Hi,

Greg has just fixed this in 9f790bc90769.  Thanks for letting us know!

--nate

On Aug 2, 2012, at 3:34 PM, Fields, Christopher J wrote:

> I mentioned this on IRC, Nate indicated he was looking into it.  My 
> short-term workaround was adding a 'sleep 9' in the process initiation loops 
> in 'run.sh' and 'run_multiple_processes.sh' (just after the python call) to 
> allow time between the start of each process.  
> 
> chris
> 
> On Aug 2, 2012, at 7:46 AM, Jelle Scholtalbers <j.scholtalb...@gmail.com> 
> wrote:
> 
>> Hi,
>> 
>> I'm experiencing the same problem after I configured the "web
>> application scaling"- although I have to say I still have the june 03
>> version from central. Has this been resolved in newer updates?
>> 
>> Cheers,
>> Jelle
>> 
>> 
>> On Mon, Jul 30, 2012 at 7:03 PM, Fields, Christopher J
>> <cjfie...@illinois.edu> wrote:
>>> I'm seeing a possible latency issue or race condition when starting Galaxy 
>>> after the latest hg upgrade (July 20) from galaxy-dist; the prior upgrade 
>>> doesn't have this problem.  We have small setup with one job manager/runner 
>>> and two web front-ends for testing load balancing:
>>> 
>>> …from universe_wsgi.ini:
>>> ------------------------------
>>> [server:web0]
>>> use = egg:Paste#http
>>> port = 8080
>>> host = 127.0.0.1
>>> use_threadpool = true
>>> threadpool_workers = 7
>>> 
>>> [server:web1]
>>> use = egg:Paste#http
>>> port = 8081
>>> host = 127.0.0.1
>>> use_threadpool = true
>>> threadpool_workers = 7
>>> 
>>> [server:manager]
>>> use = egg:Paste#http
>>> port = 8079
>>> host = 127.0.0.1
>>> use_threadpool = true
>>> threadpool_workers = 5
>>> ------------------------------
>>> 
>>> If I run:
>>> 
>>>   GALAXY_RUN_ALL=1 sh run.sh --daemon
>>> 
>>> I will intermittently see the following in the paster log for any of the 
>>> above services (example below is web1, but I have seen this for manager and 
>>> web0 as well).  The traceback and error is the same in all cases ('File 
>>> exists: /home/a-m/galaxy/dist-database/tmp/work_tmp'):
>>> 
>>> ------------------------------
>>> galaxy.tool_shed.tool_shed_registry DEBUG 2012-07-30 11:40:10,194 Loading 
>>> references to tool sheds from tool_sheds_conf.xml
>>> galaxy.tool_shed.tool_shed_registry DEBUG 2012-07-30 11:40:10,194 Loaded 
>>> reference to tool shed: Galaxy main tool shed
>>> galaxy.tool_shed.tool_shed_registry DEBUG 2012-07-30 11:40:10,194 Loaded 
>>> reference to tool shed: Galaxy test tool shed
>>> galaxy.model.migrate.check DEBUG 2012-07-30 11:40:10,650 psycopg2 egg 
>>> successfully loaded for postgres dialect
>>> galaxy.model.migrate.check INFO 2012-07-30 11:40:10,845 At database version 
>>> 103
>>> galaxy.tool_shed.migrate.check DEBUG 2012-07-30 11:40:10,940 psycopg2 egg 
>>> successfully loaded for postgres dialect
>>> galaxy.tool_shed.migrate.check INFO 2012-07-30 11:40:10,986 At 
>>> migrate_tools version 3
>>> galaxy.model.custom_types DEBUG 2012-07-30 11:40:10,994 psycopg2 egg 
>>> successfully loaded for postgres dialect
>>> Traceback (most recent call last):
>>> File "/home/a-m/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in 
>>> app_factory
>>>   app = UniverseApplication( global_conf = global_conf, **kwargs )
>>> File "/home/a-m/galaxy/galaxy-dist/lib/galaxy/app.py", line 66, in __init__
>>>   self.installed_repository_manager.load_proprietary_datatypes()
>>> File "/home/a-m/galaxy/galaxy-dist/lib/galaxy/tool_shed/__init__.py", line 
>>> 47, in load_proprietary_datatypes
>>>   installed_repository_dict = 
>>> galaxy.util.shed_util.load_installed_datatypes( self.app, 
>>> tool_shed_repository, relative_install_dir )
>>> File "/home/a-m/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py", line 
>>> 1269, in load_installed_datatypes
>>>   work_dir = make_tmp_directory()
>>> File "/home/a-m/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py", line 
>>> 1305, in make_tmp_directory
>>>   os.makedirs( work_dir )
>>> File "/usr/lib64/python2.6/os.py", line 157, in makedirs
>>>   mkdir(name, mode)
>>> OSError: [Errno 17] File exists: 
>>> '/home/a-m/galaxy/dist-database/tmp/work_tmp'
>>> Removing PID file web1.pid
>>> ------------------------------
>>> 
>>> I was also seeing this using separate runner/webapp ini files and 
>>> 'run_multiple_processes.sh --daemon', but we decided to go ahead and 
>>> migrate over to a unified universe_wsgi.ini file.
>>> 
>>> Anyway, we found a workaround by rerunning 'GALAXY_RUN_ALL=1 sh run.sh 
>>> --daemon' which skips any running services, but I'm curious whether anyone 
>>> else has seen this and whether there is a fix (or maybe added config 
>>> setting we are missing?)
>>> 
>>> chris
>>> 
>>> 
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> 
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