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CWL-metrics

CWL-metrics is a framework to collect and analyze computational resource usage of workflows defined in Common Workflow Language (CWL). CWL-metrics provides a command line tool to run a CWL workflow, collect resource usage, and integrate with the workflow information. CWL-metrics uses Telegraf to collect the resource usage via docker API, and Elasticsearch to store the collected data in. You can specify an Elasticsearch server to send out the collected resource usage.

Changes on ver 2.0

  • CWL-metrics no longer uses the Perl daemon, provides cwl-metrics run command to run a CWL workflow and collect metrics instead.

Prerequisites

Install

Clone this repository and execute the script cwl-metrics

$ git clone https://github.com/inutano/cwl-metrics
$ cd cwl-metrics
$ ./cwl-metrics
cwl-metrics: 2.0.0
Usage:
  cwl-metrics [subcommand] [options] <wf.cwl> <wf.conf>

Subcommand:
  up                      Start metrics collector containers
  down                    Stop metrics collector containers
  run                     Run given workflow via cwltool and collect metrics
  fetch                   Start Virtuoso and load data; add data to the existing
  ps                      Show status of metrics collector containers
  logs                    Show docker-compose logs
  clean                   Clean up tmpdir (./tmp)
  help (-h|--help)        Show this help message
  version (-v|--version)  Show version information

Options:
  --es-host  Set Elasticsearch host name (default: localhost)
  --es-port  Set Elasticsearch port number (default: 9200)

Getting started

Use subcommands to control CWL-metrics system as follows:

$ ./cwl-metrics up
Creating network "tmp_default" with the default driver
Creating cwl-metrics-elasticsearch ... done
Creating cwl-metrics-fluentd       ... done
Creating cwl-metrics-telegraf      ... done
[2020/12/04 16:16:34] CWL-metrics: Creating ElasticSearch indexes..
{"acknowledged":true,"shards_acknowledged":true,"index":"metrics"}{"acknowledged":true,"shards_acknowledged":true,"index":"workflow"}{"metrics":{"aliases":{},"mappings":{"properties":{"timestamp":{"type":"date","format":"epoch_second"}}},"settings":{"index":{"creation_date":"1607066231035","number_of_shards":"1","number_of_replicas":"1","uuid":"6yhEsxrrSL6LXQavIYgG0Q","version":{"created":"7070099"},"provided_name":"metrics"}}}}{"workflow":{"aliases":{},"mappings":{"properties":{"end_date":{"type":"date","format":"yyyy-MM-dd HH:mm:ss"},"start_date":{"type":"date","format":"yyyy-MM-dd HH:mm:ss"}}},"settings":{"index":{"mapping":{"total_fields":{"limit":"5000"}},"number_of_shards":"1","provided_name":"workflow","creation_date":"1607066231680","number_of_replicas":"1","uuid":"TyM8DZnsQWyCg_7dGHOxrQ","version":{"created":"7070099"}}}}}%
$ ./cwl-metrics run <your CWL workflow> <your workflow job configuration>
$ ./cwl-metrics fetch
$ ./cwl-metrics down

This will do followings:

Troubleshooting

CWL-metrics starting process stopped with showing "Creating Elasticsearch index..."

This happens because Elasticsearch did not launch successfully because of the machine setting on vm.max_map_count. Follow the guide below to set it to 262144.

# Linux
$ sudo sysctl -w vm.max_map_count=262144
$ grep vm.max_map_count /etc/sysctl.conf
vm.max_map_count=262144

# On mac os
$ screen ~/Library/Containers/com.docker.docker/Data/com.docker.driver.amd64-linux/tty
$ sudo sysctl -w vm.max_map_count=262144

# Windows and macOS with Docker Toolbox
$ docker-machine ssh
$ sudo sysctl -w vm.max_map_count=262144

If you still get an error on launching CWL-metrics, please let us know by creating an issue.