Software

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We use 'modules', a commonly used software package in HPC environments: http://modules.sourceforge.net/
We use 'modules', a commonly used software package in HPC environments: http://modules.sourceforge.net/
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The 'module' command has been added to your environment, but if you have modified your environment away from the defaults, you will need to source the module env vars for your shell:
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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.
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<source lang="sh">
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For example, you may need to try something like this at the end of your .bashrc:
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  If using sh/bash/ksh/zsh, add this to your .bashrc
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    eval `tclsh /mnt/glusterfs/software/free/modules/tcl/modulecmd.tcl sh autoinit`
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  If using csh/tcsh, add this to your .cshrc
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    source /mnt/glusterfs/software/free/modules/tcl/init/csh
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  If using perl, put this in your script
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    eval `tclsh /mnt/glusterfs/software/free/modules/tcl/modulecmd.tcl perl autoinit`;
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</source>
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For example, try something like this at the end of your .bashrc:
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<source lang="sh">
<source lang="sh">
HOSTNAME=$(hostname)
HOSTNAME=$(hostname)

Revision as of 10:18, 2 July 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

Don't use /usr/pubsw

Maybe use /usr/sweet/bin, though we'll be installing new versions of software outside of AFS, use module avail instead.

more complete example

[chekh@corn24.stanford.edu] ~ [0] 
$ module avail
------------------------------------------- /mnt/glusterfs/software/free/modules/tcl/modulefiles --------------------------------------------
MATLAB-R2009b     MATLAB-R2010b     MATLAB-R2011b     StatTransfer-10.1 StatTransfer-11.2 stata-v12         


[chekh@corn24.stanford.edu] ~ [0] 
$ module load StatTransfer-10.1

[chekh@corn24.stanford.edu] ~ [0] 
$ st --version
Stat/Transfer (c) 1986-2011 Circle Systems, Inc.
www.stattransfer.com 
Version 10.1.1847.0331 - 64 Bit Linux

Serial:	BUNLM-VEAN7-JMC8
User:	Pat Box (1) - Stanford University
License Type:	Linux - Single Machine Lease
Warning: Your annual license is in its last month.
Status:	License OK - Expires April 30, 2012
Stat/Transfer is running in a remote secure shell. A workgroup license covering all users may be required.
Please contact our sales department (sales@circlesys.com) for more information.

[chekh@corn24.stanford.edu] ~ [0] 
$ module unload StatTransfer-10.1

[chekh@corn24.stanford.edu] ~ [0] 
$ module load StatTransfer-11.2

[chekh@corn24.stanford.edu] ~ [0] 
$ st --version
Stat/Transfer (c) 1986-2012 Circle Systems, Inc.
www.stattransfer.com 
Version 11.2.2013.0330 - 64 Bit Linux

Serial:	BOC59-BUAAN-ZCYF
User:	Jane Tansuwan - Stanford University
License Type:	Linux - 50 User Workgroup / Lease
Status:	License OK - Expires April 30, 2013

[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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