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] serving on http://127.0.0.1:8101 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 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(.*) 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: davide.cittaro@ifom-ieo-campus.it */