gistfile1.txt

<?xml version="1.0"?>
<!-- If job_metrics.xml exists, this file will define the default job metric
     plugin used for all jobs. Individual job_conf.xml destinations can
     disable metric collection by setting metrics="off" on that destination.
     The metrics attribute on destination definition elements can also be
     a path - in which case that XML metrics file will be loaded and used for
     that destination. Finally, the destination element may contain a job_metrics
     child element (with all options defined below) to define job metrics in an
     embedded manner directly in the job_conf.xml file.
-->
<job_metrics>
  <!-- Each element in this file corresponds to a job instrumentation plugin
       used to generate metrics in lib/galaxy/jobs/metrics/instrumenters. -->

  <!-- Core plugin captures Galaxy slots, start and end of job (in seconds
       since epoch) and computes runtime in seconds. -->
  <core />
  
  <!-- Uncomment to dump processor count for each job - linux only. -->
  <cpuinfo />
  <!-- Uncomment to dump information about all processors for for each
       job - this is likely too much data. Linux only. -->
  <!-- <cpuinfo verbose="true" /> -->

  <!-- Uncomment to dump system memory information for each job - linux
       only. -->
  <meminfo />

  <!-- Uncomment to record operating system each job is executed on - linux
       only. -->
  <!-- <uname /> -->

  <!-- Uncomment following to enable plugin dumping complete environment 
       for each job, potentially useful for debuging -->
  <!-- <env /> -->
  <!-- env plugin can also record more targetted, obviously useful variables
       as well. -->
  <!-- <env variables="HOSTNAME,SLURM_CPUS_ON_NODE,SLURM_JOBID" /> -->

  <collectl />
  <!-- Collectl (http://collectl.sourceforge.net/) is a powerful monitoring
       utility capable of gathering numerous system and process level
       statistics of running applications. The Galaxy collectl job metrics
       plugin by default will grab a variety of process level metrics
       aggregated across all processes corresponding to a job, this behavior
       is highly customiziable - both using the attributes documented below
       or simply hacking up the code in lib/galaxy/jobs/metrics.

       Warning: In order to use this plugin collectl must be available on the 
       compute server the job runs on and on the local Galaxy server as well
       (unless in this latter case summarize_process_data is set to False).

       Attributes (the follow describes attributes that can be used with
       the collectl job metrics element above to modify its behavior).

       'summarize_process_data': Boolean indicating whether to run collectl
              in playback mode after jobs complete and gather process level
              statistics for the job run. These statistics can be customized
              with the 'process_statistics' attribute. (defaults to True)

       'saved_logs_path': If set (it is off by default), all collectl logs
              will be saved to the specified path after jobs complete. These
              logs can later be replayed using collectl offline to generate
              full time-series data corresponding to a job run.

       'subsystems': Comma separated list of collectl subystems to collect
              data for. Plugin doesn't currently expose all of them or offer 
              summary data for any of them except 'process' but extensions 
              would be welcome. May seem pointless to include subsystems 
              beside process since they won't be processed online by Galaxy -
              but if 'saved_logs_path' these files can be played back at anytime.
              
              Available subsystems - 'process', 'cpu', 'memory', 'network',
              'disk', 'network'. (Default 'process').

              Warning: If you override this - be sure to include 'process'
              unless 'summarize_process_data' is set to false.

       'process_statistics': If 'summarize_process_data' this attribute can be
              specified as a comma separated list to override the statistics
              that are gathered. Each statistics is of the for X_Y where X
              if one of 'min', 'max', 'count', 'avg', or 'sum' and Y is a
              value from 'S', 'VmSize', 'VmLck', 'VmRSS', 'VmData', 'VmStk',
              'VmExe', 'VmLib', 'CPU', 'SysT', 'UsrT', 'PCT', 'AccumT' 'WKB',
              'RKBC', 'WKBC', 'RSYS', 'WSYS', 'CNCL', 'MajF', 'MinF'. Consult
              lib/galaxy/jobs/metrics/collectl/processes.py for more details
              on what each of these resource types means.

              Defaults to 'max_VmSize,avg_VmSize,max_VmRSS,avg_VmRSS,sum_SysT,sum_UsrT,max_PCT avg_PCT,max_AccumT,sum_RSYS,sum_WSYS'
              as variety of statistics roughly describing CPU and memory
              usage of the program and VERY ROUGHLY describing I/O consumption.

       'procfilt_on': By default Galaxy will tell collectl to only collect
             'process' level data for the current user (as identified)
             by 'username' (default) - this can be disabled by settting this
             to 'none' - the plugin will still only aggregate process level
             statistics for the jobs process tree - but the additional
             information can still be used offline with 'saved_logs_path'
             if set. Obsecurely, this can also be set 'uid' to identify
             the current user to filter on by UID instead of username -
             this may needed on some clusters(?).

       'interval': The time (in seconds) between data collection points.
              Collectl uses a variety of different defaults for different
              subsystems if this is not set, but process information (likely
              the most pertinent for Galaxy jobs will collect data every
              60 seconds).

       'flush': Interval (in seconds I think) between when collectl will
              flush its buffer to disk. Galaxy overrides this to disable
              flushing by default if not set. 

       'local_collectl_path', 'remote_collectl_path', 'collectl_path':
              By default, jobs will just assume collectl is on the PATH, but 
              it can be overridden with 'local_collectl_path' and 
              'remote_collectl_path' (or simply 'collectl_path' if it is not 
              on the path but installed in the same location both locally and 
              remotely).

        There are more and more increasingly obsecure options including -
        log_collectl_program_output, interval2, and interval3. Consult
        source code for more details.
  -->
</job_metrics>