[galaxy-dev] again on multiple server instances

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[galaxy-dev] again on multiple server instances

Davide Cittaro
Hi all, after successful configuration of multiple server instances (web and runner) I've placed everything behind apache proxy (actually I'm trying to).
I can see the welcome page and navigate through my history (still I have to delegate the authentication to apache), nevertheless I'm not able to perform any job...
getting data from UCSC is waiting for run after a couple of hours, uploading files is stuck...
Hence I've tried to disable the proxy thing and still have the same issues. I've then checked at the log files for the five runners and two of them report this:

[runner0]
serving on http://127.0.0.1:8100
galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 13:49:09,032 RoundRobin queue: user/session did not exist, created new jobqueue for session = 6galaxy.jobs DEBUG 2010-05-21 13:49:09,032 job 13 put in policy queue
galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 13:49:09,032 RoundRobin queue: retrieving job from job queue for session = 6
galaxy.jobs DEBUG 2010-05-21 13:49:09,032 dispatching job 13 to local runner
galaxy.jobs DEBUG 2010-05-21 13:49:09,135 job 13 dispatched
galaxy.jobs.runners.local DEBUG 2010-05-21 13:49:09,538 executing: python /data/galaxy_dist/tools/data_source/data_source.py /data/galaxy_dist/database/files
/000/dataset_60.dat 0
galaxy.jobs.runners.local ERROR 2010-05-21 13:49:09,761 Uncaught exception running job
Traceback (most recent call last):
  File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 46, in run_next
    self.run_job( job_wrapper )
  File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 101, in run_job
    job_wrapper.fail( "failure running job", exception=True )
  File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 413, in fail
    self.sa_session.refresh( job )
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/scoping.py", line 127, in do
    return getattr(self.registry(), name)(*args, **kwargs)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/session.py", line 929, in refresh
    only_load_props=attribute_names) is None:
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1500, in _get
    return q.all()[0]
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1267, in all
    return list(self)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1361, in __iter__
    return self._execute_and_instances(context)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances
    result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none())
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/session.py", line 755, in execute
    clause, params or {})
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 824, in execute
    return Connection.executors[c](self, object, multiparams, params)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement
    return self.__execute_context(context)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 901, in __execute_context
    return context.get_result_proxy()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy
    return base.BufferedRowResultProxy(self)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1415, in __init__
    self._init_metadata()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata
    self.__buffer_rows()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows
    self.__rowbuffer = self.cursor.fetchmany(size)
  File "/usr/lib/python2.5/decimal.py", line 541, in __new__
    m = _parser(value)
OperationalError: could not receive data from server: Error 0


[runner1]
galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 13:49:09,198 RoundRobin queue: user/session did not exist, created new jobqueue for session = 6
galaxy.jobs DEBUG 2010-05-21 13:49:09,199 job 13 put in policy queue
galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 13:49:09,199 RoundRobin queue: retrieving job from job queue for session = 6
galaxy.jobs DEBUG 2010-05-21 13:49:09,199 dispatching job 13 to local runner
galaxy.jobs DEBUG 2010-05-21 13:49:09,315 job 13 dispatched
galaxy.jobs.runners.local ERROR 2010-05-21 13:49:09,741 Uncaught exception running job
Traceback (most recent call last):
  File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 46, in run_next
    self.run_job( job_wrapper )
  File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 58, in run_job
    job_wrapper.fail( "failure preparing job", exception=True )
  File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 413, in fail
    self.sa_session.refresh( job )
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/scoping.py", line 127, in do
    return getattr(self.registry(), name)(*args, **kwargs)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/session.py", line 929, in refresh
    only_load_props=attribute_names) is None:
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1500, in _get
    return q.all()[0]
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1267, in all
    return list(self)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1361, in __iter__
    return self._execute_and_instances(context)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances
    result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none())
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/session.py", line 755, in execute
    clause, params or {})
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 824, in execute
    return Connection.executors[c](self, object, multiparams, params)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement
    return self.__execute_context(context)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 901, in __execute_context
    return context.get_result_proxy()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy
    return base.BufferedRowResultProxy(self)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1415, in __init__
    self._init_metadata()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata
    self.__buffer_rows()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows
    self.__rowbuffer = self.cursor.fetchmany(size)
  File "/usr/lib/python2.5/decimal.py", line 541, in __new__
    m = _parser(value)
OperationalError: could not receive data from server: Error 0

BTW, this is the proxy conf:

<IfModule mod_proxy.c>

        ProxyRequests Off

        ProxyVia Off
        <Proxy <a href="balancer://galaxy">balancer://galaxy>
                BalancerMember http://localhost:8080
                BalancerMember http://localhost:8081
        </Proxy>
</IfModule>

and the rewrite rules:

RewriteEngine on
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) /data/galaxy_dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/(.*) /data/galaxy_dist/static/$1 [L]
RewriteRule ^/galaxy/images/(.*) /data/galaxy_dist/static/images/$1 [L]
RewriteRule ^/galaxy/favicon.ico /data/galaxy_dist/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /data/galaxy_dist/static/robots.txt [L]
RewriteRule ^/galaxy(.*) <a href="http://127.0.0.1:8080$1">http://127.0.0.1:8080$1 [P]


Any hint is appreciated...

Thanks

d

/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
*/




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Re: [galaxy-dev] again on multiple server instances

Nate Coraor (nate@bx.psu.edu)
Davide Cittaro wrote:

> Hi all, after successful configuration of multiple server instances (web
> and runner) I've placed everything behind apache proxy (actually I'm
> trying to).
> I can see the welcome page and navigate through my history (still I have
> to delegate the authentication to apache), nevertheless I'm not able to
> perform any job...
> getting data from UCSC is waiting for run after a couple of hours,
> uploading files is stuck...
> Hence I've tried to disable the proxy thing and still have the same
> issues. I've then checked at the log files for the five runners and two
> of them report this:
>
> [runner0]

...

> [runner1]

This is most likely the problem.  At present we only support a single
job runner.  Try only starting runner0 and see if it works.

--nate

> BTW, this is the proxy conf:
>
> <IfModule mod_proxy.c>
>
>         ProxyRequests Off
>
>         ProxyVia Off
>         <Proxy balancer://galaxy>
>                 BalancerMember http://localhost:8080
>                 BalancerMember http://localhost:8081
>         </Proxy>
> </IfModule>
>
> and the rewrite rules:
>
> RewriteEngine on
> RewriteRule ^/galaxy$ /galaxy/ [R]
> RewriteRule ^/galaxy/static/style/(.*)
> /data/galaxy_dist/static/june_2007_style/blue/$1 [L]
> RewriteRule ^/galaxy/static/(.*) /data/galaxy_dist/static/$1 [L]
> RewriteRule ^/galaxy/images/(.*) /data/galaxy_dist/static/images/$1 [L]
> RewriteRule ^/galaxy/favicon.ico /data/galaxy_dist/static/favicon.ico [L]
> RewriteRule ^/galaxy/robots.txt /data/galaxy_dist/static/robots.txt [L]
> RewriteRule ^/galaxy(.*) <a href="http://127.0.0.1:8080$1">http://127.0.0.1:8080$1 [P]
>
>
> Any hint is appreciated...
>
> Thanks
>
> d
>
> /*
> Davide Cittaro
>
> Cogentech - Consortium for Genomic Technologies
> via adamello, 16
> 20139 Milano
> Italy
>
> tel.: +39(02)574303007
> e-mail: [hidden email]
> <mailto:[hidden email]>
> */
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> galaxy-dev mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-dev

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Re: [galaxy-dev] again on multiple server instances

Davide Cittaro

On May 21, 2010, at 3:20 PM, Nate Coraor wrote:

Davide Cittaro wrote:
Hi all, after successful configuration of multiple server instances (web and runner) I've placed everything behind apache proxy (actually I'm trying to).
I can see the welcome page and navigate through my history (still I have to delegate the authentication to apache), nevertheless I'm not able to perform any job...
getting data from UCSC is waiting for run after a couple of hours, uploading files is stuck...
Hence I've tried to disable the proxy thing and still have the same issues. I've then checked at the log files for the five runners and two of them report this:
[runner0]

...

[runner1]

This is most likely the problem.  At present we only support a single job runner.  Try only starting runner0 and see if it works.


Mmm...

galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 15:53:48,681 RoundRobin queue: inserted new job for user/session = 6
galaxy.jobs DEBUG 2010-05-21 15:53:48,681 job 24 put in policy queue
galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 15:53:48,682 RoundRobin queue: retrieving job from job queue for session = 6
galaxy.jobs DEBUG 2010-05-21 15:53:48,682 dispatching job 24 to local runner
galaxy.jobs DEBUG 2010-05-21 15:53:48,773 job 24 dispatched
galaxy.jobs.runners.local DEBUG 2010-05-21 15:53:49,018 executing: python /data/galaxy_dist/tools/data_source/upload.py /tmp/tmphIrPuJ         71:/data/galaxy_dist/database/job_working_directory/24/dataset_71_files:/data/galaxy_dist/database/files/000/dataset_71.dat   
galaxy.jobs.runners.local DEBUG 2010-05-21 15:53:49,495 execution finished: python /data/galaxy_dist/tools/data_source/upload.py /tmp/tmphIrPuJ         71:/data/galaxy_dist/database/job_working_directory/24/dataset_71_files:/data/galaxy_dist/database/files/000/dataset_71.dat   
galaxy.jobs.runners.local ERROR 2010-05-21 15:53:49,689 Job wrapper finish method failed
Traceback (most recent call last):
  File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 122, in run_job
    job_wrapper.finish( stdout, stderr )
  File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 569, in finish
    self.sa_session.flush()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do
    return getattr(self.registry(), name)(*args, **kwargs)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1356, in flush
    self._flush(objects)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1443, in _flush
    flush_context.finalize_flush_changes()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 288, in finalize_flush_changes
    self.session._register_newly_persistent(elem.state)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1015, in _register_newly_persistent
    instance_key = mapper._identity_key_from_state(state)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1085, in _identity_key_from_state
    return self.identity_key_from_primary_key(self._primary_key_from_state(state))
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1096, in _primary_key_from_state
    return [self._get_state_attr_by_column(state, column) for column in self.primary_key]
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1110, in _get_state_attr_by_column
    return self._get_col_to_prop(column).getattr(state, column)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/properties.py", line 99, in getattr
    return state.get_impl(self.key).get(state, state.dict)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get
    value = callable_()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/state.py", line 185, in __call__
    attr.impl.key in unmodified
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1878, in _load_scalar_attributes
    result = session.query(mapper)._get(identity_key, refresh_state=state, only_load_props=attribute_names)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1500, in _get
    return q.all()[0]
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all
    return list(self)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__
    return self._execute_and_instances(context)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances
    result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none())
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute
    clause, params or {})
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute
    return Connection.executors[c](self, object, multiparams, params)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement
    return self.__execute_context(context)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 901, in __execute_context
    return context.get_result_proxy()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy
    return base.BufferedRowResultProxy(self)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1415, in __init__
    self._init_metadata()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata
    self.__buffer_rows()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows
    self.__rowbuffer = self.cursor.fetchmany(size)
  File "/usr/local/lib/python2.6/decimal.py", line 540, in __new__
    m = _parser(value.strip())
OperationalError: could not receive data from server: Error 0

galaxy.jobs.runners.local ERROR 2010-05-21 15:53:49,740 Uncaught exception running job
Traceback (most recent call last):
  File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 46, in run_next
    self.run_job( job_wrapper )
  File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 125, in run_job
    job_wrapper.fail("Unable to finish job", exception=True)
  File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 413, in fail
    self.sa_session.refresh( job )
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do
    return getattr(self.registry(), name)(*args, **kwargs)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 929, in refresh
    only_load_props=attribute_names) is None:
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1500, in _get
    return q.all()[0]
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all
    return list(self)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__
    return self._execute_and_instances(context)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances
    result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none())
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute
    clause, params or {})
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute
    return Connection.executors[c](self, object, multiparams, params)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement
    return self.__execute_context(context)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 901, in __execute_context
    return context.get_result_proxy()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy
    return base.BufferedRowResultProxy(self)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1415, in __init__
    self._init_metadata()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata
    self.__buffer_rows()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows
    self.__rowbuffer = self.cursor.fetchmany(size)
  File "/usr/local/lib/python2.6/decimal.py", line 540, in __new__
    m = _parser(value.strip())
OperationalError: could not receive data from server: Error 0

d

/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
*/




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Re: [galaxy-dev] again on multiple server instances

Nate Coraor (nate@bx.psu.edu)
Davide Cittaro wrote:

> Mmm...

Do you happen to know how your Postgres was compiled?  This can happen
if --enable-thread-safety wasn't specified.

Also, if you're scrambling psycopg2 for a platform we don't provide, the
bug could be in the way I've instructed the scramble script to compile
the static libpq.

For Main on Solaris I build the egg by hand and dynamically link with
the real Postgres install instead of statically linking our
auto-compiled version:

PYTHONPATH=/path/to/galaxy/scripts/scramble/lib python setup.py
build_ext --rpath=/usr/postgres/8.3/lib/64 egg_info
--tag-build=_8.2.6_static bdist_egg

Also, is threadlocal enabled in the config?

database_engine_option_strategy = threadlocal

--nate

>
> galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 15:53:48,681
> RoundRobin queue: inserted new job for user/session = 6
> galaxy.jobs DEBUG 2010-05-21 15:53:48,681 job 24 put in policy queue
> galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 15:53:48,682
> RoundRobin queue: retrieving job from job queue for session = 6
> galaxy.jobs DEBUG 2010-05-21 15:53:48,682 dispatching job 24 to local runner
> galaxy.jobs DEBUG 2010-05-21 15:53:48,773 job 24 dispatched
> galaxy.jobs.runners.local DEBUG 2010-05-21 15:53:49,018 executing:
> python /data/galaxy_dist/tools/data_source/upload.py /tmp/tmphIrPuJ    
>    
> 71:/data/galaxy_dist/database/job_working_directory/24/dataset_71_files:/data/galaxy_dist/database/files/000/dataset_71.dat
>  
> galaxy.jobs.runners.local DEBUG 2010-05-21 15:53:49,495 execution
> finished: python /data/galaxy_dist/tools/data_source/upload.py
> /tmp/tmphIrPuJ        
> 71:/data/galaxy_dist/database/job_working_directory/24/dataset_71_files:/data/galaxy_dist/database/files/000/dataset_71.dat
>  
> galaxy.jobs.runners.local ERROR 2010-05-21 15:53:49,689 Job wrapper
> finish method failed
> Traceback (most recent call last):
>   File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 122,
> in run_job
>     job_wrapper.finish( stdout, stderr )
>   File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 569, in finish
>     self.sa_session.flush()
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py",
> line 127, in do
>     return getattr(self.registry(), name)(*args, **kwargs)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py",
> line 1356, in flush
>     self._flush(objects)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py",
> line 1443, in _flush
>     flush_context.finalize_flush_changes()
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py",
> line 288, in finalize_flush_changes
>     self.session._register_newly_persistent(elem.state)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py",
> line 1015, in _register_newly_persistent
>     instance_key = mapper._identity_key_from_state(state)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py",
> line 1085, in _identity_key_from_state
>     return
> self.identity_key_from_primary_key(self._primary_key_from_state(state))
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py",
> line 1096, in _primary_key_from_state
>     return [self._get_state_attr_by_column(state, column) for column in
> self.primary_key]
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py",
> line 1110, in _get_state_attr_by_column
>     return self._get_col_to_prop(column).getattr(state, column)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/properties.py",
> line 99, in getattr
>     return state.get_impl(self.key).get(state, state.dict)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py",
> line 377, in get
>     value = callable_()
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/state.py",
> line 185, in __call__
>     attr.impl.key in unmodified
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py",
> line 1878, in _load_scalar_attributes
>     result = session.query(mapper)._get(identity_key,
> refresh_state=state, only_load_props=attribute_names)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py",
> line 1500, in _get
>     return q.all()[0]
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py",
> line 1267, in all
>     return list(self)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py",
> line 1361, in __iter__
>     return self._execute_and_instances(context)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py",
> line 1364, in _execute_and_instances
>     result = self.session.execute(querycontext.statement,
> params=self._params, mapper=self._mapper_zero_or_none())
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py",
> line 755, in execute
>     clause, params or {})
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 824, in execute
>     return Connection.executors[c](self, object, multiparams, params)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 874, in _execute_clauseelement
>     return self.__execute_context(context)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 901, in __execute_context
>     return context.get_result_proxy()
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/postgres.py",
> line 346, in get_result_proxy
>     return base.BufferedRowResultProxy(self)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 1415, in __init__
>     self._init_metadata()
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 1704, in _init_metadata
>     self.__buffer_rows()
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 1721, in __buffer_rows
>     self.__rowbuffer = self.cursor.fetchmany(size)
>   File "/usr/local/lib/python2.6/decimal.py", line 540, in __new__
>     m = _parser(value.strip())
> OperationalError: could not receive data from server: Error 0
>
> galaxy.jobs.runners.local ERROR 2010-05-21 15:53:49,740 Uncaught
> exception running job
> Traceback (most recent call last):
>   File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 46, in
> run_next
>     self.run_job( job_wrapper )
>   File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 125,
> in run_job
>     job_wrapper.fail("Unable to finish job", exception=True)
>   File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 413, in fail
>     self.sa_session.refresh( job )
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py",
> line 127, in do
>     return getattr(self.registry(), name)(*args, **kwargs)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py",
> line 929, in refresh
>     only_load_props=attribute_names) is None:
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py",
> line 1500, in _get
>     return q.all()[0]
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py",
> line 1267, in all
>     return list(self)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py",
> line 1361, in __iter__
>     return self._execute_and_instances(context)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py",
> line 1364, in _execute_and_instances
>     result = self.session.execute(querycontext.statement,
> params=self._params, mapper=self._mapper_zero_or_none())
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py",
> line 755, in execute
>     clause, params or {})
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 824, in execute
>     return Connection.executors[c](self, object, multiparams, params)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 874, in _execute_clauseelement
>     return self.__execute_context(context)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 901, in __execute_context
>     return context.get_result_proxy()
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/postgres.py",
> line 346, in get_result_proxy
>     return base.BufferedRowResultProxy(self)
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 1415, in __init__
>     self._init_metadata()
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 1704, in _init_metadata
>     self.__buffer_rows()
>   File
> "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 1721, in __buffer_rows
>     self.__rowbuffer = self.cursor.fetchmany(size)
>   File "/usr/local/lib/python2.6/decimal.py", line 540, in __new__
>     m = _parser(value.strip())
> OperationalError: could not receive data from server: Error 0
>
> d
>
> /*
> Davide Cittaro
>
> Cogentech - Consortium for Genomic Technologies
> via adamello, 16
> 20139 Milano
> Italy
>
> tel.: +39(02)574303007
> e-mail: [hidden email]
> <mailto:[hidden email]>
> */
>
>
>

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Re: [galaxy-dev] again on multiple server instances

Davide Cittaro

On May 21, 2010, at 4:38 PM, Nate Coraor wrote:

Davide Cittaro wrote:

Mmm...

Do you happen to know how your Postgres was compiled?  This can happen if --enable-thread-safety wasn't specified.


Mmm.. I've installed the binary version provided for nexenta (i.e. apt-get install), I'll check for that

Also, if you're scrambling psycopg2 for a platform we don't provide, the bug could be in the way I've instructed the scramble script to compile the static libpq.


Using this psycopg2-2.0.13_8.4.2_static-py2.6-solaris-2.10-i86pc_64-ucs2.egg
I see that you used postgres 8.4 while I have postgres 8.3.... Mmm... the strange fact is that, before trying the multiserver I was able to run some job... 

For Main on Solaris I build the egg by hand and dynamically link with the real Postgres install instead of statically linking our auto-compiled version:

PYTHONPATH=/path/to/galaxy/scripts/scramble/lib python setup.py build_ext --rpath=/usr/postgres/8.3/lib/64 egg_info --tag-build=_8.2.6_static bdist_egg


I'll try that

Also, is threadlocal enabled in the config?

database_engine_option_strategy = threadlocal


It is

thanks

d

--nate

galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 15:53:48,681 RoundRobin queue: inserted new job for user/session = 6
galaxy.jobs DEBUG 2010-05-21 15:53:48,681 job 24 put in policy queue
galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 15:53:48,682 RoundRobin queue: retrieving job from job queue for session = 6
galaxy.jobs DEBUG 2010-05-21 15:53:48,682 dispatching job 24 to local runner
galaxy.jobs DEBUG 2010-05-21 15:53:48,773 job 24 dispatched
galaxy.jobs.runners.local DEBUG 2010-05-21 15:53:49,018 executing: python /data/galaxy_dist/tools/data_source/upload.py /tmp/tmphIrPuJ         71:/data/galaxy_dist/database/job_working_directory/24/dataset_71_files:/data/galaxy_dist/database/files/000/dataset_71.dat   galaxy.jobs.runners.local DEBUG 2010-05-21 15:53:49,495 execution finished: python /data/galaxy_dist/tools/data_source/upload.py /tmp/tmphIrPuJ         71:/data/galaxy_dist/database/job_working_directory/24/dataset_71_files:/data/galaxy_dist/database/files/000/dataset_71.dat   galaxy.jobs.runners.local ERROR 2010-05-21 15:53:49,689 Job wrapper finish method failed
Traceback (most recent call last):
 File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 122, in run_job
   job_wrapper.finish( stdout, stderr )
 File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 569, in finish
   self.sa_session.flush()
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do
   return getattr(self.registry(), name)(*args, **kwargs)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1356, in flush
   self._flush(objects)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1443, in _flush
   flush_context.finalize_flush_changes()
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 288, in finalize_flush_changes
   self.session._register_newly_persistent(elem.state)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1015, in _register_newly_persistent
   instance_key = mapper._identity_key_from_state(state)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1085, in _identity_key_from_state
   return self.identity_key_from_primary_key(self._primary_key_from_state(state))
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1096, in _primary_key_from_state
   return [self._get_state_attr_by_column(state, column) for column in self.primary_key]
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1110, in _get_state_attr_by_column
   return self._get_col_to_prop(column).getattr(state, column)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/properties.py", line 99, in getattr
   return state.get_impl(self.key).get(state, state.dict)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get
   value = callable_()
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/state.py", line 185, in __call__
   attr.impl.key in unmodified
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1878, in _load_scalar_attributes
   result = session.query(mapper)._get(identity_key, refresh_state=state, only_load_props=attribute_names)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1500, in _get
   return q.all()[0]
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all
   return list(self)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__
   return self._execute_and_instances(context)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances
   result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none())
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute
   clause, params or {})
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute
   return Connection.executors[c](self, object, multiparams, params)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement
   return self.__execute_context(context)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 901, in __execute_context
   return context.get_result_proxy()
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy
   return base.BufferedRowResultProxy(self)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1415, in __init__
   self._init_metadata()
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata
   self.__buffer_rows()
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows
   self.__rowbuffer = self.cursor.fetchmany(size)
 File "/usr/local/lib/python2.6/decimal.py", line 540, in __new__
   m = _parser(value.strip())
OperationalError: could not receive data from server: Error 0
galaxy.jobs.runners.local ERROR 2010-05-21 15:53:49,740 Uncaught exception running job
Traceback (most recent call last):
 File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 46, in run_next
   self.run_job( job_wrapper )
 File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 125, in run_job
   job_wrapper.fail("Unable to finish job", exception=True)
 File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 413, in fail
   self.sa_session.refresh( job )
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do
   return getattr(self.registry(), name)(*args, **kwargs)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 929, in refresh
   only_load_props=attribute_names) is None:
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1500, in _get
   return q.all()[0]
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all
   return list(self)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__
   return self._execute_and_instances(context)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances
   result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none())
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute
   clause, params or {})
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute
   return Connection.executors[c](self, object, multiparams, params)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement
   return self.__execute_context(context)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 901, in __execute_context
   return context.get_result_proxy()
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy
   return base.BufferedRowResultProxy(self)
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1415, in __init__
   self._init_metadata()
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata
   self.__buffer_rows()
 File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows
   self.__rowbuffer = self.cursor.fetchmany(size)
 File "/usr/local/lib/python2.6/decimal.py", line 540, in __new__
   m = _parser(value.strip())
OperationalError: could not receive data from server: Error 0
d
/*
Davide Cittaro
Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy
tel.: +39(02)574303007
e-mail: [hidden email] <[hidden email]>
*/


/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
*/




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Re: [galaxy-dev] again on multiple server instances

Modi, Amit
In reply to this post by Nate Coraor (nate@bx.psu.edu)
Re: [galaxy-dev] again on multiple server instances
Hi,

I have added a few tools in the galaxy.For one of these tools it sometime gives an error.
but everytime I execute this tool it renders this exception on console.

Can anybody please help me fix it.

galaxy.jobs DEBUG 2010-05-21 14:30:03,166 dispatching job 203 to sge runner
galaxy.jobs.runners.sge ERROR 2010-05-21 14:30:03,508 failure running job 203
Traceback (most recent call last):
  File "/export/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/sge.py", line 120, in queue_job
    job_wrapper.prepare()
  File "/export/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 390, in prepare
    self.command_line = self.tool.build_command_line( param_dict )
  File "/export/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 1343, in build_command_line
    command_line = fill_template( self.command, context=param_dict )
  File "/export/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template
    return str( Template( source=template_text, searchList=[context] ) )
  File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1244, in __init__
    self._compile(source, file, compilerSettings=compilerSettings)
  File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1538, in _compile
    keepRefToGeneratedCode=True)
  File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 745, in compile
    compiler.compile()
  File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Compiler.py", line 1670, in compile
    self._parser.parse()
  File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py", line 1488, in parse
    self.eatDirective()
  File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py", line 1610, in eatDirective
    directiveParser()
  File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py", line 1755, in eatEndDirective
    raise ParseError(self, msg='Invalid end directive')
ParseError:

Invalid end directive
Line 3, column 6

Line|Cheetah Code
----|-------------------------------------------------------------
2   |    #else: #gkelvin $confile.nonmeta
3   |    #end
          ^
4   |  

galaxy.jobs DEBUG 2010-05-21 14:30:03,509 job 203 dispatched


Regards,
Amit Modi


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Re: [galaxy-dev] again on multiple server instances

Jesse Erdmann
It looks to me like you might want to change the if/else to something like:

#if
  ## action
#else
  # set $gkelvin $confile.nonmeta
#end

I'm not certain exactly what you're trying to do, but I'm pretty sure
that the two '#' on the same line without being a '##' to indicate a
comment are part of the problem you're seeing below.

If that isn't what you're looking for, I recommend checking out the
Cheetah users guide:
http://www.cheetahtemplate.org/docs/users_guide_html/users_guide.html

On Fri, May 21, 2010 at 1:26 PM, Modi, Amit
<[hidden email]> wrote:

> Hi,
>
> I have added a few tools in the galaxy.For one of these tools it sometime
> gives an error.
> but everytime I execute this tool it renders this exception on console.
>
> Can anybody please help me fix it.
>
> galaxy.jobs DEBUG 2010-05-21 14:30:03,166 dispatching job 203 to sge runner
> galaxy.jobs.runners.sge ERROR 2010-05-21 14:30:03,508 failure running job
> 203
> Traceback (most recent call last):
>   File "/export/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/sge.py",
> line 120, in queue_job
>     job_wrapper.prepare()
>   File "/export/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
> 390, in prepare
>     self.command_line = self.tool.build_command_line( param_dict )
>   File "/export/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line
> 1343, in build_command_line
>     command_line = fill_template( self.command, context=param_dict )
>   File "/export/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line
> 9, in fill_template
>     return str( Template( source=template_text, searchList=[context] ) )
>   File
> "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py",
> line 1244, in __init__
>     self._compile(source, file, compilerSettings=compilerSettings)
>   File
> "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py",
> line 1538, in _compile
>     keepRefToGeneratedCode=True)
>   File
> "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py",
> line 745, in compile
>     compiler.compile()
>   File
> "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Compiler.py",
> line 1670, in compile
>     self._parser.parse()
>   File
> "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py",
> line 1488, in parse
>     self.eatDirective()
>   File
> "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py",
> line 1610, in eatDirective
>     directiveParser()
>   File
> "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py",
> line 1755, in eatEndDirective
>     raise ParseError(self, msg='Invalid end directive')
> ParseError:
>
> Invalid end directive
> Line 3, column 6
>
> Line|Cheetah Code
> ----|-------------------------------------------------------------
> 2   |    #else: #gkelvin $confile.nonmeta
> 3   |    #end
>           ^
> 4   |
>
> galaxy.jobs DEBUG 2010-05-21 14:30:03,509 job 203 dispatched
>
>
> Regards,
> Amit Modi
>
> ________________________________
>
> ----------------------------------------- Confidentiality Notice: The
> following mail message, including any attachments, is for the sole use of
> the intended recipient(s) and may contain confidential and privileged
> information. The recipient is responsible to maintain the confidentiality of
> this information and to use the information only for authorized purposes. If
> you are not the intended recipient (or authorized to receive information for
> the intended recipient), you are hereby notified that any review, use,
> disclosure, distribution, copying, printing, or action taken in reliance on
> the contents of this e-mail is strictly prohibited. If you have received
> this communication in error, please notify us immediately by reply e-mail
> and destroy all copies of the original message. Thank you.
>
> _______________________________________________
> galaxy-dev mailing list
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>
>



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Masonic Cancer Center
University of Minnesota
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