Ok. Thats your problem I think.

Please note that following directories and everything inside them( assuming standard install, if not adjust your paths. ) need to be owned by user & group koha

/var/lib/koha
/var/run/koha
/var/lock/koha
/var/log/koha


Did you follow section 6 in the INSTALL.debian document in the directory where you downloaded koha?

Specifically while testing try this :

sudo -u koha zebrasrv -f /etc/koha/koha-conf.xml
    (note that the path to koha-conf.xml may be different if you chose a dev install, and that -u koha refers to the user you set up in step 2.3)

Then run ps aux|grep koha again. You should see atleast three lines of output. If yes, follow sections 6.2.1 & 6.2.2 to configure zebra server to run automatically and run zebra indexing through crontab on a set frequency.


Regards,
Koustubha Kale
Anant Corporation

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