On Sep 25, 2012, at 12:35 PM, Lukasz Lacinski wrote:

> I use start-stop-daemon that sends SIGTERM (which is a default signal sent to 
> a service that is being asked to stop) to Galaxy to let Galaxy store all 
> information in a database, close files, etc., and terminate itself. When 
> Galaxy process is terminated, both shell and python scripts (Galaxy tools) 
> are still running.
> 
> Effects of using SIGKILL/SIGSTOP are not predictable. I do not want to risk 
> that Galaxy does not insert entries to the database that should be inserted 
> to start Galaxy correctly again, or does not flush buffers to write all data 
> to files and close the files correctly.

Hi Lukasz,

Galaxy does not terminate jobs running in the local runner when the Galaxy 
server stops.  If you need to be able to restart the server without losing 
running jobs, you'll need to set up a cluster scheduler, even if it just 
submits jobs to the localhost.

--nate

> 
> Thanks,
> Lukasz
> 
> On 9/25/12 10:40 AM, Scott McManus wrote:
>> Lukasz-
>> 
>> How are you stopping the process? It's possible that the python
>> task for galaxy is still running. I would recommend trying to
>> send a "kill" signal to that process. Something like
>> "kill -9 PID", where PID is the process id for galaxy, should
>> work.
>> 
>> -Scott
>> 
>> ----- Original Message -----
>>> On 9/24/12 12:40 PM, Nate Coraor wrote:
>>>> On Sep 19, 2012, at 9:50 AM, Jennifer Jackson wrote:
>>>> 
>>>>> repost to galaxy-dev
>>>>> 
>>>>> On 9/7/12 6:39 PM, Lukasz Lacinski wrote:
>>>>>> Dear All,
>>>>>> 
>>>>>> I use an init script that comes with Galaxy in the contrib/
>>>>>> subdirectory
>>>>>> to start Galaxy. The log file
>>>>>> 
>>>>>> --log-file /home/galaxy/galaxy.log
>>>>>> 
>>>>>> specified in the script grows really quickly. How to logrotate
>>>>>> the file?
>>>> Hi Lukasz,
>>>> 
>>>> I'd suggest using whatever log rotation utility is provided by your
>>>> OS.  You'll need to restart the Galaxy process to begin writing to
>>>> the new log once the old one has been rotated.
>>> Hi Nate,
>>> 
>>> When Galaxy is started again, it fails because it cannot bind a
>>> socket to port 8080, that is already bound by child Galaxy processes
>>> orphaned by the former Galaxy process.
>>> 
>>> When Galaxy forks to run tools, a child process does not close open
>>> files/sockets that the child process does not need.
>>> 
>>> Thanks,
>>> Lukasz
>>> 
>>>> --nate
>>>> 
>>>>>> Thanks,
>>>>>> Lukasz
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>>>>> --
>>>>> Jennifer Jackson
>>>>> http://galaxyproject.org
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> 
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