Omero logging¶
All OMERO components written in Java use the
SLF4J logging facade, typically backed
by Logback; all
components written in python use the built-in logging module.
Warning
Refrain from calling logging.basicConfig() anywhere in your
module except in if __name__ == "__main__" blocks.
Java clients¶
Java clients log to $HOME/omero/log. The number of files and their
size are limited.
logback-cli.xml controls the output for the command line importer: all logging goes to standard err, while useful output (pixel ids, or used files) goes to standard out. It is contained within the blitz.jar itself. Therefore, to modify the settings use -Dlogback.configurationFile=/path/to/logback.xml or similar.
OMERO.insight logging is configured via logback.xml which is available in the config/ directory of any OMERO.insight install.
Java servers¶
Java server components are configured by passing
-Dlogback.configurationFile=etc/logback.xml to each Java process.
logback.xml includes the scan attribute so
that changes to the logging configuration are automatically reloaded at
regular intervals.
By default, the output from logback is sent to:
var/log/<servername>.log. Once files reach a size of 500MB, they are
rolled over to <servername>.log.1, <servername>.log.2, etc. Once
the files have rolled over, you can safely delete or compress (bzip2,
gzip, zip) them. Alternatively, once you are comfortable with the
stability of your server, you can either reduce logging or the number
and size of the files kept. Note: if something goes wrong with your
server installation, the log files can be very useful in tracking down
issues.
In addition, each import process logs to a file under the managed
repository which matches the timestamped fileset directory’s name.
For example, if an imported fileset is uploaded to
/OMERO/ManagedRepository/userA_1/2013-06/17/12-00-00.000, then
the log file can be found under
/OMERO/ManagedRepository/userA_1/2013-06/17/12-00-00.000.log.
Python servers¶
Python servers are configured by a call to
omero.util.configure_server_logging(props). The property values are
taken from the configuration file passed to the server via icegridnode.
For example, the config file for Processor-0 can be found in
var/master/servers/Processor-0/config/config. These values come from
etc/grid/templates.xml.
All the “omero.logging.*” properties can be overwritten in your
etc/grid/default.xml file. See the “Profile” properties block
for how to configure for your site.
Similar to logback, logging is configured to be written to
var/log/<servername>.log and to maintain 9 backups of at most 500MB.
stdout and stderr¶
Though all components try to avoid it, some output will still go to
stdout/stderr. On non-Windows systems, all of this output will be sent
to the var/log/master.out and var/log/master.err files.
Windows stdout and stderr¶
On Windows, the state of stdout and stderr is somewhat different. No information will be written to master.out, master.err, or similar files. Instead, what logging is produced will go to the Windows Event Viewer, but finding error situations can be considerably more challenging (See #1449 for more information).
