11. Frequently Asked Questions

Here are some answers to frequently-asked questions. Got a question that isn’t answered here? Open an issue in the RADICAL-Pilot github issue tracker.

11.1. Error “OperationFailure: too many namespaces/collections”

Traceback (most recent call last):
  File "application.py", line 120, in __init__
  File "/lib/python3.6/site-packages/radical/pilot/controller/pilot_manager_controller.py", line 88, in __init__
  File "/lib/python3.6/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

This can happen if too many RADICAL-Pilot sessions are piling up in the back-end database. Database entries are removed when a RADICAL-Pilot session is closed via session.close(cleanup=True). However, if the application fails and is not able to close the session, or if the session entry remains purposefully 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.

11.2. Error “Permission denied (publickey,keyboard-interactive).” in AGENT.STDERR or STDERR

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

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

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 HPC 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: https://linuxize.com/post/how-to-setup-passwordless-ssh-login/)

11.3. Error “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)

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

11.4. Errors from setuptools when trying to use a virtualenv

This happens most likely because an upgrade of pip or setuptools failed.

We have seen occurrences 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. The easiest approach seems 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.

11.5. Error “Received message too long 1903391841”

This error may show up in the DEBUG level logs during file staging or pilot startup, when sftp is used as a transfer protocol. We have seen this error being caused by verbose .bashrc files (or other login files), which confuses sftp startup. Please make sure that any parts of the bashrc which print information are only executed on interactive shell (i.e., on shells which have a prompt set as $PS1). The snippet below shows how to do that:

if [ ! -z "$PS1" ]
  echo "hello $USER"

11.6. Pop-up “Do you want the application python to accept incoming network connections?” on macOS

Currently, we do not support RADICAL-Pilot on macOS. If macOS support is critical for you, please open an issue.

11.7. Error “Could not detect shell prompt (timeout)”

We support sh and bash as login shells on the target machines. Please try to switch to those shells if you use others like zsh and csh/tcsh. If you need other shells supported, please open an issue.

Prompt detecting behavior can be improved by calling touch $HOME/.hushlogin on the target machine, which will suppress some system messages on login. If the problem persists, please open an issue.

Details: we implement a rather cumbersome screen scraping via an interactive ssh session to get onto the target machine, instead of using paramiko or other modules that proven to be too buggy and unstable. This gives us better performance, but most importantly, this gives us support for gsissh, which we did not find available in any other package so far.

11.8. Number of concurrent RADICAL-Pilot scripts that can can be executed

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 concurrent SSH connections one can make.