Software

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There is also some licensed software installed: https://itservices.stanford.edu/service/sharedcomputing/software
There is also some licensed software installed: https://itservices.stanford.edu/service/sharedcomputing/software
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Notice: e /usr/pubsw, /usr/sweet/bin, and /mnt/glusterfs/software have been deprecated.  All have been replaced by /farmshare/software.
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Notice: /usr/pubsw, /usr/sweet/bin, and /mnt/glusterfs/software have been deprecated.  All have been replaced by /farmshare/software.
/farmshare/software can be accessed as follows:
/farmshare/software can be accessed as follows:
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===more complete example===
===more complete example===
<source lang="sh">
<source lang="sh">
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[chekh@corn24.stanford.edu] ~ [0]
 
$ module avail
$ module avail
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------------------------------------------- /mnt/glusterfs/software/free/modules/tcl/modulefiles --------------------------------------------
 
-
MATLAB-R2009b    MATLAB-R2010b    MATLAB-R2011b    StatTransfer-10.1 StatTransfer-11.2 stata-v12       
 
 +
---------------------------------------- /farmshare/software/free/lmod-5.0-install/lmod/lmod/modulefiles/Core -----------------------------------------
 +
  lmod/lmod    settarg/settarg
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[chekh@corn24.stanford.edu] ~ [0]
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------------------------------------------------------------ /farmshare/software/mf/raring ------------------------------------------------------------
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$ module load StatTransfer-10.1
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  cplex/12.4    gams/24.1              mathematica/9.0   matlab/r2013a  (D)    statamp/12.1    stattransfer/12
 +
  cuda/5.5      gaussian/g09gview50    matlab/r2012b      sas/9.2                statase/12.1
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[chekh@corn24.stanford.edu] ~ [0]
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-------------------------------------------------------- /farmshare/software/mf/raring-compat ---------------------------------------------------------
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$ st --version
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  CPLEX-12.4    GAMS-24.1   MATLAB-R2012b    MATLAB-R2013a    Mathematica-9.0    SAS-v9.2    StatTransfer-v12    StataMP-12.1    StataSE-12.1
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Stat/Transfer (c) 1986-2011 Circle Systems, Inc.
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www.stattransfer.com
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Version 10.1.1847.0331 - 64 Bit Linux
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Serial: BUNLM-VEAN7-JMC8
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  Where:
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User: Pat Box (1) - Stanford University
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  (D): Default Module
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License Type: Linux - Single Machine Lease
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Warning: Your annual license is in its last month.
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Status: License OK - Expires April 30, 2012
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Stat/Transfer is running in a remote secure shell. A workgroup license covering all users may be required.
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Please contact our sales department (sales@circlesys.com) for more information.
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[chekh@corn24.stanford.edu] ~ [0]
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See http://farmshare.stanford.edu for description of how to use modules
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$ module unload StatTransfer-10.1
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[chekh@corn24.stanford.edu] ~ [0]
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To load latest version of matlab: module load matlab
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$ module load StatTransfer-11.2
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You can load a specific version by: module load matlab/r2012b or module load MATLAB-R2012b
 +
</source>
 +
 
 +
<source lang="sh">
 +
$ module load StatTransfer-v12
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[chekh@corn24.stanford.edu] ~ [0]
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bishopj@scorn:~$ st --version
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$ st --version
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Stat/Transfer (c) 1986-2013 Circle Systems, Inc.
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Stat/Transfer (c) 1986-2012 Circle Systems, Inc.
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www.stattransfer.com  
www.stattransfer.com  
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Version 11.2.2013.0330 - 64 Bit Linux
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Version 12.0.56.0613 - 64 Bit Linux
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Serial: BOC59-BUAAN-ZCYF
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Serial: B2CNR-FZAS7-LPHI
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User: Jane Tansuwan - Stanford University
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User: Software Licensing - Stanford University
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License Type: Linux - 50 User Workgroup / Lease
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License Type: 25 User Workgroup / Lease
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Status: License OK - Expires April 30, 2013
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Status: License OK - Expires April 30, 2014
[chekh@corn24.stanford.edu] ~ [0]  
[chekh@corn24.stanford.edu] ~ [0]  

Revision as of 10:54, 14 September 2013

There is a lot of software available on the FarmShare systems. The systems run Ubuntu, so a lot of Ubuntu packages are installed.

There is also some licensed software installed: https://itservices.stanford.edu/service/sharedcomputing/software

Notice: /usr/pubsw, /usr/sweet/bin, and /mnt/glusterfs/software have been deprecated. All have been replaced by /farmshare/software.

/farmshare/software can be accessed as follows:

more complete example

$ module avail

---------------------------------------- /farmshare/software/free/lmod-5.0-install/lmod/lmod/modulefiles/Core -----------------------------------------
   lmod/lmod    settarg/settarg

------------------------------------------------------------ /farmshare/software/mf/raring ------------------------------------------------------------
   cplex/12.4    gams/24.1              mathematica/9.0    matlab/r2013a   (D)    statamp/12.1    stattransfer/12
   cuda/5.5      gaussian/g09gview50    matlab/r2012b      sas/9.2                statase/12.1

-------------------------------------------------------- /farmshare/software/mf/raring-compat ---------------------------------------------------------
   CPLEX-12.4    GAMS-24.1    MATLAB-R2012b    MATLAB-R2013a    Mathematica-9.0    SAS-v9.2    StatTransfer-v12    StataMP-12.1    StataSE-12.1

  Where:
   (D):  Default Module

See http://farmshare.stanford.edu for description of how to use modules 

To load latest version of matlab: module load matlab 
You can load a specific version by: module load matlab/r2012b or module load MATLAB-R2012b

$ module load StatTransfer-v12

bishopj@scorn:~$ st --version
Stat/Transfer (c) 1986-2013 Circle Systems, Inc.
www.stattransfer.com 
Version 12.0.56.0613 - 64 Bit Linux

Serial:	B2CNR-FZAS7-LPHI
User:	Software Licensing - Stanford University
License Type:	25 User Workgroup / Lease
Status:	License OK - Expires April 30, 2014

[chekh@corn24.stanford.edu] ~ [0] 
$ module help StatTransfer-11.2
-------------------------------------------------------------------
Module Specific Help for /mnt/glusterfs/software/free/modules/tcl/modulefiles/StatTransfer-11.2:

	 ITS-maintained Stat/Transfer v11.2 (in GlusterFS)
	 use st for command-line version
	 use stattransfer for X11 GUI version
-------------------------------------------------------------------

modules

We use 'modules', a commonly used software package in HPC environments: http://modules.sourceforge.net/

The 'module' command has been added to your environment, but if you have modified your environment away from the defaults, you may need to source the module env vars for your shell.

For example, you may need to try something like this at the end of your .bashrc:

HOSTNAME=$(hostname)
if [ "${HOSTNAME:0:4}" = "corn" ]; then
  #source farmshare modules
  echo "on a corn! try module avail"
  eval `tclsh /mnt/glusterfs/software/free/modules/tcl/modulecmd.tcl sh autoinit`
fi

Then you can do something like:

module avail
module load stata
stata


Link: https://www.stanford.edu/group/hpcc/cgi-bin/mediawiki/index.php/Modules

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