10. Frequently Asked Questions¶

10.1. Q: I see the error “OperationFailure: too many namespaces/collections”¶

Traceback (most recent call last):
  File "application.py", line 120, in __init__
    db_connection_info=session._connection_info)
  File "/lib/python2.7/site-packages/radical/pilot/controller/pilot_manager_controller.py", line 88, in __init__
    pilot_launcher_workers=pilot_launcher_workers
  File "/lib/python2.7/site-packages/radical/pilot/db/database.py", line 253, in insert_pilot_manager
    result = self._pm.insert(pilot_manager_json)
  File "build/bdist.linux-x86_64/egg/pymongo/collection.py", line 412, in insert
  File "build/bdist.linux-x86_64/egg/pymongo/mongo_client.py", line 1121, in _send_message
  File "build/bdist.linux-x86_64/egg/pymongo/mongo_client.py", line 1063, in __check_response_to_last_error
pymongo.errors.OperationFailure: too many namespaces/collections

10.2. A: Try Cleaning-up MongoDB.¶

This can happen if radical.pilot too many sessions are piling up in the back-end database. Normally, all database entries are removed when a RADICAL-Pilot session is closed via session.close() (or more verbose via session.close(cleanup=True), which is the default. However, if the application fails and is not able to close the session, or if the session entry remains puprosefully in place for later analysis with radicalpilot-stats, then those entries add up over time.

RADICAL-Pilot provides two utilities which can be used to address this problem: radicalpilot-close-session can be used to close a session when it is not used anymore; radicalpilot-cleanup can be used to clean up all sessions older than a specified number of hours or days, to purge orphaned session entries in a bulk.

10.3. Q: I see the error “Permission denied (publickey,keyboard-interactive).” in AGENT.STDERR or STDERR.¶

The AGENT.STDERR file or the STDERR file in the unit directory shows the following error and the pilot or unit never starts running:

Permission denied (publickey,keyboard-interactive).
kill: 19932: No such process

10.4. A: Set up password-less, intra-node SSH access.¶

Even though this should already be set up by default on many HPC clusters, it is not always the case. The following instructions will help you to set up password-less SSH between the cluster nodes correctly.

Log-in to the head-node or login-node of the cluster and run the following commands:

cd ~/.ssh/
ssh-keygen -t rsa

Do not enter a passphrase. The result should look something like this:

Generating public/private rsa key pair.
Enter file in which to save the key (/home/e290/e290/oweidner/.ssh/id_rsa):
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/e290/e290/oweidner/.ssh/id_rsa.
Your public key has been saved in /home/e290/e290/oweidner/.ssh/id_rsa.pub.
The key fingerprint is:
73:b9:cf:45:3d:b6:a7:22:72:90:28:0a:2f:8a:86:fd oweidner@eslogin001

Next, add you newly generated key to ~/.ssh/authorized_keys:

cat id_rsa.pub >> ~/.ssh/authorized_keys

This should be all. Next time you run radical.pilot, you shouldn’t see that error message anymore.

(For more general information on SSH keys, check out this link: http://www.linuxproblem.org/art_9.html)

10.5. Q: On Gordon I see “Failed to execvp() ‘mybinary’: No such file or directory (2)”¶

The full error in STDERR is something like:

[gcn-X-X.sdsc.edu:mpispawn_0][spawn_processes] Failed to execvp() 'mybinary': No such file or directory (2)

10.6. A: You need to specify the full path of the executable as mpirun_rsh is not able to find it in the path¶

10.7. Q: How many concurrent RADICAL-Pilot scripts can I execute?¶

A: From a RADICAL-Pilot perspective there is no limit, but as SSH is used to access many systems, there is a resource specific limit of the number of SSH connections one can make.

10.8. Q: Why do I get errors from setuptools when trying to use a virtualenv?¶

10.9. A: Most likely because an upgrade of pip or setuptools failed¶

We have seen occurences where an update of setuptools or pip can make a virtualenv unusable. We don’t have any suggestion on how to get the affected virtualenv clean again - it seems easiest to just start over with a new virtualenv. If the problem persists, try to use the default version of setuptools and pip, i.e. do not upgrade them.