2018/Data Project: Difference between revisions

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==Stage 1: Collecting System Data==
==Stage 1: Collecting System Data==


===COMPLETED Phase 1a: Netdata===
See [[2018/Data Project/Stage 1]]


First, we set up [[Netdata]].
==Stage 2: Spy==
* '''Pros:''' Netdata has a fantastic dashboard with all kinds of stuff all ready to go.
* '''Cons:''' Netdata is custom-built for monitoring compute nodes, and not for general visualization.
* [[Netdata]]
* Link to Netdata scripts: https://charlesreid1.com:3000/data/netdata


Netdata is a useful tool for monitoring an individual machine instance remotely and it works excellent.
dahak-spy project:
* lightweight server (may want larger disk, okay if non-free)
* running mongodb
* running mongoexpress
* running prometheus
* running grafana
* running netdata


===NOPE Phase 1b: Prometheus===
additional components before real world testing:
* netdata on the build node
* netdata python plugin from another process, monitoring.....???
* metrics:
** is snakemake running (binary yes/no)
** current stage of snakemake (adjust snakemake file to write into a dotfile)
** cpu/memory/network/disk io


<s>Second, we set up [[Netdata]] to dump to a [[Prometheus]] database.
netdata python plugin workflow?
* '''Pros:''' Prometheus was fairly easy to integrate with Netdata.
* does it need to be installed and netdata restarted, or can it push data into netdata?
* '''Cons:''' Prometheus was not a particularly outstanding tool, don't know much about how to use it.
* [[Prometheus]]


Need to get more involved with Prometheus and/or Grafana to monitor more than one machine.</s>
real yeti:
* get a yeti node
* debug the snakemake file one step at a time using already-downloaded files (faster step)
* let the snakemake file run with netdata and friends running


===COMPLETED Phase 2a: MongoDB and MongoExpress===
=Flags=


We then set up [[MongoDB]] and [[MongoExpress]] in Docker containers. MongoDB listens for incoming data on the VPN. MongoExpress is connected to MongoDB and exposes a web interface to interact with MongoDB. We used MongoDB to store edit history and page graph data from the charlesreid1 wiki.
[[Category:Data Engineering]]
[[Category:Data Project]]


Pros and cons:
[[Category:MongoDB]]
* '''Pros:''' MongoDB is a containerized solution with persistent data. MongoDB had (has?) a high setup barrier, but a low usage barrier. Very easy to do basic CRUD operations, make new databases as needed, etc.
[[Category:MongoExpress]]
* '''Cons:''' No visualization tools baked in, need to define own tools. Collectd cannot dump to MongoDB because of a bunch of installation stupidity.
[[Category:Graphite]]
[[Category:Grafana]]
[[Category:Netdata]]
[[Category:Collectd]]
[[Category:Prometheus]]


Links:
[[Category:2018]]
* [[MongoDB]]
[[Category:January 2018]]
* [[MongoExpress]]
[[Category:February 2018]]
* [[Pywikibot]]
* Link to MongoDB docker files: https://charlesreid1.com:3000/docker/d-mongodb
* Link to MongoExpress docker files: https://charlesreid1.com:3000/docker/d-mongoexpress
* Link to wiki scraping scripts: https://charlesreid1.com:3000/wiki/charlesreid1-wiki-data
 
===NOPE Phase 2b: Collectd===
 
<s>We struggled a LOT with [[Collectd]], mainly because we wanted to use the collectd plugin to write to MongoDB. Unfortunately, this was the only plugin that seemed impossible to install.
 
See [[Collectd]] page.
 
(This is all installation stupidity. I tried installing collectd with aptitude, no plugins. Then the core, no plugins. Then installing from source, and MongoDB plugin did not work. Struggling to get collectd to link to MongoDB. Needed custom config or something. Then I just gave up, and re-installed collectd core, and the library was there, but it was complaining it couldn't find it. In the end, I totally abandoned the attempt to get collectd to talk to mongodb. Could probably use a collectd docker and fix this whole issue.)</s>
 
===NOPE Phase 3a: Graphite===
 
<s>Next, we deployed a [[Graphite]] container to hold time series from [[Collectd]].
 
Pros and cons:
* '''Pros:''' Containerized solution. Collectd graphite plugin worked fine.
* '''Cons:''' Graphite comes with Carbon (web interface), which is utter awful. It provides the absolute bare minimum, and it looks like it's trapped in a miserable 1998 computer prison.
 
Links:
* [[Graphite]]
* Link to Graphite docker files: https://charlesreid1.com:3000/docker/d-graphite</s>
 
===NOPE Phase 3b: Visualizing Graphite===
 
<s>A few years back we explored [[Cubism]] and Cube (difference?) as a way of visualizing time series from Graphite. It took some effort to get a basic dashboard, and Cubism is (ultimately) D3, the most frustratingly stupidly over-designed and over-complicated library ever, implemented in a totally irrational programming language.
 
So, no.


We're going to focus on Mongo, which is more transparent and more flexible for all purposes.</s>


===Stage 1 Conclusion: Netdata, Not Collectd===


All of the struggle to get collectd working with mongo was a waste of effort, and led to the graphite distraction in the first place. A broken build procedure (collectd) led to an unknown, mediocre tool (graphite).
<!--


Ultimately, if we need to run collectd, interface with the collectd API via Python: https://collectd.org/wiki/index.php/Plugin:Python
==Stage 2: Finalized Data Collection System==
 
==Stage 2: Finalizing Data Collection==


===Phase 4: Netdata and Mongo===
===Phase 4: Netdata and Mongo===
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This is a (micro)service design pattern - small, lightweight, standalone daemons act as instruments that continuously read whatever they read, available to be queried but otherwise not saving or doing anything with the data themselves. The data is handled by an application that queries each service it manages to collect data about those services (and coordinate if necessary).
This is a (micro)service design pattern - small, lightweight, standalone daemons act as instruments that continuously read whatever they read, available to be queried but otherwise not saving or doing anything with the data themselves. The data is handled by an application that queries each service it manages to collect data about those services (and coordinate if necessary).
-->
<!--


==Stage 3: Visualizing Data==
==Stage 3: Visualizing Data==
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[[Grafana]] container to create dashboards from it.
[[Grafana]] container to create dashboards from it.


Link to Grafana docker files: https://charlesreid1.com:3000/docker/d-graphite
Link to Grafana docker files: https://charlesreid1.com:3000/docker/d-grafana


Need to fix grafana user on jupiter.
Need to fix grafana user on jupiter.


We're basically after something like this, except MongoDB instead of Prometheus: https://github.com/firehol/netdata/wiki/Netdata,-Prometheus,-and-Grafana-Stack
We're basically after something like this: https://github.com/firehol/netdata/wiki/Netdata,-Prometheus,-and-Grafana-Stack
 
==Next Steps==
 
Bioconda and biocontainers - start to adopt their approach to doing things, and be able to replicate workflows
 
Slang some cluster workflows around
 
=Flags=
 
[[Category:Data Engineering]]
[[Category:Data Project]]


[[Category:MongoDB]]
-->
[[Category:MongoExpress]]
[[Category:Graphite]]
[[Category:Grafana]]
[[Category:Netdata]]
[[Category:Collectd]]
[[Category:Prometheus]]
 
[[Category:2018]]
[[Category:January 2018]]
[[Category:February 2018]]

Latest revision as of 08:18, 3 March 2018

Project Overview

The 2018 data project is an ongoing effort to figure out how to set up "painless" dashboards for monitoring metrics.

Stage 1: Collecting System Data

See 2018/Data Project/Stage 1

Stage 2: Spy

dahak-spy project:

  • lightweight server (may want larger disk, okay if non-free)
  • running mongodb
  • running mongoexpress
  • running prometheus
  • running grafana
  • running netdata

additional components before real world testing:

  • netdata on the build node
  • netdata python plugin from another process, monitoring.....???
  • metrics:
    • is snakemake running (binary yes/no)
    • current stage of snakemake (adjust snakemake file to write into a dotfile)
    • cpu/memory/network/disk io

netdata python plugin workflow?

  • does it need to be installed and netdata restarted, or can it push data into netdata?

real yeti:

  • get a yeti node
  • debug the snakemake file one step at a time using already-downloaded files (faster step)
  • let the snakemake file run with netdata and friends running

Flags



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