What about the file itself (i.e., /mnt/galaxy/galaxy-app/main.log) - who
owns it? It could be that Galaxy was started manually during the build
phase by a user other than galaxy and so it can't rewrite that file now?
Either way, you can just delete that file and try it again.
As an image is built, the installation procedure itself leaves some
artifacts that need to be cleaned up so the cleanup step is required just
before bundling the AMI.
On Mon, Jun 22, 2015 at 6:43 PM, Alexander Vowinkel <
I didn't do the cleanup, because I didn't change anything on the generated
I now created a new clean instance and get this error:
2015-06-22 22:35:37,190 DEBUG master:2482 Monitor done adding service Galaxy
> 2015-06-22 22:35:37,190 DEBUG decorators:59 Cluster not yet ready (STARTING),
skipping method cm.master->ConsoleMonitor.newFunction
> 2015-06-22 22:35:41,192 DEBUG master:2478 Monitor adding service
> 2015-06-22 22:35:41,192 INFO __init__:347 Galaxy service prerequisites OK;
starting the service
> 2015-06-22 22:35:41,196 DEBUG galaxy:84 Using Galaxy from
> 2015-06-22 22:35:41,212 DEBUG decorators:83 Delay trigger not met (delta: 0;
delay: 10. skipping method cm.services.apps.galaxy->GalaxyService.status
> 2015-06-22 22:35:41,217 DEBUG galaxy:248 Galaxy UI does not seem to be
> 2015-06-22 22:35:41,217 DEBUG galaxy:138 Starting Galaxy...
> 2015-06-22 22:35:41,246 DEBUG galaxy_conf:32 Attemping to chown to galaxy for
> 2015-06-22 22:35:41,281 DEBUG galaxy_conf:190 Rewriting Galaxy's main config
> 2015-06-22 22:35:41,282 DEBUG galaxy_conf:32 Attemping to chown to galaxy for
> 2015-06-22 22:35:41,917 ERROR misc:848 ---> PROBLEM, running command
'/bin/su - galaxy -c "export GALAXY_HOME='/mnt/galaxy/galaxy-app'; export
TMPDIR='/mnt/galaxy/tmp'; export TEMP='/mnt/galaxy/tmp'; source
$GALAXY_HOME/.venv/bin/activate; sh $GALAXY_HOME/run.sh --pid-file=main.pid
--log-file=main.log --daemon"' returned code '2', the following stderr:
'' and stdout: 'Activating virtualenv at /mnt/galaxy/galaxy-app/.venv
> Error: Unable to write to log file: [Errno 13] Permission denied: 'main.log'
> The directory /mnt/galaxy/galaxy-app is owned by galaxy.
Where is cloudman trying to write the logfile to?
2015-06-19 10:16 GMT-05:00 Enis Afgan <enis.afgan(a)irb.hr>:
> Hi Alexander,
> When you build the image, did you run the image cleanup step? RabbitMQ's
> database needs to be cleaned up before building the image otherwise the
> application won't start properly and the AMQP connection will never be
> You can also post the entire CloudMan's log somewhere and I can take a
> look there for other clues.
> On Tue, Jun 16, 2015 at 4:07 PM, Alexander Vowinkel <
> vowinkel.alexander(a)gmail.com> wrote:
>> Maybe connected. this error (happening multiple times):
>>> Exception happened during processing of request from ('127.0.0.1',
>>> Traceback (most recent call last):
>>> line 1068, in process_request_in_thread
>>> self.finish_request(request, client_address)
>>> File "/usr/lib/python2.7/SocketServer.py", line 334, in
>>> self.RequestHandlerClass(request, client_address, self)
>>> File "/usr/lib/python2.7/SocketServer.py", line 651, in __init__
>>> File "/usr/lib/python2.7/SocketServer.py", line 710, in finish
>>> File "/usr/lib/python2.7/socket.py", line 279, in close
>>> File "/usr/lib/python2.7/socket.py", line 303, in flush
>>> error: [Errno 32] Broken pipe
>> 2015-06-16 13:59 GMT-05:00 Alexander Vowinkel <
>>> I have the following problem:
>>> First, the job scheduling didn't work.
>>> I tried to upload a file, but the job was waiting.
>>> Then I checked "squeue", which timed out.
>>> The slurm service was running.
>>> Then I restarted the cluster.
>>> Now I even have problems access the cloudman admin page.
>>> Meaning, the page is loading endless.
>>> The machine is not busy (CPU and mem @ htop)
>>> In the paster.log it tries this every 4 seconds:
>>> 2015-06-16 18:35:56,547 DEBUG master:2579 Trying to setup AMQP
>>>> connection; conn = '<cm.util.comm.CMMasterComm object at
>>>> 2015-06-16 18:35:56,547 DEBUG comm:30 Setting up a new
>>>> AMQP connection
>>>> 2015-06-16 18:35:56,548 DEBUG comm:49 AMQP Connection
>>>> Failure: [Errno 111] Connection refused
>>> Any idea what this might be?
>>> Something seems to be really weird.
>>> I am using the next version of CloudMan (dev).
>>> I created an own instance with the Cloud Man playbook.
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