User Tools
biac:cluster
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision | ||
|
biac:cluster [2012/06/15 14:54] mm265 [Tutorials] |
biac:cluster [2023/04/06 18:31] (current) cmp12 |
||
|---|---|---|---|
| Line 3: | Line 3: | ||
| ===== User guides ===== | ===== User guides ===== | ||
| - | * [[biac: | + | * [[biac: |
| - | * [[biac: | + | * [[biac: |
| - | * [[biac: | + | * [[biac: |
| - | * [[biac: | + | * [[biac: |
| - | * [[biac: | + | * [[biac: |
| - | * [[biac: | + | * [[biac: |
| - | * [[biac: | + | * [[biac: |
| * [[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. |
| - | Or see: {{: | + | |
| + | 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. | + | |
| - | | + | |
| - | + | ||
| - | | + | |
| - | here http:// | + | |
| - | + | ||
| - | You will also need a cluster account. Please send an email to help@biac.duke.edu requesting a cluster account. | + | |
| - | | + | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | == 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). | qinteract is also known as the ‘interactive node,’ because it allows you to interact directly with your data on Munin (or whatever server). | ||
| * List of packages: http:// | * List of packages: http:// | ||
| - | * 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! | * Congratulations! | ||
| == Useful Commands == | == Useful Commands == | ||
| - | + | * ls - "list scripts" | |
| - | Command lines | + | |
| - | ls | + | |
| - | ls -ltr | + | * mkdir - "make directory," |
| - | mkdir | + | * gedit - will open a text editor, to be followed by the name of the text file you'd like to edit |
| - | cd | + | |
| - | .. | + | |
| - | 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.1339772077.txt.gz · Last modified: 2014/08/04 16:03 (external edit)
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 4.0 International
