icegridnode not started

[gael.pawlak]

Hello,

I installed omero on scientific linux 6.
I followed installation step and at starting I got an timeout start error.

I give you my "diagnostics" result

Code: Select all

================================================================================
OMERO Diagnostics 4.3.2-8fc94b85-b2882
================================================================================
       
Commands:   java -version                  1.6.0     (/usr/bin/java)
Commands:   python -V                      2.6.6     (/usr/bin/python)
Commands:   icegridnode --version          3.3.1     (/opt/Ice-3.3/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/opt/Ice-3.3/bin/icegridadmin)
Commands:   psql --version                 8.4.9     (/usr/local/PostgreSQL/8.4/bin/psql)

[b]Server:     icegridnode                    not started[/b]

Log dir:    /usr/local/omero/omero/var/log exists

Log files:  Blitz-0.log                    n/a
Log files:  DropBox.log                    n/a
Log files:  FileServer.log                 n/a
Log files:  Indexer-0.log                  n/a
Log files:  MonitorServer.log              n/a
Log files:  OMEROweb.log                   9.0 KB        errors=15   warnings=0   
Log files:  Processor-0.log                n/a
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB       
Log files:  master.out                     0.0 KB       
Log files:  Total size                     0.01 MB

Error while parsing logs

Environment:OMERO_HOME=/usr/local/omero/omero
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:PATH=/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lib/jvm/jre-1.6.0-openjdk.x86_64/bin:/usr/lib/jvm/jre-1.6.0-openjdk.x86_64/bin:/opt/Ice-3.3/bin:/usr/local/PostgreSQL/8.4/bin:/usr/local/omero/omero/bin:/usr/local/omero/bin
Environment:ICE_HOME=/opt/Ice-3.3         
Environment:LD_LIBRARY_PATH=/opt/Ice-3.3:/usr/share/java:/usr/lib:/usr/lib64
Environment:DYLD_LIBRARY_PATH=/opt/Ice-3.3:/usr/share/java:/usr/lib:/usr/lib64

OMERO data dir: '/mnt/omerodata/OMERO'   Exists? True   Is writable? True
OMERO.web status... DEVELOPMENT: You will have to check status by hand!


my environment variables in .bashrc

Code: Select all

# User specific aliases and functions
export JAVA_HOME=/usr/lib/jvm/jre-1.6.0-openjdk.x86_64
export JRE_HOME=/usr/lib/jvm/jre-1.6.0-openjdk.x86_64
export ICE_HOME=/opt/Ice-3.3
export POSTGRES_HOME=/usr/local/PostgreSQL/8.4
export PYTHONPATH=/usr/lib/python2.6:/usr/lib64/python2.6:/opt/Ice-3.3/python:$PYTHONPATH
export DYLD_LIBRARY_PATH=$ICE_HOME:/usr/share/java:/usr/lib:/usr/lib64
export LD_LIBRARY_PATH=$ICE_HOME:/usr/share/java:/usr/lib:/usr/lib64
export OMERO_HOME=/usr/local/omero/omero
export PATH=$PATH:$JAVA_HOME/bin:$JRE_HOME/bin:$ICE_HOME/bin:$POSTGRES_HOME/bin:$OMERO_HOME/bin


Ice is compiled from source.
my master.err is empty, I have no prompted error anywhere and I don't know how to continue.

If anyone may help me...
Thanks

Gael

[cxallan]

What is the output you get when executing bin/omero admin start? On an unrelated note OpenJDK is not supported and you will run into issues without installing the Oracle JDK.

[gael.pawlak]

the output on "omero admin start" is

Code: Select all

[omero@vbioimage-omero ~]$ omero admin start
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
.............................
Failed to startup some components after 5 minutes
Calling "stop" on remaining components
Server not running
[omero@vbioimage-omero ~]$


I will install Oracle JDK, thanks for the advice ...

Gael

[gael.pawlak]

I installed oracle jdk and configure it in JAVA_HOME and JRE_HOME...

Regards
Gael

[cxallan]

And that made a difference? I assume now that you still have nothing in master.err or master.out in var/log? If you run Python, does the following work?

Code: Select all

$ python
Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import Ice
>>>
...


[gael.pawlak]

It seems ok...

Code: Select all

[omero@vbioimage-omero omero]$ python
Python 2.6.6 (r266:84292, May 20 2011, 16:42:11)
[GCC 4.4.5 20110214 (Red Hat 4.4.5-6)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Ice
>>>


Gael

[gael.pawlak]

Sorry, too quick response...
installation of oracle JDK didn't make change for my ice problem

Regards
Gael

[cxallan]

A couple things. It looks like you've set OMERO_HOME. Where are you executing these commands? Do you actually have permissions to write in /usr/local/omero as the user you are executing omero as? Who owns /usr/local/omero?

[gael.pawlak]

An unix user "omero" owns /usr/local/omero. It's its home directory.

the software omero is installed in /usr/local/omero/omero. This directory defined as OMERO_HOME.

Commands are executed from this directory (/usr/local/omero/omero).

edit :
permissions on directories are

Code: Select all

[omero@vbioimage-omero local]$ ls -l | grep omero
drwxr-xr-x. 4 omero omero 4096 Oct 14 15:38 omero
[omero@vbioimage-omero local]$ ls -l omero
total 4
drwxr-xr-x. 13 omero omero 4096 Oct 13 13:58 omero
[omero@vbioimage-omero local]$ ls -l omero/omero
total 324
drwxr-xr-x. 2 omero omero   4096 Sep 14 14:35 bin
drwxr-xr-x. 3 omero omero   4096 Sep 14 14:35 docs
drwxr-xr-x. 4 omero omero   4096 Oct 14 10:33 etc
drwxr-xr-x. 3 omero omero   4096 Sep 14 14:34 include
drwxr-xr-x. 8 omero omero   4096 Sep 14 14:35 lib
drwxr-xr-x. 2 omero omero   4096 Sep 14 14:35 licenses
-rw-r--r--. 1 omero omero  17987 Sep 14 14:35 LICENSE.txt
drwxrwxr-x. 2 omero omero   4096 Oct 13 11:42 log
-rw-rw-r--. 1 omero omero 264201 Oct 13 12:04 OMERO4.3__0.sql
drwxrwxr-x. 2 omero omero   4096 Oct 13 11:42 sessions
drwxr-xr-x. 4 omero omero   4096 Sep 14 14:35 sql
drwxrwxr-x. 3 omero omero   4096 Oct 13 12:01 tmp
drwx------. 5 omero omero   4096 Oct 13 16:52 var
[omero@vbioimage-omero local]$


Gael

[cxallan]

Okay. If you:

Code: Select all

unset OMERO_HOME
cd /usr/local/omero/omero
bin/omero admin start


Is there any difference to what you are seeing?