Ubuntu13TransitionGuide

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== Transition Guide for Farmshare Ubuntu 12.04 based systems to Ubuntu 13.04 ==
== Transition Guide for Farmshare Ubuntu 12.04 based systems to Ubuntu 13.04 ==
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Ubuntu 13.04 is being introduced to Farmshare systems starting September 12, 2013.
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Ubuntu 13.04 is now live on Farmshare systems as of September 19, 2013.
You can access the new Ubuntu 13.04 systems by:
You can access the new Ubuntu 13.04 systems by:
<source lang="sh">
<source lang="sh">
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ssh corn-new.stanford.edu
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ssh corn.stanford.edu
</source>
</source>
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ssh corn-old.stanford.edu
ssh corn-old.stanford.edu
</source>
</source>
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For the next week or so '''corn.stanford.edu''' will be an alias for corn-old.stanford.edu.  After which, corn.stanford.edu will become an alias for corn-new.stanford.edu.
 
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* As of 9/15/2013 There are 20 corn running Ubuntu 13.04.
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* As of 9/19/2013 There are 20 corn running Ubuntu 13.04.
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* As of 9/15/2013 There are 5 barley running Ubuntu 13.04.  
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* As of 9/19/2013 There are 9 barley running Ubuntu 13.04.  

Revision as of 14:52, 19 September 2013

Contents

Transition Guide for Farmshare Ubuntu 12.04 based systems to Ubuntu 13.04

Ubuntu 13.04 is now live on Farmshare systems as of September 19, 2013.

You can access the new Ubuntu 13.04 systems by:

ssh corn.stanford.edu

You can access the old Ubuntu 12.04 systems by:

ssh corn-old.stanford.edu


The barley cluster is accessible from both the old corns and the new corns, each seeing the portion of barley systems running their respective Ubuntu version.


  • As of 9/19/2013 There are 20 corn running Ubuntu 13.04.
  • As of 9/19/2013 There are 9 barley running Ubuntu 13.04.


It is anticipated that every 2 days another barley system will be converted to Ubuntu 13.04. The rate depends somewhat on how many jobs are queued from corn-new vs corn-old.


This guide walks through the changes and new features.

Changes

/mnt/glusterfs is retired

If you used /mnt/glusterfs/<sunetid> for storing files, the replacement is /farmshare/user_data/<sunetid>

If you used /mnt/glusterfs/software/... for matlab, R, stata etc, the replacement is /farmshare/software. See Quick Start Guide below.

/usr/sweet/bin is retired

If you have been using stata, gaussian, matlab, etc from /usr/sweet/bin, the replacement is /farmshare/software. See Quick Start Guide.

/usr/pubsw is retired

If you have been using software from pubsw then let us know by sending an email to research-computing-support@stanford.edu. There are a lot of historical dependencies which we are currently tracing.

If you are not sure if you were using /usr/pubsw then you can check this way:

ssh corn-new and run your program. If you are getting an error then: ssh corn-old and run your program. If it works then type: "which <program name>" to find out the path. One you have the name of the program and the path, send us an email to research-computing-support@stanford.edu

100TB of shared storage

Farmshare now has 100TB of shared storage. see New Features below for details.

unix groups for collaboration

Farmshare now supports collaboration by unix groups. See New Features below for details.


Quick Start Guide for transitioning to Ubuntu 13.04

If you have been used to logging into a corn system and then executing matlab or mathematica then most likely you were using these programs from /usr/sweet/bin. On the new Farmshare you will need to execute a command to load these programs into your environment.

To help you get started quickly you can pick from these common examples:

See available software

 module avail

Matlab

If you used to run

matlab -nodesktop

then you can now run

module load matlab
matlab -nodesktop

Gaussian

If you used to run

g09

Then you can now run

module load gaussian
g09

Stata

If you used to run

stata

Then you can now run

module load statase
stata

or for Stata-MP

module load statamp
stata

Mathematica

If you used to run

math

Then you can now run

module load mathematica
math

or

If you used to run

Mathematica

Then you can now run

module load mathematica
Mathematica


SAS

If you used to run

sas

Then you can now run

module load sas
sas

R

If you were using module load R-2.15.1-precise then you can just execute R from ubuntu. If we get requests for R libraries which Ubuntu 13.04 does not have then we will build a local R package as we did with R-2.15.1-precise.

New Features

GPU's

Farmshare has GPU's. There are two systems available which have 8 Nvidia GPU each. See Rye-GPU for details

100TB shared space

Farmshare has 100TB usable shared disk space provided by a NetApp E-series storage system. You may use this space by accessing /farmshare/user_data/<your sunetid> when logged into corn, barley, rye, or cardinal systems.

Unix groups for collaboration

We can support sharing files in /farmshare/user_data between users via standard unix groups. Send us an email at research-computing-support@stanford.edu to request a group for your project.

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