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.


On 26 Feb 2016 15:21, "Nate Coraor" <nate@bx.psu.edu> wrote:
On Wed, Feb 24, 2016 at 5:37 AM, Ziphozakhe Mashologu <zipho@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.




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