biac:cluster
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biac:cluster [2012/06/15 14:44] – [Tutorials] mm265 | biac:cluster [2023/04/06 18:31] – cmp12 | ||
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===== User guides ===== | ===== User guides ===== | ||
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* [[huettel: | * [[huettel: | ||
- | ===== Tutorials ===== | + | === Basic Primer |
- | A [[http:// | + | 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. |
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+ | To connect | ||
+ | * [[biac: | ||
- | Hugin for dummies | ||
- | 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 | + | == The Interactive Node == |
- | line at a time. In order to set up access to Hugin on your computer, you need to be behind the firewall. | + | |
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- | here http:// | + | |
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- | You will also need a cluster account. Please send an email to help@biac.duke.edu requesting a cluster account. | + | |
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- | On an 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). |
- | Cd findexp | + | |
+ | * List of packages: http:// | ||
+ | * Getting on: log onto the cluster, in the command line (username@cluster: | ||
+ | * Congratulations! | ||
- | Command lines | + | == Useful Commands == |
- | ls | + | |
- | ls -ltr | + | |
- | mkdir | + | |
- | cd | + | * mkdir - "make directory," |
- | .. | + | * gedit - will open a text editor, to be followed by the name of the text file you'd like to edit |
- | Tab to complete | + | |
- | Gedit . nedit | + | |
- | Commenting out | + | |
- | saving | + | |
- | & | + | |
- | bash | + | |
- | rm | + | |
- | Up arrow | + | |
- | cp | + | |
- | qdel | + | |
- | qstatall | + | |
- | Blue “directories” are equivalent to folders, “cd”ing is like double clicking | + | |
- | Getting files from munin onto hugin, and mounting experiments? | + | |
- | Print from terminal window | + | |
+ | == 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