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BIAC Cluster
User guides
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Advanced Bash/Python Submission Scripts - Provided by Dr. Scott Huettel's lab, the scripts included here will check FSL parameters to make sure jobs do not get “stuck” running on the cluster, and submit multiple jobs in a smart way so individual users do not tie up the cluster at any one time.
Tutorials
Hugin for dummies ...or really smart people who aren't used to this system yet!
The BIAC cluster, Hugin, is a Linux base processor put in place to analyze any type of data. You will work on Hugin though a terminal window by writing commands one
line at a time. In order to set up access to Hugin on your computer, you need to be behind the firewall. Being at BIAC or on "Diamonds" or "Clubs" puts you
behind this firewall.
First, you will need X-Win. On BIAC computers, X-Win comes standard but it can also be downloaded through OIT’s website
here http://oit.duke.edu/comp-print/software/index.php (select “Browse and order software”).
You will also need a cluster account. Please send an email to help@biac.duke.edu requesting a cluster account.
Include your BIAC Windows username in the email (see http://wiki.biac.duke.edu/biac:accounts).
Opening Hugin
Begin by running X-Win Config under the X-Win tab in your programs
Select your cluster profile, aptly named “Hugin,” and hit launch
Alternative:
Under the X-Win tab in your programs select X-Win32 2012 (or whatever year)
The X-Win icon will appear next to the time and date in the bottom right hand corner of your screen
Right click it then scroll down to “My Connections”
Select your profile by clicking “Hugin”
If, prompted, enter your cluster password and hit enter (your cluster password may be different from your BIAC password)
Your command line should appear with username@hugin (this is your home directory on the cluster) in a terminal window
Now you are “on the cluster,” aka Hugin
the Interactive Node
qinteract is also known as the ‘interactive node,’ because it allows you to interact directly with your data on Munin (or whatever server). It also contains the “packages” (FSL, CMTK, FreeSurfer) that BIAC has installed. You can access the GUI’s for these packages by typing in their appropriate commands once in qinteract.
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Getting on: log onto Hugin, in the command line (username@hugin: ___) type “qinteract” if prompted, type yes, and then enter your cluster password.
Congratulations! You are now on the “interactive node.” Access your study data by typing “cd `findexp Study.01`”
Useful Commands
ls - “list scripts” displays the contents of the directory
ls -ltr - ls w/ time and date
cd - “change directory,” to be followed by the name of the directory you want to go to
mkdir - “make directory,” to be followed by the name of the directory you want to make
gedit - will open a text editor, to be followed by the name of the text file you'd like to edit
rm - “remove” followed by what you'd like to remove - be careful!
cp - copy
qdel - delete job
qstatall - display active jobs
Blue “directories” are equivalent to folders, “cd”ing is like double clicking on the folder
If you command line is gone in Hugin, as in you don’t have the prompt to type something, make sure nothing is open in gedit (for example batchMakeFSL_Data is open using gedit – click out), click ctrl+c
In order to avoid this, follow commands with an &
Hit the up arrow in order to go to the previous written command
Hit tab in order to fill in a file, script, or directory name
If there are multiple files with that name it’ll fill in up to where they differ
If you’d like to work the command on all files with that particular prefix, immediately follow the prefix with * (for example “gedit batch*” would open all scripts that start with batch)
To cd to previous folder type cd ..
Scripts with tildes (~) are there as a backup service, ignore, don’t use, can be deleted if you make sure the proper script is current (example batch_QA versus batch_QA~)
By typing qstatall (no folloing arguments necessary), you can look at the active jobs on the cluster
By typing ls –ltr you’ll have a list of files with a timestamp/ more details
In order to paste from windows into linux (example gedit or the FSL
GUI), copy using right click and paste using the center scroll button
Administration guides
Support
For issues and discussions related to the cluster, visit the Cluster Forum