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The transition took place in the middle of December, Dec 15 - Dec 18. Right now, you can SSH to 'corn' or 'corn-new' and you will be on an Ubuntu 14.04 machine instead of an Ubuntu 13.10 machine. It will be very similar, but the output of 'module avail' will be different, and the q commands will point to a new grid engine environment. You can SSH to "corn-old" if you want the old environment.

We'll be working on the systems in this order: corn, barley, rye, cardinal.

To see which corn machines belong to which group, you can run a bash for loop like this:

 for i in corn corn-old corn-new; do echo $i; dig +short +noedns -t txt $i.best.stanford.edu @lbdns1.stanford.edu; done 

To see which barley machines belong to which group, try a 'qhost' on a corn vs a 'qhost' on a corn-new.

For any machine, you can see the distro version with:

 lsb_release -a


new features

  • new version of Julia from ppa:staticfloat/julia-deps + ppa:staticfloat/juliareleases
 $ julia --version
 julia version 0.3.3
  • new version of FSL, from regular Ubuntu 14.04 repos
 fsl-5.0-complete  5.0.7-1~nd14.04+1  metapackage for the entire FSL suite (tools and data)
  • Xmipp 3.1
 $ xmipp --version
 Xmipp version 3.1
  • Mathematica 10.0
 module load mathematica
 module show mathematica

You'll probably get an error like "libGL error: failed to load driver" but that's safe to ignore, you just won't have 3D-acceleration in Mathematica.

  • MATLAB R2014b
 module load matlab

You'll probably see an error like:

libGL error: failed to load driver: swrast
MATLAB is selecting SOFTWARE OPENGL rendering.

A doc about new features in R2014b: http://www.mathworks.com/products/matlab/matlab-graphics/index.html


  • barley environment 'fah' is now called 'shm'
  • qsub does "-R y" by default, which should help with jobs larger than 1 slot
  • barley queues limited to 48hr run time, ask us about longer run time
  • qsub warning about AFS credentials works again
 {No Kerberos credentials, AFS access won't work inside job!}
 {Please do a kinit if you want AFS access inside job!}
  • qsub option '-V' is broken with the recent changes to bash, I updated the template scripts and recommend you explicitly set up your job environment instead of passing in your current environment. If you use the '-V' option, you'll get an error like
     error: JSV stderr: bad variable name "jsv_env_BASH_FUNC_module()": upvar won't create a scalar variable that looks like an array element
  • SAS v9.2 removed
  • SAS v9.3 license will expire on Nov 30 2014, use SAS v9.4 instead

things that don't work

  • module meep only works on corn01-10 and not on higher-numbered corns, due to some details about CPU architecture features.
  • pymol crashes when loading pdb file, e.g. /usr/share/pymol/data/chempy/water.pdb Workaround: run on a Rye-GPU and not on a corn.
  • R is only from OS, need to rebuild a newer one
  • For qsub, if you have no kerberos TGT, you'll get the "no Kerberos TGT message', and if you have a renewable one, it'll work, but if you have one and it's not renewable, you'll get a crazy JSV stack trace. So just 'kinit' again.


  • Some MATLAB users are reporting various errors which are resolved by deleting or moving aside the $HOME/.matlab directory (which has your old MATLAB settings)
  • Some FarmVNC users are having various problems. Usually they are resolved by moving aside your old desktop-/GNOME-related settings. Try move aside or delete your ~/.config , ~/.gvfs , ~/.gconf
  rm -rf .config .gvfs .gnome .gnome2 .gnome2_private .gconf
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