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

Up until October 2012 we were saying: Currently, everyone gets tcsh as default shell.

As of October 18, 2012, we can change your shell to bash University-wide:

To change your shell, please compose an email to research-computing-support@stanford.edu using your stanford email address and include following text:

Dear research computing, please change my default shell to /bin/bash.
I understand that this setting will be a global change and will affect
the farmshare systems (corn/rye/barley/etc) as well as other systems at stanford
(for example the myth systems in computer science dept).

As of early 2014 new SUNetIDs get bash as their default shell.

"error: failed receiving gdi request response for mid=1 (got syncron message receive timeout error)."

This is a cryptic error that means the master system is overloaded and did not respond before the timeout period. Try again in a couple of minutes.

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

where is GView version 5?

Gauss View (GV5) is available via gaussian module.

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), module load 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 or that you're providing the correct password.

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.

Why does pressing 'd' cause my windows to disappear?

The GNOME keybinding for d may be broken when using VNC for remote display. You can edit the relevant keyboard shortcut ("Hide All Normal Windows and Set Focus to the Desktop") using the GNOME Control Center (gnome-control-center). Alternatively, you can edit ~/.gconf/apps/metacity/global_keybindings/%gconf.xml manually. For example:

<?xml version="1.0"?>
  <entry name="show_desktop" mtime="0123456789" type="string">

We added this setting system-wide to cardinal+corn on 2012-04-18

I get a CPLEX license error, what should I do?

You may see something like:

corn04:~> cplex
Failed to initialize CPLEX environment.
CPLEX Error 32201: ILM Error 8: CPLEX: access key has expired.

Check that you're using the latest version of CPLEX:

[chekh@corn05.stanford.edu] ~ [0] 
$ module load cplex
[chekh@corn05.stanford.edu] ~ [0] 
$ which cplex

My job errored out, what should I do?

First, check what the error message is, something like

 qstat -f -j $JOBID | grep err

If you think that the error is not with your job script or the job parameters, try to just resubmit.

If your job is now in state E or in state Eqw, probably the best thing to do is something like:

 qresub $JOBID # this will resubmit the job with a new job id
 qdel $JOBID # delete the old errored one

If the job failed because you have an error in your script, it'll error out again. Sometimes we have intermittent filesystem problems, so the job will run fine when you resubmit.

You can also log in to machine 'senpai1' and try a 'qacct -j $JOBID' there, it will give you the accounting info written at end of job, there can be a different error message there.

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.

"failed searching requested shell because:" or other execvp errors

Often these come up because you created your job script on a Windows machine and then copied it over without adjusting the line endings. To see the exact line endings, try a 'cat -ve' on your file , or try to open it in a text editor. To convert the line endings, run 'dos2unix' on it, or re-upload with "ASCII" instead of "binary" mode.

Another example error:

error reason    1:          11/05/2014 12:16:26 [233269:25790]: execvp(/farmshare/software/free/oge/2011.11p1/FSsaucy/spool/barley09/job_scripts/2171682, "/farmshare/software/free/oge/2011.11p1/FSsaucy/spool/barley09/job_scripts/2171682") failed: No such file or directory
                            Job is in error state

For more info, see https://en.wikipedia.org/wiki/Newline

Is HIPAA data or other PHI/PII allowed on these systems?

No, this system is not HIPAA compliant and may not be used to process any PHI or PII.

Are my data backed up?

Data in your home directory (/afs/ir.stanford.edu/users/<etc>) are backed up. Data in /farmshare/user_data are not backed up; this is shared scratch space. If you have important files there, you should keep a copy on your own machine or elsewhere.

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