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Created August 13, 2014 10:28
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gistfile1.py
(sqmpy-env)pc-p282(/W5/sade/workspace/simple-queue-manager) SAGA_VERBOSE=DEBUG python run.py
2014:08:13 12:27:00 MainThread saga : [INFO ] saga-python version: 0.17
* Running on http://0.0.0.0:5001/
* Restarting with reloader
2014:08:13 12:27:02 MainThread saga : [INFO ] saga-python version: 0.17
in submit.... before wrapper initialization
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.myproxy
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.context.myproxy for saga.Context API with URL scheme(s) ['myproxy://']
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.x509
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.context.x509 for saga.Context API with URL scheme(s) ['x509://']
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.ssh
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.context.ssh for saga.Context API with URL scheme(s) ['ssh://']
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.userpass
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.context.userpass for saga.Context API with URL scheme(s) ['userpass://']
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.shell.shell_job
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Service API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://']
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Job API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://']
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.shell.shell_file
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_file for saga.namespace.Directory API with URL scheme(s) ['file://', 'local://', 'sftp://', 'gsisftp://', 'ssh://', 'gsissh://']
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_file for saga.namespace.Entry API with URL scheme(s) ['file://', 'local://', 'sftp://', 'gsisftp://', 'ssh://', 'gsissh://']
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_file for saga.filesystem.Directory API with URL scheme(s) ['file://', 'local://', 'sftp://', 'gsisftp://', 'ssh://', 'gsissh://']
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_file for saga.filesystem.File API with URL scheme(s) ['file://', 'local://', 'sftp://', 'gsisftp://', 'ssh://', 'gsissh://']
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.shell.shell_resource
2014:08:13 12:27:05 Dummy-1 saga.Engine : [WARNING ] Skipping adaptor saga.adaptors.shell.shell_resource: beta versions are disabled (v0.1.beta)
2014:08:13 12:27:05 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.redis.redis_advert
2014:08:13 12:27:06 Dummy-1 saga.Engine : [WARNING ] Skipping adaptor saga.adaptors.redis.redis_advert: beta versions are disabled (v0.2.beta)
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.sge.sgejob
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Service API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Job API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.pbs.pbsjob
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Service API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Job API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.lsf.lsfjob
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Service API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Job API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.irods.irods_replica
2014:08:13 12:27:06 Dummy-1 saga.Engine : [ERROR ] Skipping adaptor saga.adaptors.irods.irods_replica: failed self test: Could not run iRODS/ils. Check iRODSenvironment and certificates ('module' object has no attribute 'logger') (/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/adaptors/irods/irods_replica.py +200 (sanity_check) : "environment and certificates (%s)" % ex))
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.condor.condorjob
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Service API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Job API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.slurm.slurm_job
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.slurm.slurm_job for saga.job.Service API with URL scheme(s) ['slurm://', 'slurm+ssh://', 'slurm+gsissh://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.slurm.slurm_job for saga.job.Job API with URL scheme(s) ['slurm://', 'slurm+ssh://', 'slurm+gsissh://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.http.http_file
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.http.http_file for saga.namespace.Entry API with URL scheme(s) ['http://', 'https://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.http.http_file for saga.filesystem.File API with URL scheme(s) ['http://', 'https://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.aws.ec2_resource
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.aws.ec2_resource for saga.Context API with URL scheme(s) ['ec2://', 'ec2_keypair://', 'openstack://', 'eucalyptus://', 'euca://', 'aws://', 'amazon://', 'http://', 'https://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.aws.ec2_resource for saga.resource.Manager API with URL scheme(s) ['ec2://', 'ec2_keypair://', 'openstack://', 'eucalyptus://', 'euca://', 'aws://', 'amazon://', 'http://', 'https://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.aws.ec2_resource for saga.resource.Compute API with URL scheme(s) ['ec2://', 'ec2_keypair://', 'openstack://', 'eucalyptus://', 'euca://', 'aws://', 'amazon://', 'http://', 'https://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Loading adaptor saga.adaptors.loadl.loadljob
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Service API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://']
2014:08:13 12:27:06 Dummy-1 saga.Engine : [INFO ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Job API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://']
2014:08:13 12:27:06 Dummy-1 saga.saga.adaptor.ssh : [INFO ] default ssh key at /home/sade/.ssh/id_rsa
2014:08:13 12:27:06 Dummy-1 saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /home/sade/.ssh/authorized_keys (no public key: /home/sade/.ssh/authorized_keys.pub)
2014:08:13 12:27:07 Dummy-1 saga.saga.adaptor.ssh : [INFO ] default ssh key at /home/sade/.ssh/id_dsa
2014:08:13 12:27:07 Dummy-1 saga.saga.adaptor.ssh : [INFO ] default ssh key at /home/sade/.ssh/identity
2014:08:13 12:27:07 Dummy-1 saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /home/sade/.ssh/authorized_keys2 (no public key: /home/sade/.ssh/authorized_keys2.pub)
2014:08:13 12:27:07 Dummy-1 saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /home/sade/.ssh/known_hosts__ (no public key: /home/sade/.ssh/known_hosts__.pub)
2014:08:13 12:27:07 Dummy-1 saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /home/sade/.ssh/known_hosts (no public key: /home/sade/.ssh/known_hosts.pub)
2014:08:13 12:27:07 Dummy-1 saga.DefaultSession : [DEBUG ] adding context : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/id_rsa.pub', 'UserKey' : '/home/sade/.ssh/id_rsa'}
2014:08:13 12:27:07 Dummy-1 saga.ContextSSH : [INFO ] init SSH context for key at '/home/sade/.ssh/id_rsa' done
2014:08:13 12:27:07 Dummy-1 saga.DefaultSession : [DEBUG ] default context [saga.adaptor.ssh ] : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/id_rsa.pub', 'UserKey' : '/home/sade/.ssh/id_rsa'}
2014:08:13 12:27:07 Dummy-1 saga.DefaultSession : [DEBUG ] adding context : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/id_dsa.pub', 'UserKey' : '/home/sade/.ssh/id_dsa'}
2014:08:13 12:27:07 Dummy-1 saga.ContextSSH : [INFO ] init SSH context for key at '/home/sade/.ssh/id_dsa' done
2014:08:13 12:27:07 Dummy-1 saga.DefaultSession : [DEBUG ] default context [saga.adaptor.ssh ] : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/id_dsa.pub', 'UserKey' : '/home/sade/.ssh/id_dsa'}
2014:08:13 12:27:07 Dummy-1 saga.DefaultSession : [DEBUG ] adding context : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/identity.pub', 'UserKey' : '/home/sade/.ssh/identity'}
2014:08:13 12:27:07 Dummy-1 saga.ContextSSH : [INFO ] init SSH context for key at '/home/sade/.ssh/identity' done
2014:08:13 12:27:07 Dummy-1 saga.DefaultSession : [DEBUG ] default context [saga.adaptor.ssh ] : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/identity.pub', 'UserKey' : '/home/sade/.ssh/identity'}
2014:08:13 12:27:07 Dummy-1 saga.saga.Session : [DEBUG ] adding context : {'LifeTime' : '-1', 'Type' : 'ssh'}
2014:08:13 12:27:07 Dummy-1 saga.PTYShell : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7facfc48a650>
2014:08:13 12:27:07 Dummy-1 saga.PTYShell : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$
2014:08:13 12:27:07 Dummy-1 saga.PTYShell : [DEBUG ] open master pty for [ssh] [joe223423] sade: /usr/bin/env TERM=vt100 "/usr/bin/ssh" -t -o IdentityFile=/home/sade/.ssh/id_rsa -o IdentityFile=/home/sade/.ssh/id_dsa -o IdentityFile=/home/sade/.ssh/identity -o ControlMaster=yes -o ControlPath=/tmp/saga_ssh_sade_%h_%p.ctrl joe223423'
2014:08:13 12:27:07 Dummy-1 saga.PTYShell : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7facfc7e4250>
2014:08:13 12:27:07 Dummy-1 saga.PTYShell : [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/home/sade/.ssh/id_rsa -o IdentityFile=/home/sade/.ssh/id_dsa -o IdentityFile=/home/sade/.ssh/identity -o ControlMaster=yes -o ControlPath=/tmp/saga_ssh_sade_%h_%p.ctrl joe223423
2014:08:13 12:27:07 Dummy-1 saga.PTYShell : [DEBUG ] write: [ 10] [ 51] ( export PS1='$' > /dev/null 2>&1 || set prompt='$'\n)
127.0.0.1 - - [13/Aug/2014 12:27:07] "POST /job/submit HTTP/1.1" 500 -
Traceback (most recent call last):
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/flask/app.py", line 1836, in __call__
return self.wsgi_app(environ, start_response)
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/flask/app.py", line 1820, in wsgi_app
response = self.make_response(self.handle_exception(e))
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/flask/app.py", line 1403, in handle_exception
reraise(exc_type, exc_value, tb)
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/flask/app.py", line 1817, in wsgi_app
response = self.full_dispatch_request()
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/flask/app.py", line 1477, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/flask/app.py", line 1381, in handle_user_exception
reraise(exc_type, exc_value, tb)
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/flask/app.py", line 1475, in full_dispatch_request
rv = self.dispatch_request()
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/flask/app.py", line 1461, in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/flask_login.py", line 758, in decorated_view
return func(*args, **kwargs)
File "/W5/sade/workspace/simple-queue-manager/sqmpy/job/views.py", line 110, in submit
description=form.description.data)
File "/W5/sade/workspace/simple-queue-manager/sqmpy/job/services.py", line 37, in submit_job
**kwargs)
File "/W5/sade/workspace/simple-queue-manager/sqmpy/job/manager.py", line 85, in submit_job
saga_wrapper = SagaJobWrapper(job)
File "/W5/sade/workspace/simple-queue-manager/sqmpy/job/saga_helper.py", line 65, in __init__
session=self._session)
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/job/service.py", line 109, in __init__
url, session, ttype=_ttype)
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/base.py", line 99, in __init__
self._init_task = self._adaptor.init_instance (adaptor_state, *args, **kwargs)
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/adaptors/cpi/decorators.py", line 51, in wrap_function
return sync_function (self, *args, **kwargs)
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/adaptors/sge/sgejob.py", line 316, in init_instance
self.shell = saga.utils.pty_shell.PTYShell(pty_url, self.session)
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/utils/pty_shell.py", line 224, in __init__
self.pty_info = self.factory.initialize (self.url, self.session, self.prompt, self.logger)
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/utils/pty_shell_factory.py", line 183, in initialize
self._initialize_pty (info['pty'], info, is_shell=True)
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/utils/pty_shell_factory.py", line 386, in _initialize_pty
raise ptye.translate_exception (e)
NoSuccess: process I/O failed: (/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/utils/pty_process.py +512 (read) : raise se.NoSuccess ("process I/O failed: %s" % self.tail))
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