biac:cluster
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biac:cluster [2012/06/15 15:00] – [Tutorials] mm265 | biac:cluster [2024/06/21 15:54] (current) – cmp12 | ||
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===== User guides ===== | ===== User guides ===== | ||
- | * [[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. |
+ | |||
+ | To connect | ||
+ | * [[biac: | ||
- | Or see {{: | ||
- | === 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. | + | |
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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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- | == Opening Hugin == | + | |
- | * Begin by running X-Win Config under the X-Win tab in your programs | + | |
- | * Select your cluster profile, aptly named “Hugin, | + | |
- | * 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 | + | |
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- | + | ||
- | == 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" | ||
+ | * ls -ltr - ls w/ time and date | ||
+ | * 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 | ||
+ | * rm - " | ||
+ | * cp - copy | ||
+ | * qdel - delete job | ||
+ | * qstatall - display active jobs | ||
- | Command lines | ||
- | ls | ||
- | ls -ltr | ||
- | mkdir | ||
- | 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 == | == EXTRA TIPS == | ||
- | * 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 | ||
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* 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) | * 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 .. | * To cd to previous folder type cd .. | ||
- | * Scripts with tilda’s | + | * Scripts with tildes |
* By typing qstatall (no folloing arguments necessary), you can look at the active jobs on the cluster | * 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 | * 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 | * 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 | ||
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===== Administration guides ===== | ===== Administration guides ===== | ||
- | * [[biac: | + | * <del>[[biac: |
- | * [[biac: | + | |
* [[biac: | * [[biac: | ||
* [[biac: | * [[biac: |
biac/cluster.txt · Last modified: 2024/06/21 15:54 by cmp12