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radical-cybertools / radical.pilot

RADICAL-Pilot
http://radical-cybertools.github.io/radical-pilot/index.html
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Session creation failure, OperationFailure: None #725

Closed vivek-bala closed 9 years ago

vivek-bala commented 9 years ago

Justin from Rice has been facing this issue while using ExTASY, the failure seems to be during session creation. The mongodb being used is mongodb://extasy:extasyproject@extasy-db.epcc.ed.ac.uk/radicalpilot. This is reproducible from his machine, although I have not been able to reproduce this on mine.

ExTASY documentation: http://extasy.readthedocs.org/en/latest/index.html (please install using the devel link)

2015:09:15 14:31:21 2420   MainThread   saga                  : [INFO    ] saga-python          version: 0.35
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] radical.pilot        version: 0.35
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.myproxy
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.myproxy for saga.Context API with URL scheme(s) ['myproxy://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.x509
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.x509 for saga.Context API with URL scheme(s) ['x509://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.ssh
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.ssh for saga.Context API with URL scheme(s) ['ssh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.userpass
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.userpass for saga.Context API with URL scheme(s) ['userpass://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.shell.shell_job
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Service API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Job API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.shell.shell_file
2015:09:15 14:31:21 2420   MainThread   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://']
2015:09:15 14:31:21 2420   MainThread   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://']
2015:09:15 14:31:21 2420   MainThread   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://']
2015:09:15 14:31:21 2420   MainThread   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://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.shell.shell_resource
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [WARNING ] Skipping adaptor saga.adaptors.shell.shell_resource: beta versions are disabled (v0.1.beta)
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.redis.redis_advert
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [WARNING ] Skipping adaptor saga.adaptors.redis.redis_advert 1: module loading failed: No module named redis
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.sge.sgejob
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Service API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Job API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.pbs.pbsjob
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Service API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Job API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.lsf.lsfjob
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Service API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Job API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.condor.condorjob
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Service API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Job API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.slurm.slurm_job
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.slurm.slurm_job for saga.job.Service API with URL scheme(s) ['slurm://', 'slurm+ssh://', 'slurm+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.slurm.slurm_job for saga.job.Job API with URL scheme(s) ['slurm://', 'slurm+ssh://', 'slurm+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.http.http_file
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.http.http_file for saga.namespace.Entry API with URL scheme(s) ['http://', 'https://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.http.http_file for saga.filesystem.File API with URL scheme(s) ['http://', 'https://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.aws.ec2_resource
2015:09:15 14:31:21 2420   MainThread   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://']
2015:09:15 14:31:21 2420   MainThread   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://']
2015:09:15 14:31:21 2420   MainThread   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://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.loadl.loadljob
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Service API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Job API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.globus_online.go_file
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.namespace.Directory API with URL scheme(s) ['go://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.namespace.Entry API with URL scheme(s) ['go://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.filesystem.Directory API with URL scheme(s) ['go://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.filesystem.File API with URL scheme(s) ['go://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.torque.torquejob
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.torque.torquejob for saga.job.Service API with URL scheme(s) ['torque://', 'torque+ssh://', 'torque+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.torque.torquejob for saga.job.Job API with URL scheme(s) ['torque://', 'torque+ssh://', 'torque+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.pbspro.pbsprojob
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbspro.pbsprojob for saga.job.Service API with URL scheme(s) ['pbspro://', 'pbspro+ssh://', 'pbspro+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbspro.pbsprojob for saga.job.Job API with URL scheme(s) ['pbspro://', 'pbspro+ssh://', 'pbspro+gsissh://']
2015:09:15 14:31:21 2420   MainThread   saga.saga.adaptor.ssh : [INFO    ] ignore ssh key at /home/jchen/.ssh/known_hosts (no public key: /home/jchen/.ssh/known_hosts.pub)
2015:09:15 14:31:21 2420   MainThread   saga.saga.adaptor.ssh : [WARNING ] ignore  ssh key at /home/jchen/.ssh/id_rsa (requires passphrase)
2015:09:15 14:31:21 2420   MainThread   saga.saga.adaptor.ssh : [INFO    ] ignore ssh key at /home/jchen/.ssh/jc49@stampede.tacc.utexas.edu (no public key: /home/jchen/.ssh/jc49@stampede.tacc.utexas.edu.pub)
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] using database url  mongodb://extasy:extasyproject@extasy-db.epcc.ed.ac.uk/radicalpilot
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] using database path radicalpilot
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/stfc.json
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for stfc.joule
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/radical.json
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for radical.tutorial
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/rice.json
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for rice.biou
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for rice.davinci
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/local.json
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for local.localhost
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/aliases.json
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/nersc.json
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.hopper_ccm
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.hopper
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.edison
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.edison_ccm
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/xsede.json
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.blacklight
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.supermic
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.lonestar
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.comet
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.stampede
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.trestles
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.gordon
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/futuregrid.json
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.xray
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.echo
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.india
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.bravo
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.xray_ccm
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.delta
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/ornl.json
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ornl.titan
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/epsrc.json
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for epsrc.archer
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/ncsa.json
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ncsa.bw_ccm
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ncsa.bw
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/ncar.json
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ncar.yellowstone
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/das4.json
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for das4.fs2
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/lrz.json
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for lrz.supermuc
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/iu.json
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for iu.bigred2
2015:09:15 14:31:21 2420   MainThread   radical.pilot         : [INFO    ] Load resource configurations for iu.bigred2_ccm
2015:09:15 14:31:22 2420   MainThread   radical.pilot         : [ERROR   ] session create failed
Traceback (most recent call last):
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/session.py", line 226, in __init__
    db_name = self._database_name)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/db/database.py", line 104, in new
    dbs = Session(db_url, db_name)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/db/database.py", line 75, in __init__
    mongo, db, dbname, pname, cname = ru.mongodb_connect (url)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/utils/misc.py", line 86, in mongodb_connect
    mongo = pymongo.MongoClient (host=host, port=port)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 374, in __init__
    self._ensure_connected(True)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 939, in _ensure_connected
    self.__ensure_member()
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 813, in __ensure_member
    member, nodes = self.__find_node()
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 873, in __find_node
    member, nodes = self.__try_node(candidate)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 720, in __try_node
    {'ismaster': 1})
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 703, in __simple_command
    helpers._check_command_response(response, None, msg)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/helpers.py", line 133, in _check_command_response
    response)
OperationFailure: None
2015:09:15 14:31:22 2420   MainThread   radical.pilot         : [DEBUG   ] session rp.session.jchen-Vostro-260.jchen.016693.0006 closing
Exception AttributeError: "'Session' object has no attribute '_dbs'" in <bound method Session.__del__ of <radical.pilot.session.Session object at 0x7f2bbd5350d0>> ignored
TensorDuck commented 9 years ago

I should add that as far as I know, I have no firewalls up (I checked the two typical firewalls on Ubuntu).

andre-merzky commented 9 years ago

The error is not reported correctly, I'll fix that. But at the core, this does look like a connection setup error toward mongodb.

Could you please, from your machine, try: telnet extasy-db.epcc.ed.ac.uk 27017 to see if the connection gets through? If you have the mongodb client tools installed, you can also run:

$ mongo extasy-db.epcc.ed.ac.uk:27017
MongoDB shell version: 2.4.5
connecting to: extasy-db.epcc.ed.ac.uk:27017/test
Error while trying to show server startup warnings: not authorized on admin to execute command { getLog: "startupWarnings" }
> 
bye

It might be a firewall between your box and epcc kicking in...

TensorDuck commented 9 years ago

With Telnet, I think it works. I get:

$ telnet extasy-db.epcc.ed.ac.uk 27017 Trying 129.215.62.213... Connected to extasy-db.epcc.ed.ac.uk. Escape character is '^]'.

Using mongoDB as well, I get:

$ mongo extasy-db.epcc.ed.ac.uk:27017 mongo: /home/jchen/miniconda/lib/libcrypto.so.1.0.0: no version information available (required by mongo) mongo: /home/jchen/miniconda/lib/libssl.so.1.0.0: no version information available (required by mongo) MongoDB shell version: 2.4.9 connecting to: extasy-db.epcc.ed.ac.uk:27017/test Error while trying to show server startup warnings: not authorized on admin to execute command { getLog: "startupWarnings" }

I do get errors related to miniconda, but it still connect nonetheless.

Best -Justin

vivek-bala commented 9 years ago

Are you currently using anaconda (in user mode) or python ?

andre-merzky commented 9 years ago

yeah, miniconda is an environment which we do not yet test again, and I can't day much on how RP would behave there I'm afraid. At this point we usually expect plain python, virtualenv and pip as deployment route.

Having said that: I pushed a branch fix/dbs_var which should help to get a better error message, which would at least verify that we are using the right dburl when connecting. Would you mind giving this a try?

Thanks!

TensorDuck commented 9 years ago

So right now I have anaconda, but I installed a separate python and made a new virtualenv with the new python.

Anyways, with the new branch fix/dbs_var, I get this error. It looks like a different error that it's having trouble importing something?

2015:09:15 15:30:43 4739   MainThread   saga                  : [INFO    ] saga-python          version: 0.35
Traceback (most recent call last):
  File "/home/jchen/ExTASY/ExTASY-tools/bin/extasy", line 9, in <module>
    load_entry_point('radical.ensemblemd.extasy===0.1-20-g347657f', 'console_scripts', 'extasy')()
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pkg_resources/__init__.py", line 558, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2682, in load_entry_point
    return ep.load()
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2355, in load
    return self.resolve()
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2361, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/runme.py", line 3, in <module>
    import radical.pilot
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/__init__.py", line 20, in <module>
    from .scheduler  import *
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/scheduler/__init__.py", line 14, in <module>
    from direct_submission import DirectSubmissionScheduler
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/scheduler/direct_submission.py", line 16, in <module>
    from ..utils    import logger
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/utils/__init__.py", line 21, in <module>
    logger = ru.get_logger('radical.pilot')
AttributeError: 'module' object has no attribute 'get_logger'
andre-merzky commented 9 years ago

Ah - I am really sorry, I branched from the wrong base. I used devel, which in turn requires the devel branches for saga-python and radical.utils. Let me fix this, brb...

andre-merzky commented 9 years ago

Would you please try fix/dbs_var_2 ? Sorry for the trouble...

TensorDuck commented 9 years ago

No problem, thanks for your help!

I get the following output from the extasy.log:

2015:09:15 16:06:07 5175   MainThread   saga                  : [INFO    ] saga-python          version: 0.35
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] radical.pilot        version: v0.35-1-g846e6ce@detached-846e6ce
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.myproxy
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.myproxy for saga.Context API with URL scheme(s) ['myproxy://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.x509
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.x509 for saga.Context API with URL scheme(s) ['x509://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.ssh
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.ssh for saga.Context API with URL scheme(s) ['ssh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.userpass
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.userpass for saga.Context API with URL scheme(s) ['userpass://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.shell.shell_job
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Service API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Job API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.shell.shell_file
2015:09:15 16:06:07 5175   MainThread   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://']
2015:09:15 16:06:07 5175   MainThread   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://']
2015:09:15 16:06:07 5175   MainThread   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://']
2015:09:15 16:06:07 5175   MainThread   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://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.shell.shell_resource
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [WARNING ] Skipping adaptor saga.adaptors.shell.shell_resource: beta versions are disabled (v0.1.beta)
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.redis.redis_advert
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [WARNING ] Skipping adaptor saga.adaptors.redis.redis_advert 1: module loading failed: No module named redis
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.sge.sgejob
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Service API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Job API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.pbs.pbsjob
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Service API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Job API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.lsf.lsfjob
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Service API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Job API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.condor.condorjob
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Service API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Job API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.slurm.slurm_job
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.slurm.slurm_job for saga.job.Service API with URL scheme(s) ['slurm://', 'slurm+ssh://', 'slurm+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.slurm.slurm_job for saga.job.Job API with URL scheme(s) ['slurm://', 'slurm+ssh://', 'slurm+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.http.http_file
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.http.http_file for saga.namespace.Entry API with URL scheme(s) ['http://', 'https://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.http.http_file for saga.filesystem.File API with URL scheme(s) ['http://', 'https://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.aws.ec2_resource
2015:09:15 16:06:07 5175   MainThread   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://']
2015:09:15 16:06:07 5175   MainThread   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://']
2015:09:15 16:06:07 5175   MainThread   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://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.loadl.loadljob
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Service API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Job API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.globus_online.go_file
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.namespace.Directory API with URL scheme(s) ['go://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.namespace.Entry API with URL scheme(s) ['go://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.filesystem.Directory API with URL scheme(s) ['go://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.filesystem.File API with URL scheme(s) ['go://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.torque.torquejob
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.torque.torquejob for saga.job.Service API with URL scheme(s) ['torque://', 'torque+ssh://', 'torque+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.torque.torquejob for saga.job.Job API with URL scheme(s) ['torque://', 'torque+ssh://', 'torque+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.pbspro.pbsprojob
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbspro.pbsprojob for saga.job.Service API with URL scheme(s) ['pbspro://', 'pbspro+ssh://', 'pbspro+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbspro.pbsprojob for saga.job.Job API with URL scheme(s) ['pbspro://', 'pbspro+ssh://', 'pbspro+gsissh://']
2015:09:15 16:06:07 5175   MainThread   saga.saga.adaptor.ssh : [INFO    ] ignore ssh key at /home/jchen/.ssh/known_hosts (no public key: /home/jchen/.ssh/known_hosts.pub)
2015:09:15 16:06:07 5175   MainThread   saga.saga.adaptor.ssh : [WARNING ] ignore  ssh key at /home/jchen/.ssh/id_rsa (requires passphrase)
2015:09:15 16:06:07 5175   MainThread   saga.saga.adaptor.ssh : [INFO    ] ignore ssh key at /home/jchen/.ssh/jc49@stampede.tacc.utexas.edu (no public key: /home/jchen/.ssh/jc49@stampede.tacc.utexas.edu.pub)
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] using database url  mongodb://extasy:extasyproject@extasy-db.epcc.ed.ac.uk/radicalpilot
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] using database path radicalpilot
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/stfc.json
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for stfc.joule
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/radical.json
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for radical.tutorial
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/rice.json
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for rice.biou
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for rice.davinci
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/local.json
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for local.localhost
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/aliases.json
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/nersc.json
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.hopper_ccm
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.hopper
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.edison
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.edison_ccm
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/xsede.json
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.blacklight
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.supermic
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.lonestar
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.comet
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.stampede
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.trestles
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.gordon
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/futuregrid.json
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.xray
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.echo
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.india
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.bravo
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.xray_ccm
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.delta
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/ornl.json
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ornl.titan
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/epsrc.json
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for epsrc.archer
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/ncsa.json
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ncsa.bw_ccm
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ncsa.bw
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/ncar.json
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ncar.yellowstone
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/das4.json
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for das4.fs2
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/lrz.json
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for lrz.supermuc
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/iu.json
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for iu.bigred2
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [INFO    ] Load resource configurations for iu.bigred2_ccm
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [ERROR   ] session create failed
Traceback (most recent call last):
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/session.py", line 226, in __init__
    db_name = self._database_name)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/db/database.py", line 104, in new
    dbs = Session(db_url, db_name)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/db/database.py", line 75, in __init__
    mongo, db, dbname, pname, cname = ru.mongodb_connect (url)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/utils/misc.py", line 86, in mongodb_connect
    mongo = pymongo.MongoClient (host=host, port=port)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 374, in __init__
    self._ensure_connected(True)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 939, in _ensure_connected
    self.__ensure_member()
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 813, in __ensure_member
    member, nodes = self.__find_node()
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 873, in __find_node
    member, nodes = self.__try_node(candidate)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 720, in __try_node
    {'ismaster': 1})
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 703, in __simple_command
    helpers._check_command_response(response, None, msg)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/helpers.py", line 133, in _check_command_response
    response)
OperationFailure: None
2015:09:15 16:06:07 5175   MainThread   radical.pilot         : [DEBUG   ] session rp.session.jchen-Vostro-260.jchen.016693.0010 closing
Exception AttributeError: "'Session' object has no attribute '_dbs'" in <bound method Session.__del__ of <radical.pilot.session.Session object at 0x7fa5c6e10150>> ignored
andre-merzky commented 9 years ago

I pushed another fix to the same branch - would you mind giving it another try? Thanks!

TensorDuck commented 9 years ago

I get:

2015:09:15 16:55:16 5516   MainThread   saga                  : [INFO    ] saga-python          version: 0.35
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] radical.pilot        version: v0.35-2-g73fa285@detached-73fa285
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.myproxy
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.myproxy for saga.Context API with URL scheme(s) ['myproxy://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.x509
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.x509 for saga.Context API with URL scheme(s) ['x509://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.ssh
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.ssh for saga.Context API with URL scheme(s) ['ssh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.userpass
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.userpass for saga.Context API with URL scheme(s) ['userpass://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.shell.shell_job
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Service API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Job API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.shell.shell_file
2015:09:15 16:55:16 5516   MainThread   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://']
2015:09:15 16:55:16 5516   MainThread   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://']
2015:09:15 16:55:16 5516   MainThread   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://']
2015:09:15 16:55:16 5516   MainThread   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://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.shell.shell_resource
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [WARNING ] Skipping adaptor saga.adaptors.shell.shell_resource: beta versions are disabled (v0.1.beta)
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.redis.redis_advert
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [WARNING ] Skipping adaptor saga.adaptors.redis.redis_advert 1: module loading failed: No module named redis
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.sge.sgejob
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Service API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Job API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.pbs.pbsjob
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Service API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Job API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.lsf.lsfjob
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Service API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Job API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.condor.condorjob
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Service API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Job API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.slurm.slurm_job
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.slurm.slurm_job for saga.job.Service API with URL scheme(s) ['slurm://', 'slurm+ssh://', 'slurm+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.slurm.slurm_job for saga.job.Job API with URL scheme(s) ['slurm://', 'slurm+ssh://', 'slurm+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.http.http_file
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.http.http_file for saga.namespace.Entry API with URL scheme(s) ['http://', 'https://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.http.http_file for saga.filesystem.File API with URL scheme(s) ['http://', 'https://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.aws.ec2_resource
2015:09:15 16:55:16 5516   MainThread   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://']
2015:09:15 16:55:16 5516   MainThread   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://']
2015:09:15 16:55:16 5516   MainThread   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://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.loadl.loadljob
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Service API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Job API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.globus_online.go_file
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.namespace.Directory API with URL scheme(s) ['go://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.namespace.Entry API with URL scheme(s) ['go://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.filesystem.Directory API with URL scheme(s) ['go://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.filesystem.File API with URL scheme(s) ['go://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.torque.torquejob
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.torque.torquejob for saga.job.Service API with URL scheme(s) ['torque://', 'torque+ssh://', 'torque+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.torque.torquejob for saga.job.Job API with URL scheme(s) ['torque://', 'torque+ssh://', 'torque+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.pbspro.pbsprojob
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbspro.pbsprojob for saga.job.Service API with URL scheme(s) ['pbspro://', 'pbspro+ssh://', 'pbspro+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbspro.pbsprojob for saga.job.Job API with URL scheme(s) ['pbspro://', 'pbspro+ssh://', 'pbspro+gsissh://']
2015:09:15 16:55:16 5516   MainThread   saga.saga.adaptor.ssh : [INFO    ] ignore ssh key at /home/jchen/.ssh/known_hosts (no public key: /home/jchen/.ssh/known_hosts.pub)
2015:09:15 16:55:16 5516   MainThread   saga.saga.adaptor.ssh : [WARNING ] ignore  ssh key at /home/jchen/.ssh/id_rsa (requires passphrase)
2015:09:15 16:55:16 5516   MainThread   saga.saga.adaptor.ssh : [INFO    ] ignore ssh key at /home/jchen/.ssh/jc49@stampede.tacc.utexas.edu (no public key: /home/jchen/.ssh/jc49@stampede.tacc.utexas.edu.pub)
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] using database url  mongodb://extasy:extasyproject@extasy-db.epcc.ed.ac.uk/radicalpilot
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] using database path radicalpilot
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/stfc.json
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for stfc.joule
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/radical.json
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for radical.tutorial
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/rice.json
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for rice.biou
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for rice.davinci
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/local.json
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for local.localhost
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/aliases.json
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/nersc.json
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.hopper_ccm
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.hopper
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.edison
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.edison_ccm
2015:09:15 16:55:16 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/xsede.json
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.blacklight
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.supermic
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.lonestar
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.comet
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.stampede
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.trestles
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.gordon
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/futuregrid.json
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.xray
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.echo
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.india
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.bravo
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.xray_ccm
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.delta
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/ornl.json
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ornl.titan
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/epsrc.json
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for epsrc.archer
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/ncsa.json
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ncsa.bw_ccm
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ncsa.bw
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/ncar.json
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ncar.yellowstone
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/das4.json
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for das4.fs2
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/lrz.json
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for lrz.supermuc
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/iu.json
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for iu.bigred2
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [INFO    ] Load resource configurations for iu.bigred2_ccm
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [ERROR   ] session create failed
Traceback (most recent call last):
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/session.py", line 225, in __init__
    db_name = self._database_name)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/db/database.py", line 104, in new
    dbs = Session(db_url, db_name)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/db/database.py", line 75, in __init__
    mongo, db, dbname, pname, cname = ru.mongodb_connect (url)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/utils/misc.py", line 86, in mongodb_connect
    mongo = pymongo.MongoClient (host=host, port=port)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 374, in __init__
    self._ensure_connected(True)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 939, in _ensure_connected
    self.__ensure_member()
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 813, in __ensure_member
    member, nodes = self.__find_node()
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 873, in __find_node
    member, nodes = self.__try_node(candidate)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 720, in __try_node
    {'ismaster': 1})
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/mongo_client.py", line 703, in __simple_command
    helpers._check_command_response(response, None, msg)
  File "/home/jchen/ExTASY/ExTASY-tools/lib/python2.7/site-packages/pymongo/helpers.py", line 133, in _check_command_response
    response)
OperationFailure: None
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [DEBUG   ] session None closing
2015:09:15 16:55:17 5516   MainThread   radical.pilot         : [ERROR   ] Session object already closed.
andre-merzky commented 9 years ago

Thanks for you patience! The error is now caught correctly on RP layer -- what I don't understand why the correct error code is still not showing up though. Could it be that the script you are running is excepting the error, but then ignoring it, ie. not printing it in any way? Vivek, do you have some insight?

Basically, we see the session create failed message from https://github.com/radical-cybertools/radical.pilot/blob/fix/dbs_var_2/src/radical/pilot/session.py#L243 -- but not the exception which is raised straight after. That would tell us what URL is being used...

I'll now added the information to the log message, please run again and post the line which contains session create failed. Thanks!

TensorDuck commented 9 years ago

Hi,

The error I now get is:

2015:09:15 18:42:58 6673   MainThread   radical.pilot         : [ERROR   ] session create failed with 'None' for 'mongodb://extasy:extasyproject@extasy-db.epcc.ed.ac.uk/radicalpilot'
andre-merzky commented 9 years ago

Well, so much effort just to get stuck again -- that URL seems to trickle down to the session creation layer all right then, and I am left with no idea why the connection setup would fail.... :/

At this point it seems like we need to debug this on pymongo level. Would it be possible to get access to your machine, by any chance?

Best, Andre.

TensorDuck commented 9 years ago

Hi Andre,

It would be, I'm heading out of the office now-ish, so let me know if you want to do this now or tomorrow.

Could this still be related to the anaconda install? I can probably test a fresh install again on a separate partition if you think it would help.

Best -Justin

andre-merzky commented 9 years ago

I think I'll finish up for today as well, so rather tomorrow then.

I don't have any experience with Anaconda, so can't really say one way or the other. I don't want to send you on a wild goose chase -- but if it is not too much effort, testing a plain python install from the same machine might make sense.

TTYT, Andre.

TensorDuck commented 9 years ago

I tried a user with no anaconda settings and the mongoDB error goes away. It appears my virtualenv package was an anaconda package to begin with, which is likely why it was causing problems. I've since rectified this and it connects properly. Thanks for all of your help, sorry the issue turned out to be something silly.

Best -Justin

andre-merzky commented 9 years ago

Thanks for the ping-back! No worries about silliness, at all: we are seeing an increasing number of questions about anaconda, so for us its useful to know what the potential pitfalls are...

Best, Andre.