biac:cluster
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biac:cluster [2011/10/27 19:26] – [Tutorials] favorini | biac:cluster [2023/03/29 20:05] – cmp12 | ||
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====== BIAC Cluster ====== | ====== BIAC Cluster ====== | ||
+ | ===== User guides ===== | ||
+ | * [[biac: | ||
+ | * [[biac: | ||
+ | * [[biac: | ||
+ | * [[biac: | ||
+ | * [[biac: | ||
+ | * [[biac: | ||
+ | * [[biac: | ||
+ | * [[biac: | ||
+ | * [[huettel: | ||
+ | === Basic Primer === | ||
+ | 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. | ||
+ | |||
+ | To connect to the cluster, you will need XWin/Putty from windows, or Terminal with Xquartz from Mac | ||
+ | * [[biac: | ||
+ | == 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). | ||
- | ===== User guides ===== | + | |
- | + | * Getting on: log onto the cluster, in the command line (username@cluster: | |
- | | + | * Congratulations! |
- | * [[biac:cluster: | + | |
- | * [[biac:cluster:submit|Job submission]] | + | |
- | * [[biac: | + | |
- | * [[biac: | + | |
- | * [[biac: | + | |
- | * [[huettel: | + | |
- | + | ||
- | + | ||
- | ===== Tutorials ===== | + | |
- | A [[http://wiki.biac.duke.edu/ | + | == Useful Commands == |
+ | * ls - "list scripts" | ||
+ | * 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 - " | ||
+ | * cp - copy | ||
+ | * qdel - delete | ||
+ | * qstatall - display active jobs | ||
+ | == EXTRA TIPS == | ||
+ | * 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 & | ||
+ | * 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 ===== | ===== Administration guides ===== | ||
- | * [[biac: | + | * <del>[[biac: |
- | * [[biac: | + | |
* [[biac: | * [[biac: | ||
* [[biac: | * [[biac: |
biac/cluster.txt · Last modified: 2024/06/21 15:54 by cmp12