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 ==
-
Ubuntu 13.04 is being introduced to farmshare systems starting September 12, 2013.
+
Ubuntu 13.04 is now live on Farmshare systems as of September 19, 2013.
 +
 
 +
You can access the new Ubuntu 13.04 systems by:
 +
 
 +
<source lang="sh">
 +
ssh corn.stanford.edu
 +
</source>
 +
 
 +
You can access the old Ubuntu 12.04 systems by:
 +
 
 +
<source lang="sh">
 +
ssh corn-old.stanford.edu
 +
</source>
 +
 
 +
 
 +
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.
This guide walks through the changes and new features.
Line 9: Line 32:
=== /mnt/glusterfs is retired ===
=== /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/<sunetid> for storing files, the replacement is /farmshare/user_data/<sunetid> .  Like /mnt/glusterfs, /farmshare/user_data is not backed up.
If you used /mnt/glusterfs/software/... for matlab, R, stata etc, the replacement is /farmshare/software.  See Quick Start Guide below.
If you used /mnt/glusterfs/software/... for matlab, R, stata etc, the replacement is /farmshare/software.  See Quick Start Guide below.
Line 19: Line 42:
=== /usr/pubsw is retired ===
=== /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 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:
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-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
+
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 ===
=== 100TB of shared storage ===
-
Farmshare now has 100TB of shared storage.  see New Features below for details.
+
Farmshare now has 100TB of shared storage.  Like the old glusterfs space, this is for temporary files only; it is not backed up. See New Features below for details.
=== unix groups for collaboration ===
=== unix groups for collaboration ===
Line 40: Line 63:
To help you get started quickly you can pick from these common examples:
To help you get started quickly you can pick from these common examples:
 +
 +
=== See available software ===
 +
  module avail
=== Matlab ===
=== Matlab ===
 +
 +
If you used to run
 +
<source lang="sh">
 +
matlab -nodesktop
 +
</source>
 +
 +
then you can now run
<source lang="sh">
<source lang="sh">
Line 49: Line 82:
=== Gaussian ===
=== Gaussian ===
 +
 +
If you used to run
 +
<source lang="sh">
 +
g09
 +
</source>
 +
 +
Then you can now run
<source lang="sh">
<source lang="sh">
module load gaussian
module load gaussian
g09
g09
 +
gview
</source>
</source>
=== Stata ===
=== Stata ===
 +
 +
If you used to run
 +
<source lang="sh">
 +
stata
 +
</source>
 +
 +
Then you can now run
<source lang="sh">
<source lang="sh">
Line 62: Line 110:
</source>
</source>
-
or
+
or for Stata-MP
<source lang="sh">
<source lang="sh">
Line 70: Line 118:
=== Mathematica ===
=== Mathematica ===
 +
 +
If you used to run
 +
<source lang="sh">
 +
math
 +
</source>
 +
 +
Then you can now run
<source lang="sh">
<source lang="sh">
module load mathematica
module load mathematica
math
math
 +
</source>
 +
 +
or
 +
 +
If you used to run
 +
<source lang="sh">
 +
Mathematica
 +
</source>
 +
 +
Then you can now run
 +
<source lang="sh">
 +
module load mathematica
 +
Mathematica
 +
</source>
 +
 +
=== pine ===
 +
 +
If you used to run
 +
<source lang="sh">
 +
pine
 +
</source>
 +
 +
Then you can now run
 +
<source lang="sh">
 +
alpine
</source>
</source>
=== SAS ===
=== SAS ===
 +
 +
If you used to run
 +
<source lang="sh">
 +
sas
 +
</source>
 +
 +
Then you can now run
<source lang="sh">
<source lang="sh">
Line 87: Line 174:
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.
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 ===
+
== 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.  This storage is intended for temporary files; it is NOT backed up.
 +
 
 +
=== 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.
 +
 
 +
== Known problems ==
 +
 
 +
=== msgs/biff command not found ===
 +
 
 +
If you see this when you login:
 +
<source lang="sh">
 +
msgs: Command not found.
 +
biff: Command not found.
 +
</source>
 +
 
 +
To fix, (unless you have edited your .login file) you can just move it to the side by running this command:
 +
 
 +
<source lang="sh">
 +
mv .login .login.movedaside
 +
</source>

Latest revision as of 10:26, 1 May 2015

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> . Like /mnt/glusterfs, /farmshare/user_data is not backed up.

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. Like the old glusterfs space, this is for temporary files only; it is not backed up. 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
gview

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

pine

If you used to run

pine

Then you can now run

alpine

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. This storage is intended for temporary files; it is NOT backed up.

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.

Known problems

msgs/biff command not found

If you see this when you login:

msgs: Command not found.
biff: Command not found.

To fix, (unless you have edited your .login file) you can just move it to the side by running this command:

mv .login .login.movedaside
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