[ome-users] false positive errors in logs?

Tjelvar Olsson (JIC) Tjelvar.Olsson at jic.ac.uk
Wed May 11 15:38:56 BST 2016

Dear OME team,

When I run the "./bin/omero diagnositcs" command I get a load of, what I presume to be, false positive hits for errors.

omero at v0600 OMERO.server]$ ./bin/omero admin diagnostics

OMERO Diagnostics 5.2.3-ice35-b22

Commands:   java -version                  1.8.0     (/usr/bin/java)
Commands:   python -V                      2.7.5     (/usr/bin/python)
Commands:   icegridnode --version          3.5.1     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.5.1     (/usr/bin/icegridadmin)
Commands:   psql --version                 9.4.5     (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 1847, enabled)
Server:     DropBox                        active (pid = 1859, enabled)
Server:     FileServer                     active (pid = 1860, enabled)
Server:     Indexer-0                      active (pid = 1872, enabled)
Server:     MonitorServer                  active (pid = 1893, enabled)
Server:     OMERO.Glacier2                 active (pid = 1862, enabled)
Server:     OMERO.IceStorm                 active (pid = 1876, enabled)
Server:     PixelData-0                    active (pid = 1880, enabled)
Server:     Processor-0                    active (pid = 1865, enabled)
Server:     Tables-0                       active (pid = 1895, enabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /home/omero/OMERO.server-5.2.3-ice35-b22/var/log exists
Log files:  Blitz-0.log                    1.0 MB        errors=17   warnings=2
Log files:  DropBox.log                    1.0 KB
Log files:  FileServer.log                 0.0 KB
Log files:  Indexer-0.log                  1.0 KB
Log files:  MonitorServer.log              1.0 KB
Log files:  OMEROweb.lock                  0.0 KB
Log files:  OMEROweb.log                   12.0 KB       errors=0    warnings=4
Log files:  OMEROweb_brokenrequest.lock    0.0 KB
Log files:  OMEROweb_brokenrequest.log     0.0 KB
Log files:  PixelData-0.log                2.0 KB
Log files:  Processor-0.log                63.0 KB       errors=17   warnings=0
Log files:  Tables-0.log                   0.0 KB
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB        errors=0    warnings=1
Log files:  master.out                     0.0 KB
Log files:  Total size                     1.25 MB


OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir:'/OMERO'                       Exists? True      Is writable? True
OMERO temp dir:'/home/omero/omero/tmp'        Exists? True      Is writable? True   (Size: 0)

JVM settings: Blitz-${index}                -Xmx1230m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx820m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx1230m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx820m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [ERROR] You are deploying OMERO.web using Apache and mod_wsgi. OMERO.web does not provide any management for the daemon process which communicates with Apache child processes using UNIX sockets to handle a request. Please check Apache directly.
Django version: 1.8.7

I believe the error messages appear when I start the apache daeamon.

Below are sample lines form the Blitz and Processor log files:


2016-05-11 15:26:48,139 INFO  [        ome.services.util.ServiceHandler] (l.Server-5)  Args:    [Error]


2016-05-11 15:26:48,173 INFO  [                omero.processor.ProcessI] (Dummy-5   ) <proc:2238,rc=1,uuid=77a08124-110f-43e1-b351-ed9db64244c6> : Changed job status fro
m Running to Error

Are these messages something to worry about?

If not they make it difficult to spot real errors. Would it be possible to improve the diagnostics command not to highlight these false positives? In the meantime is there some way of making the logging less verbose, for example by only reporting warnings and errors (i.e. excluding INFO messages)?

Kind regards,


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