Open Microscopy Environment

Hi All,

I just finished the majority of an installation on my production VM -- discussed previously here. I am running CentOS 6.5 with OMERO 5.0.3. I believe that I have everything started; however, I am not able to access the webpage. When I have the nginx default.conf in the conf.d directory, I get a nice default nginx page; however, I get nothing when I moved default.conf elsewhere and replaced it with an omeronginx.conf file generated with:

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$ bin/omero web config nginx --system > omeronginx.conf

I'm not quite sure where to begin hunting for problems, so I was hoping to get some insight from the forum. Here is my diagnostics output:

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===============================================================================
OMERO Diagnostics 5.0.3-ice34-b41
================================================================================
       
Commands:   java -version                  1.7.0     (/usr/bin/java)
Commands:   python -V                      2.6.6     (/usr/bin/python)
Commands:   icegridnode --version          3.4.2     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.4.2     (/usr/bin/icegridadmin)
Commands:   psql --version                 8.4.20    (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 23922, enabled)
Server:     DropBox                        active (pid = 23940, enabled)
Server:     FileServer                     active (pid = 23941, enabled)
Server:     Indexer-0                      active (pid = 23943, enabled)
Server:     MonitorServer                  active (pid = 23944, enabled)
Server:     OMERO.Glacier2                 active (pid = 23947, enabled)
Server:     OMERO.IceStorm                 active (pid = 23956, enabled)
Server:     PixelData-0                    active (pid = 23957, enabled)
Server:     Processor-0                    active (pid = 23980, enabled)
Server:     Tables-0                       active (pid = 23981, enabled)
Server:     TestDropBox                    inactive (enabled)

OMERO:      SSL port                       4064
OMERO:      TCP port                       4063

Log dir:    /home/tech/omero/OMERO.server-5.0.3-ice34-b41/var/log exists

Log files:  Blitz-0.log                    419.0 KB      errors=4    warnings=0   
Log files:  DropBox.log                    9.0 KB        errors=0    warnings=3   
Log files:  FileServer.log                 1.0 KB       
Log files:  Indexer-0.log                  82.0 KB       errors=4    warnings=0   
Log files:  MonitorServer.log              5.0 KB       
Log files:  OMEROweb.log                   0.0 KB       
Log files:  OMEROweb_request.log           0.0 KB       
Log files:  PixelData-0.log                84.0 KB       errors=4    warnings=0   
Log files:  Processor-0.log                6.0 KB        errors=0    warnings=2   
Log files:  Tables-0.log                   6.0 KB        errors=0    warnings=3   
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB       
Log files:  master.out                     0.0 KB       
Log files:  Total size                     0.61 MB


Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_TEMPDIR=/home/tech/omero/OMERO.server/tmp
Environment:PATH=/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/tech/omero/OMERO.server/bin:/home/tech/bin:/home/tech/omero/OMERO.server/bin:/home/tech/omero/OMERO.server/bin:/root/omero/OMERO.server/bin:/home/tech/omero/OMERO.server/bin
Environment:PYTHONPATH=/usr/lib/python2.6:/usr/lib/python2.6:/usr/lib/python2.6:/usr/lib/python2.6:/usr/lib/python2.6:
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib:/usr/share/java:/usr/lib:
Environment:DYLD_LIBRARY_PATH=(unset)     

OMERO data dir: '/OMERO'   Exists? True   Is writable? True
OMERO temp dir: '/home/tech/omero/OMERO.server/tmp/omero/tmp'   Exists? True   Is writable? True   (Size: 0)
OMERO.web status... [RUNNING] (PID 24442)

A quick word about the documentation: I found the OMERO.web deployment page to be a bit on the confusing side -- not because of the terminology, but because of the brevity in some sections. I realize that it is beyond the scope of the documentation to provide detailed instructions for software like nginx, but I would certainly benefit from additional development of some sections.

Thanks!
Blair

brossetti wrote:

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$ bin/omero web config nginx --system > omeronginx.conf

This will generate a configuration that listens on port 8080, so if you go to http://localhost:8080/ you should see OMERO.web. To change the port you can either modify the config file, change

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listen       8080;

to

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listen       80;

or regenerate the config specifying the port you want:

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OMERO.server/bin/omero web config nginx --system --http 80

The original reason for this is so that OMERO.web can be run without admin permissions (since ports below 1024 require admin access). However it's something we could reconsider, especially if --system is passed.

brossetti wrote:A quick word about the documentation: I found the OMERO.web deployment page to be a bit on the confusing side -- not because of the terminology, but because of the brevity in some sections. I realize that it is beyond the scope of the documentation to provide detailed instructions for software like nginx, but I would certainly benefit from additional development of some sections.

Could you elaborate on which sections could do with more explanation, then we can look into improving the text or providing links to external resources. We've got a full example walkthrough for Linux and nginx (CentOS 6 and Ubuntu 14.04) here: https://www.openmicroscopy.org/site/sup ... rough.html

Simon

Ah, that was the trick! I changed the port to 80 and I can now see the webpage. Unfortunately, all of the images and formatting seems to be broken. I wonder if there is a path that is not correctly set?

To be honest, the walkthrough link you provided addresses all of my concerns about the documentation. I have seen this walkthrough page before, but had forgotten where the link was located. I think it would be helpful to add a walkthrough section to the Server Admin page and a link on the Server Installation page. Sometimes, the hardest part is finding the right documentation page to solve your problem

...now to figure out why I don't have any webpage formatting...

Thanks!
Blair

Hi,
It sounds like your static files (images, js, css) are not getting served correctly.

I haven't followed your setup so I don't know what your issue may be, but that's certainly the place to start looking. Good luck!

Will.

Thanks for the tip, Will!

I looked at the nginx error log and I saw a lot of "Permission denied" errors. I was wondering if this might be a permission issue, so I checked out the permissions on my nginx configs:

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-rw-r--r--. 1 root root  979 Apr 26  2013 fastcgi.conf
-rw-r--r--. 1 root root  979 Apr 26  2013 fastcgi.conf.default
-rw-r--r--. 1 root root  909 Apr 26  2013 fastcgi_params
-rw-r--r--. 1 root root  909 Apr 26  2013 fastcgi_params.default
-rw-r--r--. 1 root root 2837 Apr 26  2013 koi-utf
-rw-r--r--. 1 root root 2223 Apr 26  2013 koi-win
-rw-r--r--. 1 root root 3463 Apr 26  2013 mime.types
-rw-r--r--. 1 root root 3463 Apr 26  2013 mime.types.default
-rw-r--r--. 1 root root 1152 Aug 27 10:41 nginx.conf
-rw-r--r--. 1 root root 2685 Apr 26  2013 nginx.conf.default
-rw-r--r--. 1 root root  544 Apr 26  2013 scgi_params
-rw-r--r--. 1 root root  544 Apr 26  2013 scgi_params.default
-rw-r--r--. 1 root root  570 Apr 26  2013 uwsgi_params
-rw-r--r--. 1 root root  570 Apr 26  2013 uwsgi_params.default
-rw-r--r--. 1 root root 3610 Apr 26  2013 win-utf

conf.d:
total 24
drwxr-xr-x. 2 root root 4096 Aug 26 16:50 .
drwxr-xr-x. 3 root root 4096 Aug 27 10:41 ..
-rw-r--r--. 1 root root 1187 Apr 26  2013 default.disabled
-rw-rw-r--. 1 tech tech 1396 Aug 26 15:59 omero_nginx.conf
-rw-r--r--. 1 root root  466 Apr 26  2013 ssl.conf
-rw-r--r--. 1 root root  283 Apr 26  2013 virtual.conf

The only thing that seemed out of place was omero_nginx.conf. I changed the permissions and ownership to

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-rw-r--r--. 1 root root 1396 Aug 26 15:59 omero_nginx.conf

but I still seem to have an issue with serving the static files.

Is there another reason I would be getting these permission denied errors?

Can you check the permissions on the home directory of the user running omero (if it's yourself then "ls -ld $HOME"), is it world executable? Most Linux distributions default to making user directories inaccessible to other users for security, which means nginx might not be able to read the static files.

Simon

Interesting. Here is the info for the user running omero

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drwx------. 4 tech tech 4096 Aug 26 14:09 /home/tech

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chmod a+x /home/tech

as either root or the tech user should do the trick.

Perfecto! I clearly still have a lot to learn about linux.

Thanks!
Blair

After using my production version of OMERO for a bit, I seem to have stumbled across a few more bugs in my installation. I was hoping to get some tips on weeding out these last few issues.

Potential permissions issues:
- The default avatar is broken for new users. Uploading a new avatar will save properly, but the default is currently broken. Also, attempting to crop a new avatar causes a server 500 error page.

- Images appear to be uploading fine and are viewable in merged mode; however, Split Channel mode sits in the Loading state with a broken image.

OMERO Contents
- In another thread, I was given a great recommendation to make symlinks from my OMERO dir to the NSF mount point that I am using for storage.

PaulVanSchayck wrote:Using a NAS as storage is possible. I've had trouble with using CIFS/SMB, using NFS gave good performance. What I've done is kept the /OMERO directory, and only symlinked the Files, ManagedRepository, Pixels and Thumbnails directory towards the NAS mount point. This for performance reasons, as the often accessed cache and lock files are then kept local. Thumbnails for me is also that small that I think I'll move it back to local, but I haven't done that yet. Postgress is running local.

I have done this for /Files, /ManagedRepository, and /Thumbnails; however, /OMERO does not have a /Pixels directory. I'm assuming this is because I have not yet used a feature that requires this directory. For instance, I noticed that the Thumbnails directory was created only after I uploaded an image. I was planning to simply create /Pixels, but was not sure if this would cause problems elsewhere.

Thanks!
Blair