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[bioontology-support] Help for the NCBO Virtual Appliance

Alex Skrenchuk alex.skrenchuk at
Fri Mar 20 17:14:51 PDT 2015

Hi Yue,

Excessive logging is an issue with the VM which will be addressed in the
next release of the appliance.

In the mean time I can give you a couple of tips on how to reduce it.

Prior to making changes on the appliance you should top all bioportal
related services:

sudo /usr/local/bin/bpstop

1.       Delete existing logs:

sudo find /var/log ¨Ctype f ¨Cdelete

2.       Disable stderr log for unicorn:

Edit  /srv/ncbo/ontologies_api/current/config/unicorn.rb

and comment out  stderr_path "log/unicorn.stderr.log" line:

application  = 'ontologies_api'

app_path = "/srv/ncbo/#{application}"

working_directory "#{app_path}/current/"

worker_processes 8

timeout 60

preload_app true

user "ncbobp", "ncbobp"

#stderr_path "log/unicorn.stderr.log"

stdout_path "log/unicorn.stdout.log"

pid "/var/run/unicorn/"


3.       Reduce retention time for rotated logs:

Edit /etc/logrotate.d/unicorn file and change line ¡°rotate 365¡± to
¡°rotate 1¡±:

/srv/ncbo/ontologies_api/current/log/*.log {



        rotate 1





                You can do the same for /etc/logrotate.d/httpd,
/etc/logrotate.d/tomcat6  and /etc/logrotate.d/4s-httpd

Finally start all services:

sudo /usr/local/bin/bpstart


From: Ray Fergerson [mailto:ray.fergerson at]
Sent: Friday, March 20, 2015 1:49 PM
To: Íõ«h; Alex Skrenchuk
Subject: RE: [bioontology-support] Help for the NCBO Virtual Appliance


Do you understand this? Can you help sort out the problem?


From: bioontology-support [
<mailto:bioontology-support-bounces at>
mailto:bioontology-support-bounces at] On Behalf Of ??
Sent: Wednesday, March 18, 2015 7:50 PM
To:  <mailto:support at> support at
Subject: [bioontology-support] Help for the NCBO Virtual Appliance

Hi, there

I have already installed vmware and my own ncbo virtual appliance in my
local server.

My local server is (1) 6 CPU (2) 12GB RAM (3) 1TB hard disk.

The vmware is about 26GB hard disk space.

And I also manually parsed the ontology, DOID, in the vmware and I can
access the web page "http://the_vmware_offered_ip/annotator".

All the steps above is succeed.

But, when I use the NCBO virtual appliance to find DOID terms from mass
text data using my java code request the "
http://the_vmware_offered_ip/annotator", so mething went wrong.

Over a period of time (one day or more), the "
http://the_vmware_offered_ip/annotator" could not get annotations, but the
vmware looks like normal.

However, I checked the disk capacity of vmware, it shows the 26GB hard
disk space is fully used.

What's more, when I first parsed the DOID into the vmware, it shows only
4.1GB of hard disk space is used.

Also, I find the unicorn.stderr.log, as an example, is 11GB in the path of
"/var/log/unicorn"(the attachment is part of the unicorn.stderr.log),
which came out when running my code.

I don't know what's wrong.

This problem confused me for few days, and it really affecting my work

So please help me. And I hope the NCBO virtual appliance can work all the

If you have something confused, let me know. Please keep in touch.

Thank you!



Yue Wang

School of Electronic Information and Communications
Huazhong University  of Science and Technology

1037 Luoyu Road

Wuhan, Hubei 430030, China
Mobile 86-13554186936
Email    <mailto:wangyue at> wangyue at

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