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/ | ||
| - | The 'module' command has been added to your environment, but if you have modified your environment away from the defaults, you | + | 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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| - | For example, try something like this at the end of your .bashrc: | + | |
<source lang="sh"> | <source lang="sh"> | ||
HOSTNAME=$(hostname) | HOSTNAME=$(hostname) | ||
Revision as of 11:18, 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
