Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

galaxy.jobs.metrics.instrumenters package

This module describes the abstract interface for InstrumentPlugin.

These are responsible for collecting and formatting a coherent set of metrics.

class galaxy.jobs.metrics.instrumenters.InstrumentPlugin[source]

Bases: object

Describes how to instrument job scripts and retrieve collected metrics.

formatter = <galaxy.jobs.metrics.formatting.JobMetricFormatter object>
plugin_type

Short string providing labelling this plugin

pre_execute_instrument(job_directory)[source]

Optionally return one or more commands to instrument job. These commands will be executed on the compute server prior to the job running.

post_execute_instrument(job_directory)[source]

Optionally return one or more commands to instrument job. These commands will be executed on the compute server after the tool defined command is ran.

job_properties(job_id, job_directory)[source]

Collect properties for this plugin from specified job directory. This method will run on the Galaxy server and can assume files created in job_directory with pre_execute_instrument and post_execute_instrument are available.

Submodules

galaxy.jobs.metrics.instrumenters.collectl module

The module describes the collectl job metrics plugin.

class galaxy.jobs.metrics.instrumenters.collectl.CollectlPlugin(**kwargs)[source]

Bases: galaxy.jobs.metrics.instrumenters.InstrumentPlugin

Run collectl along with job to capture system and/or process data according to specified collectl subsystems.

plugin_type = 'collectl'
formatter = <galaxy.jobs.metrics.instrumenters.collectl.CollectlFormatter object>
__init__(**kwargs)[source]
pre_execute_instrument(job_directory)[source]
post_execute_instrument(job_directory)[source]
job_properties(job_id, job_directory)[source]

galaxy.jobs.metrics.instrumenters.core module

The module describes the core job metrics plugin.

class galaxy.jobs.metrics.instrumenters.core.CorePlugin(**kwargs)[source]

Bases: galaxy.jobs.metrics.instrumenters.InstrumentPlugin

Simple plugin that collects data without external dependencies. In particular it currently collects value set for Galaxy slots.

plugin_type = 'core'
formatter = <galaxy.jobs.metrics.instrumenters.core.CorePluginFormatter object>
__init__(**kwargs)[source]
pre_execute_instrument(job_directory)[source]
post_execute_instrument(job_directory)[source]
job_properties(job_id, job_directory)[source]

galaxy.jobs.metrics.instrumenters.cpuinfo module

The module describes the cpuinfo job metrics plugin.

class galaxy.jobs.metrics.instrumenters.cpuinfo.CpuInfoPlugin(**kwargs)[source]

Bases: galaxy.jobs.metrics.instrumenters.InstrumentPlugin

Gather information about processor configuration from /proc/cpuinfo. Linux only.

plugin_type = 'cpuinfo'
formatter = <galaxy.jobs.metrics.instrumenters.cpuinfo.CpuInfoFormatter object>
__init__(**kwargs)[source]
pre_execute_instrument(job_directory)[source]
job_properties(job_id, job_directory)[source]

galaxy.jobs.metrics.instrumenters.env module

The module describes the env job metrics plugin.

class galaxy.jobs.metrics.instrumenters.env.EnvPlugin(**kwargs)[source]

Bases: galaxy.jobs.metrics.instrumenters.InstrumentPlugin

Instrumentation plugin capable of recording all or specific environment variables for a job at runtime.

plugin_type = 'env'
formatter = <galaxy.jobs.metrics.instrumenters.env.EnvFormatter object>
__init__(**kwargs)[source]
pre_execute_instrument(job_directory)[source]

Use env to dump all environment variables to a file.

post_execute_instrument(job_directory)[source]
job_properties(job_id, job_directory)[source]

Recover environment variables dumped out on compute server and filter out specific variables if needed.

galaxy.jobs.metrics.instrumenters.meminfo module

The module describes the meminfo job metrics plugin.

class galaxy.jobs.metrics.instrumenters.meminfo.MemInfoPlugin(**kwargs)[source]

Bases: galaxy.jobs.metrics.instrumenters.InstrumentPlugin

Gather information about processor configuration from /proc/cpuinfo. Linux only.

plugin_type = 'meminfo'
formatter = <galaxy.jobs.metrics.instrumenters.meminfo.MemInfoFormatter object>
__init__(**kwargs)[source]
pre_execute_instrument(job_directory)[source]
job_properties(job_id, job_directory)[source]

galaxy.jobs.metrics.instrumenters.uname module

The module describes the uname job metrics plugin.

class galaxy.jobs.metrics.instrumenters.uname.UnamePlugin(**kwargs)[source]

Bases: galaxy.jobs.metrics.instrumenters.InstrumentPlugin

Use uname to gather operating system information about remote system job is running on. Linux only.

plugin_type = 'uname'
formatter = <galaxy.jobs.metrics.instrumenters.uname.UnameFormatter object>
__init__(**kwargs)[source]
pre_execute_instrument(job_directory)[source]
job_properties(job_id, job_directory)[source]