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[bioontology-support] Help for the NCBO Virtual Appliance

Alex Skrenchuk alex.skrenchuk at stanford.edu
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/unicorn.pid"

¡­¡­



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 {

        daily

        missingok

        rotate 1

        compress

        dateext

        copytruncate

}



                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



-Alex



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



Alex,



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



Ray



From: bioontology-support [
<mailto:bioontology-support-bounces at lists.stanford.edu>
mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of ??
Sent: Wednesday, March 18, 2015 7:50 PM
To:  <mailto:support at bioontology.org> support at bioontology.org
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>
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>
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
schedule.

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

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

Thank you!



BW,

Yue



--
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 hust.edu.cn> wangyue at hust.edu.cn

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