I noticed what could be an interesting point.
In the /Library/Tomcat/bin/catalina.sh file is setted the following line as 
recommended:
CATALINA_OPTS="-Xmx1G 
-Dorg.apache.jasper.compiler.Parser.STRICT_QUOTE_ESCAPING=false 
-Dcom.sun.media.jai.disableMediaLib=true -Djava.awt.headless=true"

but when I type ps -e | grep Tomcat, it gives the following:
14952 ttys000    5:31.03 /Library/Java/Home/bin/java 
-Djava.util.logging.config.file=/Library/Tomcat/conf/logging.properties 
-Xms512m -Xmx1G 
-Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m 
-Xmx1G -Dorg.apache.jasper.compiler.Parser.STRICT_QUOTE_ESCAPING=false 
-Dcom.sun.media.jai.disableMediaLib=true 
-Djava.endorsed.dirs=/Library/Tomcat/endorsed -classpath 
/Library/Tomcat/bin/bootstrap.jar -Dcatalina.base=/Library/Tomcat 
-Dcatalina.home=/Library/Tomcat -Djava.io.tmpdir=/Library/Tomcat/temp 
org.apache.catalina.startup.Bootstrap start
16845 ttys000    0:00.00 grep Tomcat

Thus the -Djava.awt.headless=true setting does not appear here.
Would it mean that the setting comes from somewhere else then the 
/Library/Tomcat/bin/catalina.sh file ?

If I do a modification on the /Library/Tomcat/bin/catalina.sh file, at what 
stage should I rester the installation procedure ? 
Just restart Tomcat (/Library/Tomcat/bin/shutdown.sh and then 
/Library/Tomcat/bin/startup.sh) ?
The other thing I noticed, confirming that the Djava.awt.headless option is not 
taken in account is that I get a windowed application named 
org.apache.catalina.startup.Bootstrap that remains as mentioned by Jari.

What surprises me is that when I type the command :
/Library/Tomcat/bin/shutdown.sh I get the following output:

Using CATALINA_BASE:   /Library/Tomcat
Using CATALINA_HOME:   /Library/Tomcat
Using CATALINA_TMPDIR: /Library/Tomcat/temp
Using JRE_HOME:        /Library/Java/Home
Using CLASSPATH:       /Library/Tomcat/bin/bootstrap.jar
Using CATALINA_PID:    /Library/Tomcat/catalina_pid.txt
PID file found but no matching process was found. Stop aborted.

And the Java process is still running…


Other informations:

Both /Library/Tomcat/work/Catalina/localhost/base2 and 
/Library/Tomcat/work/Catalina/localhost/_/ directories are empty

I have set the owner of /Library/Tomcat/work directory and inner files to 
_appserver user and _appserveradm group as defined for the tomcat process.
The other odd thing I am just discovering is that when typing the command line 
'ps auxw | grep tomcat'
I only get one time out of three the shell process 
/Library/Tomcat/bin/tomcat-launchd.sh
And each time it has an other pid. Is it supposed to be so ?
That would explain why when I want to shutdown the Tomcat process it is aborted.

Thanks again for taking of your time.
Laurent

Le 12 sept. 2013 à 20:48, Nicklas Nordborg <nicklas.nordb...@med.lu.se> a écrit 
:

> On 2013-09-12 16:22, Jari Häkkinen wrote:
>> On 2013-09-11 10:57, Laurent Troxler wrote:
>>> going through the log files here is what I can get:
>>> system.log: repeating those two lines
>>> Sep 11 10:32:00 seridi java[85937]: kCGErrorFailure: Set a breakpoint @
>>> CGErrorBreakpoint() to catch errors as they are logged.
>>> Sep 11 10:32:02 seridi com.apple.launchd[1] (org.apache.tomcat):
>>> Throttling respawn: Will start in 8 seconds
>>> 
>>> /Library/Tomcat/logs/catalina.2013-09-11.log :
>>> Sep 11, 2013 10:52:05 AM org.apache.catalina.startup.Bootstrap
>>> initClassLoaders
>>> SEVERE: Class loader creation threw exception
>>> java.lang.InternalError: Can't connect to window server - not enough
>>> permissions.
> 
> I think this could be that the Java runtime engine is starting up 
> various threads for handling GUI interactions. I have not seen this 
> preventing startup of Tomcat or BASE but it can lead to issues with 
> generating plots and other image handling (much) later.
> 
> The installation instructions mention that "headless mode" should be 
> enabled to prevent this. See 4:th bullet in the Tomcat section 
> (http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html).
>  
> 
> 
> In any case, I don't think this is related to BASE not working, but it 
> needs to be fixed sooner or later and better to rule it out as soon as 
> possible.
> 
> /Nicklas
> 
> 
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