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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