Open Microscopy Environment

Hi: I've been having a lot of trouble with omeroweb after an upgrade to omero 5.2.4
(on a Mac after an upgrade to 10.11)

Initially, I was trying to move from a 5.1 to a 5.2.4 install and it just wasn't working.

I kept getting errors in the /var/log/apache like this...

error_log

Fatal Python error: PyThreadState_Get: no current thread
Truncated or oversized response headers received from daemon process 'omeroweb' /usr/local/Cellar/omero52/5.2.4/lib/python/omeroweb/wsgi.py
AH00052: child pid 66761 exit signal Abort trap (6)

I could connect via omero.insight and command line just fine.

So, thinking I probably missed some sort of python library, I started fresh on an old MacBook Pro.
I followed the Mac/Homebrew instructions as precisely as I could, taking notes when anything deviated from the norm at all.*
* (Happy to provide those too...pytables install broke, but I found a work around.)
I set up apache, and was able to see a "it works" page in both localhost and a different computer.
I was able to write a simple wsgi "hello world" script in another place and get it working. WSGI is working okay.
I was able to switch to /var/run for the wsgi.

But I'm still getting the same errors when it comes to omero's wsgi running on Apache2.4 on a Mac running 10.11.
Something isn't working when it comes to Apache omeroweb using mod_wsgi.

Maybe doing something again and expecting different results is crazy, but I'm out of options. Something isn't right here.

omero admin diag
********************************

================================================================================
OMERO Diagnostics 5.2.4-ice35
================================================================================

Commands: java -version 1.8.0 (/usr/bin/java)
Commands: python -V 2.7.12 (/usr/local/bin/python -- 2 others)
Commands: icegridnode --version 3.5.1 (/usr/local/bin/icegridnode)
Commands: icegridadmin --version 3.5.1 (/usr/local/bin/icegridadmin)
Commands: psql --version 9.3.13 (/usr/local/bin/psql)

Server: icegridnode running
Server: Blitz-0 active (pid = 6607, enabled)
Server: DropBox active (pid = 6609, enabled)
Server: FileServer active (pid = 6608, enabled)
Server: Indexer-0 active (pid = 6610, enabled)
Server: MonitorServer active (pid = 6611, enabled)
Server: OMERO.Glacier2 active (pid = 6612, enabled)
Server: OMERO.IceStorm active (pid = 6613, enabled)
Server: PixelData-0 active (pid = 6614, enabled)
Server: Processor-0 active (pid = 6615, enabled)
Server: Tables-0 active (pid = 6616, enabled)
Server: TestDropBox inactive (enabled)

Log dir: /usr/local/Cellar/omero52/5.2.4/var/log exists
Log files: --encoding=UTF8 14.0 MB
Log files: Blitz-0.log 124.0 MB errors=1331 warnings=1678
Log files: DropBox.log 100.0 KB errors=104 warnings=50
Log files: FileServer.log 17.0 KB
Log files: Indexer-0.log 1.0 MB errors=618 warnings=0
Log files: MonitorServer.log 31.0 KB errors=30 warnings=0
Log files: OMEROweb.lock 0.0 KB
Log files: OMEROweb.log 792.0 KB errors=0 warnings=348
Log files: OMEROweb_brokenrequest.lock 0.0 KB
Log files: OMEROweb_brokenrequest.log 10.0 KB errors=0 warnings=67
Log files: PixelData-0.log 1.0 MB errors=619 warnings=9
Log files: Processor-0.log 2.0 MB errors=745 warnings=223
Log files: Tables-0.log 10.0 KB errors=0 warnings=4
Log files: TestDropBox.log n/a
Log files: master.err 8.0 MB errors=4106 warnings=4269
Log files: master.out 0.0 KB
Log files: nginx_access.log 0.0 KB
Log files: nginx_error.log 0.0 KB
Log files: omero_06272016_omero.db.dump 14.0 MB
Log files: Total size 168.29 MB


Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/usr/local/bin:/usr/local/sbin:/usr/local/lib/node_modules:/usr/local/Cellar/postgresql/9.5.3/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin
Environment:PYTHONPATH=/usr/local/lib/python2.7:/usr/local/opt/omero52/lib/python
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir:'/Volumes/Pegasus/omero/OMERO.data' Exists? True Is writable? True
OMERO temp dir:'/Users/gilroylab/omero/tmp' Exists? True Is writable? True (Size: 0)

JVM settings: Blitz-${index} -Xmx17179m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx3435m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx5153m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx3435m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [NOT STARTED]
Django version: 1.8.13
================================================================================
OMERO Diagnostics 5.2.4-ice35
================================================================================

Commands: java -version 1.8.0 (/usr/bin/java)
Commands: python -V 2.7.12 (/usr/local/bin/python -- 2 others)
Commands: icegridnode --version 3.5.1 (/usr/local/bin/icegridnode)
Commands: icegridadmin --version 3.5.1 (/usr/local/bin/icegridadmin)
Commands: psql --version 9.3.13 (/usr/local/bin/psql)

Server: icegridnode running
Server: Blitz-0 active (pid = 6607, enabled)
Server: DropBox active (pid = 6609, enabled)
Server: FileServer active (pid = 6608, enabled)
Server: Indexer-0 active (pid = 6610, enabled)
Server: MonitorServer active (pid = 6611, enabled)
Server: OMERO.Glacier2 active (pid = 6612, enabled)
Server: OMERO.IceStorm active (pid = 6613, enabled)
Server: PixelData-0 active (pid = 6614, enabled)
Server: Processor-0 active (pid = 6615, enabled)
Server: Tables-0 active (pid = 6616, enabled)
Server: TestDropBox inactive (enabled)

Log dir: /usr/local/Cellar/omero52/5.2.4/var/log exists
Log files: --encoding=UTF8 14.0 MB
Log files: Blitz-0.log 124.0 MB errors=1331 warnings=1678
Log files: DropBox.log 100.0 KB errors=104 warnings=50
Log files: FileServer.log 17.0 KB
Log files: Indexer-0.log 1.0 MB errors=618 warnings=0
Log files: MonitorServer.log 31.0 KB errors=30 warnings=0
Log files: OMEROweb.lock 0.0 KB
Log files: OMEROweb.log 792.0 KB errors=0 warnings=348
Log files: OMEROweb_brokenrequest.lock 0.0 KB
Log files: OMEROweb_brokenrequest.log 10.0 KB errors=0 warnings=67
Log files: PixelData-0.log 1.0 MB errors=619 warnings=9
Log files: Processor-0.log 2.0 MB errors=745 warnings=223
Log files: Tables-0.log 10.0 KB errors=0 warnings=4
Log files: TestDropBox.log n/a
Log files: master.err 8.0 MB errors=4106 warnings=4269
Log files: master.out 0.0 KB
Log files: nginx_access.log 0.0 KB
Log files: nginx_error.log 0.0 KB
Log files: omero_06272016_omero.db.dump 14.0 MB
Log files: Total size 168.29 MB


Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/usr/local/bin:/usr/local/sbin:/usr/local/lib/node_modules:/usr/local/Cellar/postgresql/9.5.3/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin
Environment:PYTHONPATH=/usr/local/lib/python2.7:/usr/local/opt/omero52/lib/python
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir:'/Volumes/Pegasus/omero/OMERO.data' Exists? True Is writable? True
OMERO temp dir:'/Users/gilroylab/omero/tmp' Exists? True Is writable? True (Size: 0)

JVM settings: Blitz-${index} -Xmx17179m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx3435m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx5153m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx3435m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [NOT STARTED]
Django version: 1.8.13

Hi

Could you give us more information on how you upgraded your laptop to 10.11? Did you also upgrade/recompile all your homebrew packages?

Simon

it was a straight OS upgrade using the Mac App Store's version of Mac OS X.

After the install, homebrew and postgresql weren't working so I had to get them working again. I did manage to do that, but I'm afraid I'm a bit short on details. I've been fighting with this for the better part of a month.

brew is working for downloading and updating. Is there a specific set of upgrade instructions for upgrading brew post-OS upgrade?

Last time I did a Mac OS upgrade I ended up deleting my entire homebrew installation and reinstalling everything. There were several libraries in homebrew packages which were compiled against a particular version of an OS library, and after attempting to fix them individually I just deleted the lot.

If you're not in a rush wait and see if someone else has a better suggestion.

Ergh. Well, that's messy.

I just looked up what you are supposed to do after an OS upgrade. I had done the brew update and brew doctor, but today was the first day I saw brew upgrade.

I did brew upgrade, and it upgraded a bunch of stuff. Super.

Still doesn't work.

I'm debating starting fresh; I'm imaging my test laptop right now in anticipation.

okay, on my newly imaged development machine, I think that I needed to pay extra close attention to the Mac OS X El Capitan variants to the make script of the mod_wsgi installation from source on this web page. (In case it helps anyone...

./configure --with-python=/usr/local/bin/python
make
make install LIBEXECDIR=/usr/local/httpd/modules

this was from: https://modwsgi.readthedocs.io/en/devel ... acosx.html

When I did it this way, I was able to open the omero mod_wsgi website on my development machine.

(I also had to change my apache24 conf file for the WSGISocket to go to /var/run, but that's pretty obvious.)

Okay, now off to try this in production.

Thank you for the update, good luck with it! Do let us know if you need any further help with deploying OMERO.

Cheers,
Mark