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biac:cluster [2019/02/11 21:24]
cmp12 		biac:cluster [2021/05/12 12:00]
cmp12
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 ===== User guides ===== ===== User guides =====
  
-  * [[biac:cluster:account|Requesting cluster access]]   +  * [[biac:cluster:account | Requesting cluster access]]   
-  * [[biac:cluster:access|Accessing the cluster]]   +  * [[biac:cluster:access | Accessing the cluster]]   
-  * [[biac:cluster:passwords|Cluster password]]  +  * [[biac:cluster:passwords |Cluster password]]  
-  * [[biac:cluster:submit|Job submission]] +  * [[biac:cluster:submit |Job submission]] 
-  * [[biac:cluster:packages| List of packages installed]]  +  * [[biac:cluster:modules | Software]] 
-  * [[biac:cluster:examples| BIAC Sample Scripts]] +  * [[biac:cluster:packages | List of packages installed]]  
-  * [[biac:cluster:interactive| Interactive jobs]]+  * [[biac:cluster:examples | BIAC Sample Scripts]] 
 +  * [[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.   
  
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 === Cluster for dummies... or really smart people who aren't used to this system yet! === === Cluster for dummies... or really smart people who aren't used to this system yet! ===
  
-The BIAC cluster is a Linux-based 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 DHE firewall.  Being at BIAC or on the "Clubs" wireless network puts you behind this firewall.+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 the "Clubs" wireless network puts you behind this firewall.
                                
 To connect to the cluster, you will need [[https://en.wikipedia.org/wiki/X_Window_System|X-Windows]] software. On BIAC computers X-Win32 comes standard, but it can also be downloaded from [[http://oit.duke.edu/comp-print/software/index.php|OIT’s software website]] (click “Browse and order software”). To connect to the cluster, you will need [[https://en.wikipedia.org/wiki/X_Window_System|X-Windows]] software. On BIAC computers X-Win32 comes standard, but it can also be downloaded from [[http://oit.duke.edu/comp-print/software/index.php|OIT’s software website]] (click “Browse and order software”).
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 == EXTRA TIPS == == EXTRA TIPS ==
   * Blue “directories” are equivalent to folders, “cd”ing is like double clicking on the folder   * 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+  * 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
   * 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
biac/cluster.txt · Last modified: 2023/04/06 18:31 by cmp12

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