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Problem after upgrade 5.06 to 5.1

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Re: Problem after upgrade 5.06 to 5.1

Postby phm » Tue Apr 14, 2015 9:37 am

sbesson wrote:Hi Philippe

the following line in the error log:

Code: Select all
[Tue Apr 14 10:13:42 2015] [error] [client 192.168.188.18] (13)Permission denied: access to /omero denied


hints towards a file permissions issue. Could you check the Apache agent can access the /opt/OMERO.server/var directory? If not, you may want to:

  • either fix the permissions of this folder to allow Apache to read it.
  • or move omero.fcgi to another location that Apache can access, e.g. `/var/run/omero.fcgi`.

Best regards
Sebastien


Hi Sebastien,

I fixed the permissions for /opt/OMERO.server/var now I get Internal server error:
Code: Select all
Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator, root@localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.

More information about this error may be available in the server error log.

And in the ssl-error_log :
Code: Select all
[Tue Apr 14 11:33:07 2015] [error] [client 192.168.188.18] (13)Permission denied: FastCGI: failed to connect to server "/opt/OMERO.server/var/omero.fcgi": connect() failed
[Tue Apr 14 11:33:07 2015] [error] [client 192.168.188.18] FastCGI: incomplete headers (0 bytes) received from server "/opt/OMERO.server/var/omero.fcgi"


However the stanza generation code give this lines is it correct, about the quote in the last line ?
omero.web.prefix=/omero
omero.web.static_url=/static/
Code: Select all
Alias /omero/error /opt/OMERO.server/etc/templates/error
Alias /static /opt/OMERO.server/lib/python/omeroweb/static
Alias /omero "/opt/OMERO.server/var/omero.fcgi/"



Best

Philippe
phm
 
Posts: 185
Joined: Tue Mar 19, 2013 3:39 pm

Re: Problem after upgrade 5.06 to 5.1

Postby atarkowska » Tue Apr 14, 2015 10:08 am

Hi Philippe

Could you please look at the similar thread http://www.openmicroscopy.org/community ... f=5&t=7460 Please not that we changed config in 5.1 that may not exactly match but might give you some idea. Did you try to stop OMERO server and web, delete /opt/OMERO.server/var and start everything again?

if that doesn't help could you please give us an output of bin/omero config get and what permissions are on /opt/OMERO.server/var, is that 755?

Ola
atarkowska
 
Posts: 327
Joined: Mon May 18, 2009 12:44 pm

Re: Problem after upgrade 5.06 to 5.1

Postby phm » Tue Apr 14, 2015 10:54 am

atarkowska wrote:Hi Philippe

Could you please look at the similar thread http://www.openmicroscopy.org/community ... f=5&t=7460 Please not that we changed config in 5.1 that may not exactly match but might give you some idea. Did you try to stop OMERO server and web, delete /opt/OMERO.server/var and start everything again?

if that doesn't help could you please give us an output of bin/omero config get and what permissions are on /opt/OMERO.server/var, is that 755?

Ola


Hi Ola,

After shutting down the server and the web server, deleted /opt/OMERO.server/var I got the maintenance page !!! For link http://omero.server/omero/ but internal error for http://omero.server/omero

omero config get

Code: Select all
omero.data.dir=/OMERO
omero.db.name=omero_database
omero.db.pass=******************
omero.db.user=********************
omero.jvmcfg.percent.blitz=20
omero.jvmcfg.system_memory=32000
omero.web.application_server=fastcgi-tcp
omero.web.apps=["figure", "figure"]
omero.web.debug=False
omero.web.login_logo=/static/webclient/image/logo_CIRB.jpg
omero.web.prefix=/omero
omero.web.public.enabled=False
omero.web.static_url=/static/
omero.web.ui.top_links=[["Data", "webindex", {"title": "Browse Data via Projects, Tags etc"}], ["History", "history", {"title": "History"}], ["Help", "http://help.openmicroscopy.org/", {"target": "new", "title": "Open OMERO user guide in a new tab"}], ["Figure", "figure_index", {"target": "figure"}], ["Figure", "figure_index"]]


And the permission for /opt/OMERO.server/var is
Code: Select all
ls -l /opt/OMERO.server/
total 76
drwxr-xr-x. 2 omero omero  4096 31 mars  18:42 bin
drwxr-xr-x. 6 omero omero  4096 31 mars  18:42 etc
-rw-r--r--. 1 omero omero 27229 31 mars  18:42 history.txt
drwxr-xr-x. 3 omero omero  4096 31 mars  18:40 include
drwxr-xr-x. 8 omero omero  4096 31 mars  18:45 lib
drwxr-xr-x. 2 omero omero  4096 31 mars  18:42 licenses
-rw-r--r--. 1 omero omero 17987 31 mars  18:42 LICENSE.txt
drwxr-xr-x. 4 omero omero  4096 31 mars  18:42 sql
drwxr-xr-x. 5 omero omero  4096 14 avril 12:47 var



Best

Philippe
phm
 
Posts: 185
Joined: Tue Mar 19, 2013 3:39 pm

Re: Problem after upgrade 5.06 to 5.1

Postby atarkowska » Tue Apr 14, 2015 11:08 am

Hi Philippe,

What Apache error/access log says?

Ola
atarkowska
 
Posts: 327
Joined: Mon May 18, 2009 12:44 pm

Re: Problem after upgrade 5.06 to 5.1

Postby phm » Tue Apr 14, 2015 11:14 am

atarkowska wrote:Hi Philippe,

What Apache error/access log says?

Ola


Hi Ola,

tail ssl_access_log
Code: Select all
192.168.188.18 - - [14/Apr/2015:13:09:36 +0200] "GET /omero/ HTTP/1.1" 500 27559
192.168.188.18 - - [14/Apr/2015:13:10:07 +0200] "GET /omero HTTP/1.1" 500 627


tail ssl_request_log
Code: Select all
[14/Apr/2015:13:09:36 +0200] 192.168.188.18 TLSv1.2 ECDHE-RSA-AES128-GCM-SHA256 "GET /omero/ HTTP/1.1" 27559
[14/Apr/2015:13:10:07 +0200] 192.168.188.18 TLSv1.2 ECDHE-RSA-AES128-GCM-SHA256 "GET /omero HTTP/1.1" 627


tail ssl_error_log
Code: Select all
[Tue Apr 14 13:10:07 2015] [error] [client 192.168.188.18] (13)Permission denied: FastCGI: failed to connect to server "/opt/OMERO.server/var/omero.fcgi": connect() failed
[Tue Apr 14 13:10:07 2015] [error] [client 192.168.188.18] FastCGI: incomplete headers (0 bytes) received from server "/opt/OMERO.server/var/omero.fcgi"


ls -l /opt/OMERO.server/var/
total 16
-rw-r--r--. 1 omero omero 5 14 avril 12:47 django.pid
drwxrwxr-x. 2 omero omero 4096 14 avril 12:47 log
drwxrwxr-x. 5 omero omero 4096 14 avril 12:47 master
drwxrwxr-x. 3 omero omero 4096 14 avril 12:47 registry

Best
Philippe
phm
 
Posts: 185
Joined: Tue Mar 19, 2013 3:39 pm

Re: Problem after upgrade 5.06 to 5.1

Postby atarkowska » Wed Apr 15, 2015 8:54 am

HI Philippe,

could you give one more try and double check if the entire path /opt/OMERO.server has permissions set to 755 ?
If any of the top folders not allow apache_user to see it it won't work

Ola
atarkowska
 
Posts: 327
Joined: Mon May 18, 2009 12:44 pm

Re: Problem after upgrade 5.06 to 5.1

Postby atarkowska » Wed Apr 15, 2015 9:07 am

Could you also check if all your processes are started correctly. Ideally if you could stop omero.web then

Code: Select all
ps aux | grep 'django'


If you see anything like that please kill them

Code: Select all
omero   30319  0.0  0.0 301652 67004 ?        S    Apr14   0:00 python manage.py runfcgi workdir=./ method=prefork host=127.0.0.1 port=4080 pidfile=/opt/OMERO-server/var/django.pid daemonize=true maxchildren=5 minspare=1 maxspare=5 maxrequests=400


Once you are sure nothing is run restart apache (not reload) and start omero.web by bin/omero web start

Let us know if that helps

Ola
atarkowska
 
Posts: 327
Joined: Mon May 18, 2009 12:44 pm

Re: Problem after upgrade 5.06 to 5.1

Postby phm » Wed Apr 15, 2015 9:24 am

atarkowska wrote:Could you also check if all your processes are started correctly. Ideally if you could stop omero.web then

Code: Select all
ps aux | grep 'django'


If you see anything like that please kill them

Code: Select all
omero   30319  0.0  0.0 301652 67004 ?        S    Apr14   0:00 python manage.py runfcgi workdir=./ method=prefork host=127.0.0.1 port=4080 pidfile=/opt/OMERO-server/var/django.pid daemonize=true maxchildren=5 minspare=1 maxspare=5 maxrequests=400


Once you are sure nothing is run restart apache (not reload) and start omero.web by bin/omero web start

Let us know if that helps

Ola



Hi Ola,

- I checked all /opt/OMERO.server as 755
- shutdown omero and omero web
Code: Select all
omero admin stop
omero web stop
ps aux | grep 'django' give nothing.


- stop and start apache
Code: Select all
/etc/init.d/httpd stop
/etc/init.d/httpd start


I have 6 omero processes
Code: Select all
ps aux | grep 'django'
omero    48641  0.0  0.1 298904 64324 ?        S    11:14   0:00 python manage.py runfcgi workdir=./ method=prefork host=127.0.0.1 port=4080 pidfile=/opt/OMERO.server/var/django.pid daemonize=true maxchildren=5 minspare=1 maxspare=5 maxrequests=400
omero    48642  0.0  0.1 298904 63756 ?        S    11:14   0:00 python manage.py runfcgi workdir=./ method=prefork host=127.0.0.1 port=4080 pidfile=/opt/OMERO.server/var/django.pid daemonize=true maxchildren=5 minspare=1 maxspare=5 maxrequests=400
omero    48643  0.0  0.1 298904 63760 ?        S    11:14   0:00 python manage.py runfcgi workdir=./ method=prefork host=127.0.0.1 port=4080 pidfile=/opt/OMERO.server/var/django.pid daemonize=true maxchildren=5 minspare=1 maxspare=5 maxrequests=400
omero    48644  0.0  0.1 298904 63760 ?        S    11:14   0:00 python manage.py runfcgi workdir=./ method=prefork host=127.0.0.1 port=4080 pidfile=/opt/OMERO.server/var/django.pid daemonize=true maxchildren=5 minspare=1 maxspare=5 maxrequests=400
omero    48645  0.0  0.1 298904 63760 ?        S    11:14   0:00 python manage.py runfcgi workdir=./ method=prefork host=127.0.0.1 port=4080 pidfile=/opt/OMERO.server/var/django.pid daemonize=true maxchildren=5 minspare=1 maxspare=5 maxrequests=400
omero    48646  0.0  0.1 298904 63760 ?        S    11:14   0:00 python manage.py runfcgi workdir=./ method=prefork host=127.0.0.1 port=4080 pidfile=/opt/OMERO.server/var/django.pid daemonize=true maxchildren=5 minspare=1 maxspare=5 maxrequests=400
root     48652  0.0  0.0 105316   928 pts/0    S+   11:14   0:00 grep django


And unfortunately Always the maintenance page with the permission error in ssl-error_log :
By the way I didn't have omero.fcgi in /opt/OMERO.server/var folder but a django_fcgi.sock ???

Code: Select all
[Wed Apr 15 11:22:04 2015] [error] [client 192.168.188.18] (13)Permission denied: FastCGI: failed to connect to server "/opt/OMERO.server/var/omero.fcgi": connect() failed
[Wed Apr 15 11:22:04 2015] [error] [client 192.168.188.18] FastCGI: incomplete headers (0 bytes) received from server "/opt/OMERO.server/var/omero.fcgi"


Best

Philippe
phm
 
Posts: 185
Joined: Tue Mar 19, 2013 3:39 pm

Re: Problem after upgrade 5.06 to 5.1

Postby atarkowska » Wed Apr 15, 2015 9:35 am

omero.fcgi/ doesn't actually have to exist. It's just a URL used by the Web server internally, a hook for signifying which requests at a URL should be handled by FastCGI.

Hmm I can see some difference in the output you gave us before. One of your comment above was showwing that you have pidfile in /opt/OMERO.server/var/django.pid


ls -l /opt/OMERO.server/var/
total 16
-rw-r--r--. 1 omero omero 5 14 avril 12:47 django.pid
drwxrwxr-x. 2 omero omero 4096 14 avril 12:47 log
drwxrwxr-x. 5 omero omero 4096 14 avril 12:47 master
drwxrwxr-x. 3 omero omero 4096 14 avril 12:47 registry


what is correct as seen in:

Code: Select all
omero    48644  0.0  0.1 298904 63760 ?        S    11:14   0:00 python manage.py runfcgi workdir=./ method=prefork host=127.0.0.1 port=4080 pidfile=/opt/OMERO.server/var/django.pid daemonize=true maxchildren=5 minspare=1 maxspare=5 maxrequests=400


you don't see that file anymore?

Ola
atarkowska
 
Posts: 327
Joined: Mon May 18, 2009 12:44 pm

Re: Problem after upgrade 5.06 to 5.1

Postby atarkowska » Wed Apr 15, 2015 9:43 am

You definitely shouldn't see django_fcgi.sock if you are running a threaded server on a TCP port

Can I check which apache version you use?

Ola
atarkowska
 
Posts: 327
Joined: Mon May 18, 2009 12:44 pm

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