New CloudMan Galaxy Error

Question: New CloudMan Galaxy Error

9 months ago by

rmse17 • 0

United States

rmse17 • 0 wrote:

I am trying to use Cloudman. I created a test instance using c3.large. Initially everything seemed to come up.
I added a galaxy admin email through cloudman admin interface, which triggered a Galaxy restart (as expected). Galaxy no longer comes up, all processes in the galaxy log error out in the exact same way:

127.0.0.1 - - [14/Feb/2018:15:40:34 +0000] "GET / HTTP/1.1" 200 - "-" "Python-urllib/2.7"

Exception happened during processing of request from ('127.0.0.1', 59586) Traceback (most recent call last): File "/mnt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 651, in __init__ self.finish() File "/usr/lib/python2.7/SocketServer.py", line 710, in finish self.wfile.close() File "/usr/lib/python2.7/socket.py", line 279, in close self.flush() File "/usr/lib/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe

Other than adding admin user to Galaxy through cloudman admin no other actions were made to the system.

How should I proceed with this issue?

Thanks for your help!

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modified 9 months ago by Enis Afgan • 690 • written 9 months ago by rmse17 • 0

9 months ago by

Enis Afgan • 690

United States

Enis Afgan • 690 wrote:

Have you tried (re)starting Galaxy from the Services menu lower on the Admin page? If that doesn't work, you can try Rebooting the cluster (yet lower on the same page). Finally, as it seems this is a brand new cluster, it may be easiest to just terminate this cluster and launch a brand new one. Adding admins users has not caused issues in a long time so I'm guessing this may be just an isolated issue.

(btw, not sure which version you launched, but the latest Galaxy will be available as part of the GVL appliance on CloudLaunch: https://galaxyproject.org/news/2018-01-22-gvl430/)

ADD COMMENT • link written 9 months ago by Enis Afgan • 690

Hi Enis, I tried restarting Galaxy from the Services menu, as well as rebooting the cluster. The behavior was identical (same errors, and Galaxy IP showed the Nginx page), but I agree that adding the admin user looks to be a false positive, as the user is correctly references in the galaxy.ini.

Version was 17.05 Galaxy CloudMan. So I should try out GVL instead to get the latest Galaxy?

I did get Galaxy working by installing system updates and installing "supervisor" because the one on the image was giving some missing package error: supervisorctl status Traceback (most recent call last): File "/usr/local/bin/supervisorctl", line 5, in <module> from pkg_resources import load_entry_point File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 2749, in <module> working_set = WorkingSet._build_master() File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 444, in _build_master ws.require(__requires__) File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 725, in require needed = self.resolve(parse_requirements(requirements)) File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 628, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: meld3>=0.6.5

Not sure if this was an artifact during cluster creation or some other underlying issue. In any case, having reinstalled supervisor I issued a "supervisor restart all" which brought Galaxy back to life.

Oddly enough, the original errors are still showing up from time to time in the log, but Galaxy seems to be working.

Thanks for your help!

ADD REPLY • link modified 9 months ago • written 9 months ago by rmse17 • 0

Glad you got it working. I'll try launching one (hopefully tomorrow) and see if it's a recurring issue. The error you listed initially is not a cause for concern; iirc, it stems from a timeout between the galaxy server and the proxy (magnified a bit by the frequency with which CloudMan checks Galaxy status) but it does not affect functionality of the system.

Finally, re. the GVL - yes. The current and future releases of Galaxy on AWS will come as part of the GVL so it's the recommended appliance to use.

ADD REPLY • link written 9 months ago by Enis Afgan • 690

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