13. Frequently Asked Questions¶
- How do I…
- ...avoid the error “OperationFailure: too many namespaces/collections”
- ...avoid the error “Permission denied (publickey,keyboard-interactive).” in AGENT.STDERR or STDERR.
- ...avoid the error “Failed to execvp() ‘mybinary’: No such file or directory (2)”
- ...avoid errors from setuptools when trying to use a virtualenv?
- ...avoid the error “Received message too long 1903391841”
- ...avoid the pop-up “Do you want the application python to accept incoming network connections?” on Mac OSX.
- ...avoid the error “Could not detect shell prompt (timeout)”
- Other Questions
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
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
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
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.
13.1.2. ...avoid 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
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)
This may happen specifically on Gordon. 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
This happens 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.
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 etc. are only executed on interactive shell (ie. on shells which have a prompt set as $PS1). The snippet below shows how to di that:
if [ ! -z "$PS1" ] then echo "hello $USER" date fi
13.1.6. ...avoid the pop-up “Do you want the application python to accept incoming network connections?” on Mac OSX.¶
This is coming from the firewall on your Mac. You can either:
- click “Allow” (many times)
- disable your firewall (temporarily)
- Sign the application per instructions here: http://apple.stackexchange.com/a/121010
We generally only 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 a ticket.
Prompt detecting behaviour 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 a ticket.
Details: we implement rather cumbersome screen scraping via an interactive ssh session to get onto the target machine, instead of using paramiko or other modules. 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.
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.