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biac:cluster [2015/03/13 16:32]
favorini
biac:cluster [2023/04/06 18:31] (current)
cmp12
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 ===== User guides ===== ===== User guides =====
  
-  * [[biac:cluster:account|Requesting cluster access]]   +  * [[biac:cluster:architecture System Architecture ]] 
-  * [[biac:cluster:access|Accessing the cluster]]   +  * [[biac:cluster:account Requesting cluster access]]   
-  * [[biac:cluster:passwords|Cluster password]]  +  * [[biac:cluster:access Accessing the cluster]]   
-  * [[biac:cluster:submit|Job submission]] +  * [[biac:cluster:submit |Job submission]] 
-  * [[biac:cluster:packagesList of packages installed]]  +  * [[biac:cluster:modules Software]] 
-  * [[biac:cluster:examples| BIAC Sample Scripts]] +  * [[biac:cluster:examples | BIAC Sample Scripts]] 
-  * [[biac:cluster:interactive| Interactive jobs]]+  * [[biac:cluster:interactive | Interactive jobs]]
   * [[huettel:using_the_biac_cluster | 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.      * [[huettel:using_the_biac_cluster | 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 =====+=== Basic Primer ===
  
-A [[http://wiki.biac.duke.edu/suppl/intro.htm|"Getting Started"]] tutorial on setting up access to the cluster and basic job related tasks ([[biac:cluster:submit#job submission|submission]], [[biac:cluster:submit#job status|status checking]] and [[biac:cluster:submit#job delete|deletion]] )+The BIAC cluster is a Linux-based processor put in place to analyze any type of data You will work on the cluster though a terminal window by writing commands one line at a time.  In order to set up access to the cluster on your computer, you need to be behind the DHE firewall.  Being at BIAC or on a DHE wireless network puts you within the medical center firewall.  If you are not within the med center you can request access to the DHE VPN via biac-help@duke.edu. 
 +                
 +To connect to the cluster, you will need XWin/Putty from windows, or Terminal with Xquartz from Mac 
 +  * [[biac:cluster:access Accessing the cluster]]  
  
-Or see {{:biac:infrequent_setup.doc|}} for written instructions 
  
-=== Hugin for dummies ...or really smart people who aren't used to this system yet! === +== The Interactive Node ==
- +
-                   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. 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.
  
   * List of packages: http://wiki.biac.duke.edu/biac:cluster:packages   * List of packages: http://wiki.biac.duke.edu/biac:cluster:packages
-  * Getting on: log onto Hugin, in the command line (username@hugin: ___) type “qinteract” if prompted, type yes, and then enter your cluster password.+  * Getting on: log onto the cluster, in the command line (username@cluster: ___) 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`”   * Congratulations!  You are now on the “interactive node.”  Access your study data by typing “cd `findexp Study.01`”
  
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 == EXTRA TIPS == == EXTRA TIPS ==
-  * Blue “directories” are equivalent to folders, “cd”ing is like double clicking on the folder +  * If you command line is gone in the cluster, 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
-  * 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 &   * In order to avoid this, follow commands with an &
   * Hit the up arrow in order to go to the previous written command   * Hit the up arrow in order to go to the previous written command
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 ===== Administration guides ===== ===== Administration guides =====
  
-  * [[biac:cluster:admin:architecture|System architecture]] 
   * <del>[[biac:cluster:admin:installation|Installation]]</del>    * <del>[[biac:cluster:admin:installation|Installation]]</del> 
   * [[biac:cluster:admin:manage|Management]]   * [[biac:cluster:admin:manage|Management]]
biac/cluster.1426264347.txt.gz · Last modified: 2015/03/13 16:32 by favorini