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.scholtalbers(a)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
> <cjfields(a)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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