill in the required location in Magpie
# actual auth validation is performed with Twitcher 'verify' endpoint without accessing this proxied URL
url: http://proxy:80
title: Thanos
public: true
c4i: false
type: api
sync_type: api

permissions:
- service: thanos
permission: read
group: administrators
action: create
- service: thanos
permission: write
group: administrators
action: create
- service: thanos
permission: read
group: monitoring
action: create
- service: thanos
permission: write
group: monitoring
action: create
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version: "3.4"

services:
magpie:
volumes:
- ./optional-components/thanos/config/magpie/config.yml:${MAGPIE_PERMISSIONS_CONFIG_PATH}/thanos.yml:ro
- ./optional-components/thanos/config/magpie/config.yml:${MAGPIE_PROVIDERS_CONFIG_PATH}/thanos.yml:ro
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location /thanos-query {
auth_request /secure-thanos-auth;
auth_request_set $auth_status $upstream_status;
proxy_pass http://thanos-query:19192;
proxy_set_header Host $host;
}

location /thanos-minio/ {
auth_request /secure-thanos-auth;
auth_request_set $auth_status $upstream_status;

rewrite ^/thanos-minio/(.*) /$1 break;
proxy_pass http://thanos-minio:9001;

proxy_http_version 1.1;
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection "Upgrade";
proxy_set_header Host $host;
proxy_set_header X-Real-IP $remote_addr;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header X-Forwarded-Proto $scheme;

# This allows WebSocket connections
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection "upgrade";
}

location = /secure-thanos-auth {
internal;
proxy_pass https://${BIRDHOUSE_FQDN_PUBLIC}${TWITCHER_VERIFY_PATH}/thanos$request_uri;
proxy_pass_request_body off;
proxy_set_header Host $host;
proxy_set_header Content-Length "";
proxy_set_header X-Original-URI $request_uri;
proxy_set_header X-Forwarded-Proto $real_scheme;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header X-Forwarded-Host $host:$server_port;
}
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
version: "3.4"

services:
proxy:
volumes:
- ./optional-components/thanos/config/proxy/conf.extra-service.d:/etc/nginx/conf.extra-service.d/thanos:ro
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