Open Microscopy Environment

Hello Team,
I am trying to install OMERO on aws-ubuntu instance. I tried both Open-JRE and Oracle JRE having the same issue is attached below. Can anyone please help.


root@ip-10-10-1-59:/var/OMERO.insight-5.4.1-ice36-b75-linux# ./OMEROinsight_unix.sh

Abnormal termination due to an uncaught exception.

java.awt.HeadlessException:

No X11 DISPLAY variable was set, but this program performed an operation which requires it.

at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204)

at java.awt.Window.<init>(Window.java:536)

at java.awt.Frame.<init>(Frame.java:420)

at javax.swing.JFrame.<init>(JFrame.java:233)

at org.openmicroscopy.shoola.util.ui.login.ScreenLogin.<init>(ScreenLogin.java:1039)

at org.openmicroscopy.shoola.env.ui.SplashScreenManager.initializedView(SplashScreenManager.java:178)

at org.openmicroscopy.shoola.env.ui.SplashScreenManager.<init>(SplashScreenManager.java:242)

at org.openmicroscopy.shoola.env.ui.SplashScreenProxy.<init>(SplashScreenProxy.java:123)

at org.openmicroscopy.shoola.env.ui.UIFactory.makeSplashScreen(UIFactory.java:59)

at org.openmicroscopy.shoola.env.init.SplashScreenInit.execute(SplashScreenInit.java:92)

at org.openmicroscopy.shoola.env.init.Initializer.doInit(Initializer.java:276)

at org.openmicroscopy.shoola.env.Container.runStartupProcedure(Container.java:124)

at org.openmicroscopy.shoola.env.Container.access$000(Container.java:74)

at org.openmicroscopy.shoola.env.Container$1.run(Container.java:170)

at java.lang.Thread.run(Thread.java:748)

Abnormal termination due to an uncaught exception.

java.awt.HeadlessException:

No X11 DISPLAY variable was set, but this program performed an operation which requires it.

at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204)

at java.awt.Window.<init>(Window.java:536)

at java.awt.Frame.<init>(Frame.java:420)

at javax.swing.JFrame.<init>(JFrame.java:233)

at org.openmicroscopy.shoola.util.ui.login.ScreenLogin.<init>(ScreenLogin.java:1039)

at org.openmicroscopy.shoola.env.ui.SplashScreenManager.initializedView(SplashScreenManager.java:178)

at org.openmicroscopy.shoola.env.ui.SplashScreenManager.<init>(SplashScreenManager.java:242)

at org.openmicroscopy.shoola.env.ui.SplashScreenProxy.<init>(SplashScreenProxy.java:123)

at org.openmicroscopy.shoola.env.ui.UIFactory.makeSplashScreen(UIFactory.java:59)

at org.openmicroscopy.shoola.env.init.SplashScreenInit.execute(SplashScreenInit.java:92)

at org.openmicroscopy.shoola.env.init.Initializer.doInit(Initializer.java:276)

at org.openmicroscopy.shoola.env.Container.runStartupProcedure(Container.java:124)

at org.openmicroscopy.shoola.env.Container.access$000(Container.java:74)

at org.openmicroscopy.shoola.env.Container$1.run(Container.java:170)

at java.lang.Thread.run(Thread.java:748)

Exception in thread "Initializer"





Exception: java.awt.HeadlessException thrown from the UncaughtExceptionHandler in thread "Initializer

Hi sneha,

You're installing the Insight client on a remote system - is that for testing an OMERO server also installed there?

In general, I would expect the Insight client on client systems with access to e.g. imaging data, which then connect to a remote OMERO server.

To progress past the error you're seeing to open the Insight client, you'll need an X11 server (and a window manager) which your AWS instance doesn't have at the moment. It may be possible to install it or could try to open the application with a local install of X11 on your local system using a method called X11 forwarding.

See examples like https://unix.stackexchange.com/question ... s-remotely

Best,

Kenny

Hello Kenny

I appreciate your response. We are trying to implement OMERO in our company .
Initially I started to install OMER Server from following link but I'm not sure about it.
https://docs.openmicroscopy.org/omero/5 ... ice36.html

Can you please provide any documents to implement OMERO Server,Client from scratch.




Thanks,
sneha

Hi sneha,

Our system administrator documentation at https://docs.openmicroscopy.org/omero/5 ... index.html contains all you will need to get going with an OMERO server install.

See "OMERO.server installation" - pick a walkthrough, such as "OMERO.server installation on Ubuntu 16.04" like you already tried, and follow it step-by-step.

If you are stuck on any particular section, you can get in touch with the community here, as you already have.

Cheers,

Kenny

Also, if you take a look at https://docs.openmicroscopy.org/omero/5 ... index.html - this might give you a better overview of the OMERO overall system architecture.

e.g. OMERO.insight which you were trying to run in your first post is one of the "Clients" shown on the diagram there.

All the best,

Kenny

Hi Kenny,

Thank you so much for providing useful information. I have gone through the links and trying to install Omero Server. Hope i am on the right track now. If i get any issues will get back to you.

Thanks,
sneha

Hi kenny,

I am trying to configure omero in the process of installing omero server and got stuck with the below error.

[Errno 13] Permission denied: '/home/omero/OMERO.server/etc/grid/config.xml'

Here is the screenshot of my error. Help me to resolve this issue.

root@ip-172-31-95-14:/home/omero# sudo su omero
omero@ip-172-31-95-14:~$ ls
OMERO.server OMERO.server-5.4.1-ice36-b75 OMERO.server-ice36.zip
omero@ip-172-31-95-14:~$ OMERO.server/bin/omero config set omero.data.dir "$OMERO_DATA_DIR"
[Errno 13] Permission denied: '/home/omero/OMERO.server/etc/grid/config.xml'
omero@ip-172-31-95-14:~$ su -
Password:
su: Authentication failure
omero@ip-172-31-95-14:~$ exit
exit
root@ip-172-31-95-14:/home/omero# chmod 777 omero
root@ip-172-31-95-14:/home/omero# su omero
omero@ip-172-31-95-14:~$ OMERO.server/bin/omero config set omero.data.dir "$OMERO_DATA_DIR"
[Errno 13] Permission denied: '/home/omero/OMERO.server/etc/grid/config.xml'
omero@ip-172-31-95-14:~$

Thanks,
sneha

Hi Sneha,

Did you download and unzip the OMERO server zip as the omero system user?

It looks like the OMERO system user doesn't have permissions to the OMERO distribution directory.

ls -l will show the ownership.

If that is indeed the problem, watch under each section in the install instructions for the bold "The following steps are run as" - and make sure you run each step as the relevant user.

Best,

Kenny

Hi Kenny,

Thank you that really helped me. But i got a different error. below is the screenshot of the error. Can you Please let me know your thoughts.(Is there any minimum requirements for installing omero server?)

CREATE TRIGGER
CREATE TABLE
CREATE INDEX
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE TRIGGER
CREATE TRIGGER
CREATE TRIGGER
CREATE TRIGGER
CREATE FUNCTION
CREATE FUNCTION
CREATE TRIGGER
CREATE TRIGGER
CREATE INDEX
UPDATE 1
COMMIT
omero@ip-172-31-94-213:~$ OMERO.server/bin/omero admin start
Creating /home/omero/OMERO.server/var/master
Initializing /home/omero/OMERO.server/var/log
Creating /home/omero/OMERO.server/var/registry
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
.Traceback (most recent call last):
  File "OMERO.server/bin/omero", line 125, in <module>
    rv = omero.cli.argv()
  File "/home/omero/OMERO.server/lib/python/omero/cli.py", line 1615, in argv
    cli.invoke(args[1:])
  File "/home/omero/OMERO.server/lib/python/omero/cli.py", line 1090, in invoke
    stop = self.onecmd(line, previous_args)
  File "/home/omero/OMERO.server/lib/python/omero/cli.py", line 1167, in onecmd
    self.execute(line, previous_args)
  File "/home/omero/OMERO.server/lib/python/omero/cli.py", line 1249, in execute
    args.func(args)
  File "/home/omero/OMERO.server/lib/python/omero/plugins/prefs.py", line 74, in open_and_close_config
    return func(*args, **kwargs)
  File "/home/omero/OMERO.server/lib/python/omero/plugins/admin.py", line 741, in start
    self.waitup(args)
  File "/home/omero/OMERO.server/lib/python/omero/plugins/admin.py", line 845, in waitup
    elif 0 == self.status(args, node_only=False):
  File "/home/omero/OMERO.server/lib/python/omero/install/windows_warning.py", line 26, in wrapper
    return func(self, *args, **kwargs)
  File "/home/omero/OMERO.server/lib/python/omero/plugins/admin.py", line 780, in status
    self.ctx.rv = self.ctx.popen(command).wait()  # popen
  File "/home/omero/OMERO.server/lib/python/omero/cli.py", line 1340, in popen
    stdout=stdout, stderr=stderr)
  File "/usr/lib/python2.7/subprocess.py", line 711, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1235, in _execute_child
    self.pid = os.fork()
OSError: [Errno 12] Cannot allocate memory
omero@ip-172-31-94-213:~$ df -hh

Filesystem      Size  Used Avail Use% Mounted on
udev            488M     0  488M   0% /dev
tmpfs           100M  3.3M   96M   4% /run
/dev/xvda1      7.7G  2.4G  5.3G  32% /
tmpfs           496M  4.0K  496M   1% /dev/shm
tmpfs           5.0M     0  5.0M   0% /run/lock
tmpfs           496M     0  496M   0% /sys/fs/cgroup
tmpfs           100M     0  100M   0% /run/user/1000

Thanks,
sneha

Hi Sneha,

Yes, there definitely are minimum requirements.

See the System Administrator documentation - two important pages "System requirements" and "Version requirements".

https://docs.openmicroscopy.org/omero/5 ... index.html

Best,

Kenny