started galaxy_web: ERROR (abnormal termination)

[vebaev]

Hi
in the last days everytime I want to restart Galaxy, after I install some tools I got error from galaxy_web:
sudo docker exec f187b0f37822 supervisorctl restart galaxy:
galaxy_nodejs_proxy: stopped
handler0: stopped
handler1: stopped
galaxy_web: stopped
galaxy_nodejs_proxy: started
galaxy_web: ERROR (abnormal termination)
handler0: started
handler1: started

If than If stop the container, restart docker service and start new Galaxy container, it is ok?

[bgruening]

Don't restart Docker until we found the root cause for this issue: #64

[vebaev]

Ok thanks, for notifying that this is not issue from something I did wrong, but if I do not restart Docker I cannot access anymore my Galaxy from the browser and cannot do anything, as probably the error is related to the web service?

[bgruening]

Ok, ok maybe it understood something wrong. Restarting Galaxy should work. Restarting Docker can result in some missing files in your config folder.
You you get the error message from the galaxy_web supervisord process?

[vebaev]

I'm restarting Galaxy like this:
sudo docker exec f187b0f37822 supervisorctl restart galaxy:
and I got the error from galaxy_web, than I cannot access the Galaxy via web.

Than I can only fix this to normal after restert Docker and run a new Galaxy-stable container.

[bgruening]

Can you give us more logging informations? /var/log/supervisord/* for example. Or try to start your container with this: https://github.com/bgruening/docker-galaxy-stable#advanced-logging

[vebaev]

Hi,
after Galaxy restart getting "galaxy_web: ERROR (abnormal termination)" here is the log I manage to pull:

root@80e34a802918:/var/log/supervisor# more galaxy_web-stderr---supervisor-BJvXDF.log
open("./python_plugin.so"): No such file or directory [core/utils.c line 3675]
!!! UNABLE to load uWSGI plugin: ./python_plugin.so: cannot open shared object file: No such file or directory !!!
[uWSGI] getting INI configuration from /etc/galaxy/galaxy.ini

The Galaxy was started with:
sudo docker run -d -p 8080:80 -v /home/galaxy/galaxy_storage/:/export/ bgruening/galaxy-stable
Restarted with:
sudo docker exec supervisorctl restart galaxy:

And as I mention before it is fixed when I stop, remove the container, restart Docker and run a new container with the line above.

[vebaev]

I have checked and the error is the same each time

[vebaev]

Hi, any news on the error, please let me know if you need me to provide more info from somewhere as I got this frustrating error on my all Galaxy restarts?

[bgruening]

How do you do a restart? Can you please provide a step by step guide to reproduce it?
Thanks.

[vebaev]

I just type this (while the container/galaxy is running) and got the log:
sudo docker exec 98ff81fb6066 supervisorctl restart galaxy:
galaxy_nodejs_proxy: stopped
handler0: stopped
handler1: stopped
galaxy_web: stopped
galaxy_nodejs_proxy: started
galaxy_web: ERROR (abnormal termination)
handler0: started
handler1: started

[bgruening]

Which galaxy version, Docker version? Is it still the same error from above with the uWSGI plugin: ./python_plugin.so?

[vebaev]

Yes the error is the same. How to check which version of docker-galaxy-stable I am running? The docker version is:
Client version: 1.7.1
Client API version: 1.19
Go version (client): go1.4.2
Git commit (client): 786b29d
OS/Arch (client): linux/amd64
Server version: 1.7.1
Server API version: 1.19
Go version (server): go1.4.2
Git commit (server): 786b29d
OS/Arch (server): linux/amd64

[bgruening]

How do you start galaxy-stable? You usually specify the version after the image name like :dev. Please also try the latest docker pull bgruening/galaxy-stable:15.07

[vebaev]

I'm starting it like this:
sudo docker run -d -p 8080:80 -v /home/galaxy/galaxy_storage/:/export/ bgruening/galaxy-stable

[bgruening]

Try docker pull bgruening/galaxy-stable:15.07 to be sure to have the latest version.

[vebaev]

I till try and let you know when I have to restart next time.

[bgruening]

I will close this for now. Let me know if you see this again.