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Frequently Asked Questions

How do I change my shell on a cardinal or a corn

Currently, everyone gets tcsh as default shell. If you want to use e.g. bash instead, put a code snippet like this into your .cshrc:

if ($?prompt && -x /bin/bash) then
setenv SHELL bash
exec bash

tset: standard error: Invalid argument

In your job script, you probably don't explicitly specify which shell to use. Probably your default shell is csh and your csh startup scripts are getting loaded and something there is generating that error because the job is not run under an interactive session. So the solution is to either specify a shell on the first line of your job script in the usual Unix way e.g.


or else use the -S flag to qsub, e.g.

# get rid of spurious messages about tty/terminal types
#$ -S /bin/sh

tty errors

You may see things like

tset: standard error: Invalid argument

Undefined tty
stdin: is not a tty


Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.

See the question above, and specify a shell. See the 'shell_start_mode' section of 'man sge_conf' for more info.

error: can't open output file "/afs/ir/users/c/h/chekh/YYY.oXXXX"

Check that you have your Kerberos credentials and AFS tokens per AFS

glusterfs: Transport endpoint not connected

"/mnt/glusterfs: Transport endpoint is not connected." This indicates a network or connection problem for the shared filesystem, please report this to the barley-alpha list or via HelpSU.

where is GView version 5?

Gauss View (GV5) is /usr/sweet/bin/gview

SAS error message

  When I attempt to run the command "sas", I receive the following error
  ERROR: User does not have appropriate authorization level for library
  NOTE: Unable to initialize the options subsystem.
  ERROR: Unable to initialize the SAS kernel.

Try to re-auth (kinit ; aklog), run updaterc, and source ~/.cshrc before running sas. Also check that you're not over quota with the 'fs quota' command or the '/usr/bin/check-stanford-afs-quota' command.

Received disconnect from <IP address>: 2: Too many authentication failures for...

That error message is from OpenSSH and it means it's not letting you log in because you don't have the right credentials. Check that your kerberos tickets are what you expect.

Decrypt integrity check failed

 k5start: error getting credentials: Decrypt integrity check failed

This just means that you typed your Kerberos password wrong when kinit or whatever prompted you for it.

how to submit a binary for execution

Use the '-b' flag to 'qsub', read the qsub man page for more info. But you should probably write a small wrapper script instead.

why won't my job run?

If your job is in state 'qw' for longer than you like, check its full output "qstat -f -j JOBID" and see what the scheduling reason is. It will be verbose about explaining why that job can't run in each queue instance. For full cluster information, check 'qstat -g c' and 'qstat -f -u "*"' and 'qhost -j' or e-mail us for more explanations.

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