Re: [galaxy-dev] Odd (possible latency/race?) problems post-upgrade
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
> 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
>> 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
>>>
>>>
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client. To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>
>>> http://lists.bx.psu.edu/
>
>
> ___
> Please keep all replies on the list b
Re: [galaxy-dev] Odd (possible latency/race?) problems post-upgrade
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 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
> 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
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>> http://lists.bx.psu.edu/
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
Re: [galaxy-dev] Odd (possible latency/race?) problems post-upgrade
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
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
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx.psu.edu/
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
[galaxy-dev] Odd (possible latency/race?) problems post-upgrade
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
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
