From FarmShare

Revision as of 22:49, 6 October 2014

The transition will take place in the first couple of weeks of October. Right now, you can SSH to 'corn-new' instead of 'corn' 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.

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 try an:

 lsb_release -a

new features

• new version of Julia from ppa:staticfloat/julia-deps + ppa:staticfloat/juliareleases

 $ julia --version
 julia version 0.3.1

• 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

changes

• barley test queue is not working yet
• 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!}

things that don't work

• pymol crashes when loading pdb file, e.g. /usr/share/pymol/data/chempy/water.pdb Workaround: run on a rye not on a corn.