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Remove info about cron not like . in filename.
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kjolley committed Oct 28, 2019
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Showing 1 changed file with 16 additions and 9 deletions.
25 changes: 16 additions & 9 deletions installation.rst
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Expand Up @@ -192,27 +192,34 @@ To run plugins that require a long time to complete their analyses, an offline j
jobs_db=bigsdb_jobs
max_load=8

The jobs script will not process a job if the server's load average (over the last minute) is higher than the max_load parameter. This should be set higher than the number of processor cores or you may find that jobs never run on a busy server. Setting it to double the number of cores is probably a good starting point.
The jobs script will not process a job if the server's load average (over
the last minute) is higher than the max_load parameter. This should be
set higher than the number of processor cores or you may find that jobs
never run on a busy server. Setting it to double the number of cores is
probably a good starting point.

4. Copy the job_logging.conf file to the /etc/bigsdb directory.

5. Set the script to run frequently (preferably every minute) from CRON. Note that CRON does not like '.' in executable filenames, so either rename the script to 'bigsjobs' or create a symlink and call that from CRON, e.g.::
5. Set the script to run frequently (preferably every minute) from CRON. ::

copy bigsjobs.pl to /usr/local/bin
sudo ln -s /usr/local/bin/bigsjobs.pl /usr/local/bin/bigsjobs

You should install xvfb, which is a virtual X server that may be required for third party applications called from plugins. This is required, for example, for calling splitstree4 from the Genome Comparator plugin.
You should install xvfb, which is a virtual X server that may be required
for third party applications called from plugins. This is required, for
example, for calling splitstree4 from the Genome Comparator plugin.

Add the following to /etc/crontab:::

* * * * * bigsdb xvfb-run -a /usr/local/bin/bigsjobs
* * * * * bigsdb xvfb-run -a /usr/local/bin/bigsjobs.pl

(set to run every minute from the 'bigsdb' user account).

If you'd like to run this more frequently, e.g. every 30 seconds, multiple entries can be added to CRON with an appropriate sleep prior to running, e.g.::
If you'd like to run this more frequently, e.g. every 30 seconds, multiple
entries can be added to CRON with an appropriate sleep prior to running,
e.g.::

* * * * * bigsdb xvfb-run -a /usr/local/bin/bigsjobs
* * * * * bigsdb sleep 30;xvfb-run -a /usr/local/bin/bigsjobs
* * * * * bigsdb xvfb-run -a /usr/local/bin/bigsjobs.pl
* * * * * bigsdb sleep 30;xvfb-run -a /usr/local/bin/bigsjobs.pl

6. Create a log file, bigsdb_jobs.log, in /var/log owned by 'bigsdb', e.g.::

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