Hi Nate
Thanks for the response.
It was indeed part of the problem. I needed collectl installed on the
individual cluster instances.(job runners)
Seems to be working properly now. I plan to work on using the metrics to
dynamical & intelligently choose job destination of mapping jobs for
example.
Thanks
Z
On 26 Feb 2016 15:21, "Nate Coraor" <nate(a)bx.psu.edu> wrote:
On Wed, Feb 24, 2016 at 5:37 AM, Ziphozakhe Mashologu
<zipho(a)sanbi.ac.za>
wrote:
> Hi All
>
> I have enabled job metrics on a local galaxy install, with latest code
> from dev branch. I have "<collectl /> " uncommented in
job_metrics_conf.xml
> file:
>
> Following are the errors in the logs:
>
> galaxy.jobs.metrics ERROR 2016-02-24 12:28:08,741 Failed to collect job
> properties for plugin
> <galaxy.jobs.metrics.instrumenters.collectl.CollectlPlugin object at
> 0x7ff0b6af3a50>
> Traceback (most recent call last):
> File "dev/galaxy/lib/galaxy/jobs/metrics/__init__.py", line 101, in
> collect_properties
> properties = plugin.job_properties( job_id, job_directory )
> File "dev/galaxy/lib/galaxy/jobs/metrics/instrumenters/collectl.py",
> line 105, in job_properties
> raise Exception( message )
> Exception: Failed to find collectl log in directory
>
> It seems like collectl is looking for the following files:
>
> ['__instrument_collectl_pid', '__instrument_env_vars',
'galaxy.json',
> 'metadata_kwds_HistoryDatasetAssociation_2_1rh1WC',
> 'set_metadata_N05Q24.py', '__instrument_core_galaxy_slots',
> 'metadata_results_HistoryDatasetAssociation_2_33gTDj',
> '__instrument_core_epoch_start', 'galaxy_2.sh',
> 'metadata_out_HistoryDatasetAssociation_2_G5bZYP',
> '__instrument_core_epoch_end', '__instrument_meminfo_meminfo',
> '__instrument_uname_uname',
> 'metadata_override_HistoryDatasetAssociation_2_krldDM',
> 'set_metadata_lpIXS5.py',
'metadata_in_HistoryDatasetAssociation_2_iiYW0t',
> '__instrument_cpuinfo_cpuinfo', 'tool_script.sh',
'galaxy_2.ec']
>
> Which are suppose to exist under
> galaxy/database/job_working_directory/000 job directory.
>
> Has anybody faced anything similar issue or is it a configuration issue,
> or perhaps a known issue with job_metrics (collectl)?
>
> BTW: I installed collectl packages on the host.
>
Hi Zipho,
If this Galaxy instance runs jobs on a cluster, you would also need
collectl to be installed on the cluster.
--nate
>
> Regards
> Zipho
>
>
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