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 | + | 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 === | ||
- | == Quick Start Guide | + | 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. | 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: | 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"> | <source lang="sh"> | ||
- | + | matlab -nodesktop | |
</source> | </source> | ||
+ | then you can now run | ||
+ | |||
+ | <source lang="sh"> | ||
+ | module load matlab | ||
+ | matlab -nodesktop | ||
+ | </source> | ||
=== 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 | ||
+ | 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"> | ||
module load statase | module load statase | ||
+ | stata | ||
</source> | </source> | ||
- | or | + | or for Stata-MP |
<source lang="sh"> | <source lang="sh"> | ||
module load statamp | module load statamp | ||
+ | stata | ||
</source> | </source> | ||
=== 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 | ||
+ | </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"> | ||
module load sas | module load sas | ||
+ | sas | ||
</source> | </source> | ||
+ | === 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: | ||
+ | <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 |
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
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
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