Problem after upgrade 5.06 to 5.1

[phm]

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

Oh is it because I change from fastcgi to fastcgi-tcp ???
Actually my omero config get is :

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.admins=[["Philippe Mailly", "philippe.mailly@college-de-france.fr"]]
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 my web_omero.conf apache config file :

Code: Select all

###
### Stanza for OMERO.web created 2015-04-14 09:50:59.536216
###

FastCGIExternalServer "/opt/OMERO.server/var/omero.fcgi" -host 127.0.0.1:4080 -idle-timeout 60

<Directory "/opt/OMERO.server/var">
    Options -Indexes FollowSymLinks
    Order allow,deny
    Allow from all
</Directory>

<Directory "/opt/OMERO.server/lib/python/omeroweb/static">
    Options -Indexes FollowSymLinks
    Order allow,deny
    Allow from all
</Directory>

<Directory "/opt/OMERO.server/etc/templates/error">
    Options -Indexes FollowSymLinks
    Order allow,deny
    Allow from all
</Directory>

<Location /omero/>
    ErrorDocument 500 /omero/error/maintainance.html
</Location>

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/"


Philippe

[phm]

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

Hi Ola,

Server version: Apache/2.2.15 (Unix)
I shutdown everything and remove django_fcgi.sock and restart all
Now I have only django.pid in /opt/OMERO.server/var

Code: Select all

ls -l /opt/OMERO.server/var/
total 16
-rw-r--r--. 1 omero omero    5 15 avril 12:14 django.pid
drwxr-xr-x. 2 omero omero 4096 14 avril 12:47 log
drwxr-xr-x. 5 omero omero 4096 14 avril 12:47 master
drwxr-xr-x. 3 omero omero 4096 14 avril 12:47 registry


But always the ssl_error_log

Code: Select all

[Wed Apr 15 12:22:48 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 12:22:48 2015] [error] [client 192.168.188.18] FastCGI: incomplete headers (0 bytes) received from server "/opt/OMERO.server/var/omero.fcgi"


[atarkowska]

Actually my omero config get is :

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.admins=[["Philippe Mailly", "philippe.mailly@college-de-france.fr"]]
    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"]]

In 5.1 we simplified web configuration, where omero.web.application_server is no longer needed. You can remove it by running:

Code: Select all

bin/omero config set omero.web.application_server

I'd also recommend to change

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bin/omero config set omero.web.static_url '/omero/static/'

and then apache config

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Alias /omero/static /opt/OMERO.server/lib/python/omeroweb/static

to avoid issue reported in viewtopic.php?f=5&t=7721&p=15272#p15272


Ola

[atarkowska]

And my web_omero.conf apache config file :

Code: Select all

###
### Stanza for OMERO.web created 2015-04-14 09:50:59.536216
###

FastCGIExternalServer "/opt/OMERO.server/var/omero.fcgi" -host 127.0.0.1:4080 -idle-timeout 60

<Directory "/opt/OMERO.server/var">
    Options -Indexes FollowSymLinks
    Order allow,deny
    Allow from all
</Directory>

<Directory "/opt/OMERO.server/lib/python/omeroweb/static">
    Options -Indexes FollowSymLinks
    Order allow,deny
    Allow from all
</Directory>

<Directory "/opt/OMERO.server/etc/templates/error">
    Options -Indexes FollowSymLinks
    Order allow,deny
    Allow from all
</Directory>

<Location /omero/>
    ErrorDocument 500 /omero/error/maintainance.html
</Location>

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/"

Comming back to the error, did you try to change the location of omero.fcgi?
For example to path where you ssl-error_log file is?

FastCGIExternalServer "/path_to_ssl-error_log/omero.fcgi" -host 127.0.0.1:4080 -idle-timeout 60

are you running omero web and apache on the same server right? I am asking because by default FastCGI is looking for a localhost 127.0.0.1:4080. If you think this cause some issues you may change it to 0.0.0.0:4080

Ola

[phm]

Comming back to the error, did you try to change the location of omero.fcgi?
For example to path where you ssl-error_log file is?

FastCGIExternalServer "/path_to_ssl-error_log/omero.fcgi" -host 127.0.0.1:4080 -idle-timeout 60

The two paths are the same in ssl-error_log and omero.conf

are you running omero web and apache on the same server right? I am asking because by default FastCGI is looking for a localhost 127.0.0.1:4080. If you think this cause some issues you may change it to 0.0.0.0:4080

The omero server and apache server are on the same machine.

[phm]

In the documentation you mention :

The default configuration file installed with mod_fastcgi may be incompatible with OMERO. In particular, the FastCGIWrapper option conflicts with FastCGIExternalServer required by OMERO and must be removed or commented out.

Should we just comment out the line concerning the FastCGIWrapper option as this fastcgi.conf file :

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## The User/Group for httpd need to be set before we can load mod_fastcgi,
## but /etc/httpd/conf.d/fastcgi.conf on RHEL gets loaded before
## /etc/httpd/conf/httpd.conf, so we need to set them here :(
## mod_fcgid does not have this bug,
## but it does not handle child PHP processes appropriately per
## http://serverfault.com/questions/303535/a-single-php-fastcgi-process-blocks-all-other-php-requests/305093#305093

User apache
Group apache

LoadModule fastcgi_module modules/mod_fastcgi.so

# dir for IPC socket files
#FastCgiIpcDir /var/run/mod_fastcgi

# wrap all fastcgi script calls in suexec
#FastCgiWrapper On

# global FastCgiConfig can be overridden by FastCgiServer options in vhost config
#FastCgiConfig -idle-timeout 20 -maxClassProcesses 1

# sample PHP config
# see /usr/share/doc/mod_fastcgi-2.4.6 for php-wrapper script
# don't forget to disable mod_php in /etc/httpd/conf.d/php.conf!
#
# to enable privilege separation, add a "SuexecUserGroup" directive
# and chown the php-wrapper script and parent directory accordingly
# see also http://www.brandonturner.net/blog/2009/07/fastcgi_with_php_opcode_cache/
#
#FastCgiServer /var/www/cgi-bin/php-wrapper
#AddHandler php-fastcgi .php
#Action php-fastcgi /cgi-bin/php-wrapper
#AddType application/x-httpd-php .php
#DirectoryIndex index.php
#
#<Location /cgi-bin/php-wrapper>
#    Order Deny,Allow
#    Deny from All
#    Allow from env=REDIRECT_STATUS
#    Options ExecCGI
#    SetHandler fastcgi-script
#</Location>



Philippe

[atarkowska]

Hi Philippe,

We had similar question about FastCGIWrapper in the past see http://www.openmicroscopy.org/community ... f=5&t=7355. Did it help?

My fastcgi.conf on CentOS looks like:

Code: Select all

User apache
Group apache

LoadModule fastcgi_module modules/mod_fastcgi.so

# FastCgiIpcDir /var/run/mod_fastcgi
# FastCgiWrapper On

FastCgiConfig -idle-timeout 20 -maxClassProcesses 1

... and everyting else is commented out


Ola

[phm]

Hi Philippe,

We had similar question about FastCGIWrapper in the past see http://www.openmicroscopy.org/community ... f=5&t=7355. Did it help?

My fastcgi.conf on CentOS looks like:

Code: Select all

User apache
Group apache

LoadModule fastcgi_module modules/mod_fastcgi.so

# FastCgiIpcDir /var/run/mod_fastcgi
# FastCgiWrapper On

FastCgiConfig -idle-timeout 20 -maxClassProcesses 1

... and everyting else is commented out


Ola

Hi Ola

It is like mine.

Philippe

[phm]

Hi all,

I tried something :
If I disable SELinux I got the login page .....

and with some error in log :

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==> /var/log/httpd/ssl_access_log <==
192.168.188.18 - - [15/Apr/2015:17:44:29 +0200] "GET /omero/static/webgateway/img/activity_light_24.png HTTP/1.1" 200 7439
192.168.188.18 - - [15/Apr/2015:17:44:29 +0200] "GET /omero/static/webgateway/img/icon_basket.png HTTP/1.1" 200 1344
192.168.188.18 - - [15/Apr/2015:17:44:29 +0200] "GET /omero/static/3rdparty/jquery.jstree-1.0-rc3/themes/default/style.css HTTP/1.1" 200 7944
192.168.188.18 - - [15/Apr/2015:17:44:29 +0200] "GET /omero/static/3rdparty/jquery.jstree-1.0-rc3/themes/default/throbber.gif HTTP/1.1" 200 4567
192.168.188.18 - - [15/Apr/2015:17:44:29 +0200] "GET /omero/webclient/activities/ HTTP/1.1" 200 534
192.168.188.18 - - [15/Apr/2015:17:44:29 +0200] "GET /omero/webclient/load_data/?view=tree HTTP/1.1" 200 2851
192.168.188.18 - - [15/Apr/2015:17:44:30 +0200] "GET /omero/static/webgateway/img/folder_open.png HTTP/1.1" 200 164
192.168.188.18 - - [15/Apr/2015:17:44:30 +0200] "GET /omero/static/webclient/image/icon_user.png HTTP/1.1" 200 1657
192.168.188.18 - - [15/Apr/2015:17:44:30 +0200] "GET /omero/static/webgateway/img/folder_closed.png HTTP/1.1" 200 159
192.168.188.18 - - [15/Apr/2015:17:44:30 +0200] "GET /omero/static/webclient/image/folder_yellow16.png HTTP/1.1" 200 1186

==> /var/log/httpd/ssl_error_log <==
[Wed Apr 15 17:41:39 2015] [error] [client 192.168.188.18] File does not exist: /var/www/html/static, referer: https://omero.college-de-france.fr/omero/webclient/login/?url=%2Fomero%2Fwebclient%2F


==> /var/log/httpd/ssl_request_log <==
[15/Apr/2015:17:44:29 +0200] 192.168.188.18 TLSv1.2 ECDHE-RSA-AES128-GCM-SHA256 "GET /omero/static/webgateway/img/activity_light_24.png HTTP/1.1" 7439
[15/Apr/2015:17:44:29 +0200] 192.168.188.18 TLSv1.2 ECDHE-RSA-AES128-GCM-SHA256 "GET /omero/static/webgateway/img/icon_basket.png HTTP/1.1" 1344
[15/Apr/2015:17:44:29 +0200] 192.168.188.18 TLSv1.2 ECDHE-RSA-AES128-GCM-SHA256 "GET /omero/static/3rdparty/jquery.jstree-1.0-rc3/themes/default/style.css HTTP/1.1" 7944
[15/Apr/2015:17:44:29 +0200] 192.168.188.18 TLSv1.2 ECDHE-RSA-AES128-GCM-SHA256 "GET /omero/static/3rdparty/jquery.jstree-1.0-rc3/themes/default/throbber.gif HTTP/1.1" 4567
[15/Apr/2015:17:44:29 +0200] 192.168.188.18 TLSv1.2 ECDHE-RSA-AES128-GCM-SHA256 "GET /omero/webclient/activities/ HTTP/1.1" 534
[15/Apr/2015:17:44:29 +0200] 192.168.188.18 TLSv1.2 ECDHE-RSA-AES128-GCM-SHA256 "GET /omero/webclient/load_data/?view=tree HTTP/1.1" 2851
[15/Apr/2015:17:44:30 +0200] 192.168.188.18 TLSv1.2 ECDHE-RSA-AES128-GCM-SHA256 "GET /omero/static/webgateway/img/folder_open.png HTTP/1.1" 164
[15/Apr/2015:17:44:30 +0200] 192.168.188.18 TLSv1.2 ECDHE-RSA-AES128-GCM-SHA256 "GET /omero/static/webclient/image/icon_user.png HTTP/1.1" 1657
[15/Apr/2015:17:44:30 +0200] 192.168.188.18 TLSv1.2 ECDHE-RSA-AES128-GCM-SHA256 "GET /omero/static/webgateway/img/folder_closed.png HTTP/1.1" 159
[15/Apr/2015:17:44:30 +0200] 192.168.188.18 TLSv1.2 ECDHE-RSA-AES128-GCM-SHA256 "GET /omero/static/webclient/image/folder_yellow16.png HTTP/1.1" 1186



Philippe

[atarkowska]

Hi Philippe,

I think I answered some of your posts before on our forum. Which webserver did you use with 5.0.6? I remember you had some issues with nginx and php-fpm. DId you manage to start it or you permanently switched to apache and didn't use nginx anymore?

Disabling SELinux seems to be a big security hole.
Ola