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Support setting and displaying timezone with the core metrics plugin
This commit is contained in:
Nate Coraor
@@ -27,24 +27,38 @@ If no configuration is specified, the default is to load only the ``core`` plugi
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Available Job Metrics Plugins
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-----------------------------
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The list of metrics plugins implemented in the code can be found at ``lib/galaxy/job_metrics/instrumenters``.
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The list of metrics plugins implemented in the code can be found at ``lib/galaxy/job_metrics/instrumenters``. A list of
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available plugins and example configurations follows.
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core
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~~~~
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The core plugin captures the number of cores allocated to the job (``$GALAXY_SLOTS``), the start and end time of job (in
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seconds since epoch) and computes the runtime in seconds.
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It has no options.
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.. code-block:: yaml
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- type: core
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timezone: UTC
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The core plugin captures the number of cores allocated to the job (``$GALAXY_SLOTS``), the start and end time of job (in
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seconds since epoch) and computes the runtime in seconds.
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The optional ``timezone`` option (default: ``null``) controls how times are displayed in the UI. If unset, times are
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displayed in server local time. Note that not all values respect daylight savings time; for example, ``US/Eastern``,
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``America/New_York``, and ``EST5EDT`` do, whereas ``EST`` does not. Possible values are determined by the server time
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zone library and can be listed with the following command:
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.. code-block:: shell
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python3 -c 'import zoneinfo; list(map(print, sorted(zoneinfo.available_timezones())))'
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cpuinfo
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~~~~~~~
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.. code-block:: yaml
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- type: cpuinfo
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verbose: false
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The cpuinfo plugin captures the processor count on the system that that job ran on (note that this may differ from the
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number of CPUs actually allocated to the job).
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@@ -53,54 +67,43 @@ The optional ``verbose`` option (default: ``false``) captures details (likely fa
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The cpuinfo plugin works on Linux only.
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.. code-block:: yaml
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- type: cpuinfo
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verbose: false
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meminfo
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~~~~~~~
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.. code-block:: yaml
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- type: meminfo
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The meminfo plugin captures the memory information on the system that the job ran on (note that this may differ from the
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amount of memory actually allocated to the job).
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It has no options.
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.. code-block:: yaml
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- type: meminfo
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hostname
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~~~~~~~~
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The hostname plugin captures the output of ``hostname`` on the system that the job ran on.
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It has no options.
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.. code-block:: yaml
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- type: hostname
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uname
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~~~~~
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The uname plugin captures the output of ``uname -a`` on the system that the job ran on.
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The hostname plugin captures the output of ``hostname`` on the system that the job ran on.
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It has no options.
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uname
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~~~~~
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.. code-block:: yaml
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- type: uname
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The uname plugin captures the output of ``uname -a`` on the system that the job ran on.
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It has no options.
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env
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~~~
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The env plugin captures environment variables set in the job's executing environment.
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By default, it captures **all** environment variables, which is likely excessive but may be useful for debugging. The
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optional ``variables`` option can be set to a list of variables to capture (if set). For legacy purposes, this can also
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be a comma-separated string of variable names.
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.. code-block:: yaml
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- type: env
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@@ -109,9 +112,24 @@ be a comma-separated string of variable names.
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- SLURM_CPUS_ON_NODE
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- SLURM_JOBID
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The env plugin captures environment variables set in the job's executing environment.
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By default, it captures **all** environment variables, which is likely excessive but may be useful for debugging. The
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optional ``variables`` option can be set to a list of variables to capture (if set). For legacy purposes, this can also
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be a comma-separated string of variable names.
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cgroup
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~~~~~~
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.. code-block:: yaml
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- type: cgroup
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verbose: false
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version: 2
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params:
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- cpu.stat
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- memory.peak
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The cgroup plugin captures values set by `Linux Control Groups (cgroups)
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<https://docs.kernel.org/admin-guide/cgroup-v2.html>`_. This is most useful if your jobs run in unique per-job Cgroups
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(as Slurm does `if so configured <https://slurm.schedmd.com/cgroups.html>`_).
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@@ -132,15 +150,6 @@ comma-separated string of cgroup parameter names.
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The cgroup plugin works on Linux only.
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.. code-block:: yaml
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- type: cgroup
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verbose: false
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version: 2
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params:
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- cpu.stat
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- memory.peak
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Overriding the Global Job Metrics Configuration
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-----------------------------------------------
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@@ -1,12 +1,14 @@
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"""The module describes the ``core`` job metrics plugin."""
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import datetime
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import json
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import logging
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import time
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import zoneinfo
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from typing import (
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Any,
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Dict,
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List,
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Optional,
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)
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from . import InstrumentPlugin
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@@ -29,6 +31,16 @@ CONTAINER_TYPE = "container_type"
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class CorePluginFormatter(JobMetricFormatter):
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def __init__(self, timezone: Optional[str]):
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self.tz = None
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self.strftime_format = "%Y-%m-%d %H:%M:%S"
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self.__init_tz(timezone)
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def __init_tz(self, timezone: Optional[str]):
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if timezone:
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self.tz = zoneinfo.ZoneInfo(timezone)
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self.strftime_format = "%Y-%m-%d %H:%M:%S %Z (%z)"
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def format(self, key: str, value: Any) -> FormattedMetric:
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if key == CONTAINER_ID:
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return FormattedMetric("Container ID", value)
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@@ -42,9 +54,9 @@ class CorePluginFormatter(JobMetricFormatter):
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elif key == RUNTIME_SECONDS_KEY:
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return FormattedMetric("Job Runtime (Wall Clock)", seconds_to_str(value))
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else:
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# TODO: Use localized version of this from galaxy.ini
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title = "Job Start Time" if key == START_EPOCH_KEY else "Job End Time"
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return FormattedMetric(title, time.strftime("%Y-%m-%d %H:%M:%S", time.localtime(value)))
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dt = datetime.datetime.fromtimestamp(value, tz=self.tz)
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return FormattedMetric(title, dt.strftime(self.strftime_format))
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class CorePlugin(InstrumentPlugin):
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@@ -53,11 +65,15 @@ class CorePlugin(InstrumentPlugin):
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"""
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plugin_type = "core"
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formatter = CorePluginFormatter()
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formatter = None
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default_safety = Safety.SAFE
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def __init__(self, **kwargs):
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pass
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self.__init_formatter(kwargs.get("timezone"))
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def __init_formatter(self, timezone: Optional[str]):
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if CorePlugin.formatter is None:
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CorePlugin.formatter = CorePluginFormatter(timezone)
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def pre_execute_instrument(self, job_directory: str) -> List[str]:
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commands = []
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