biac:cluster:interactive
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biac:cluster:interactive [2011/11/03 19:27] – [using MATLAB] petty | biac:cluster:interactive [2023/03/26 20:38] – [Accessing experiments] cmp12 | ||
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====== Job restrictions ====== | ====== Job restrictions ====== | ||
- | Each node has a finite amount of memory installed and due to the disk-less nature of the nodes there are restrictions set on the amount of ram used. Currently, the default is to assign | + | Each node has a finite amount of memory installed and due to the disk-less nature of the nodes there are restrictions set on the amount of ram used. Currently, the default is to assign |
- | > qrsh -l h_vmem=5G bash -li | + | > qrsh -q interact.q -V -verbose -N interact |
- | The above example will request/ | + | The above example will request/ |
- | The maximum available is 94.5GB | + | The maximum available is 187GB on any node, so if you request more than that, the job will just sit in the queue waiting indefinitely. |
//Please do not request additional resources unless you absolutely need them. If additional resources are requested, they are deducted from the amount available to everyone else. If unneeded resources are requested, this reduces the capacity on a given node for other potential usage.// | //Please do not request additional resources unless you absolutely need them. If additional resources are requested, they are deducted from the amount available to everyone else. If unneeded resources are requested, this reduces the capacity on a given node for other potential usage.// | ||
- | There is a 1GB cumulative quota on all HOME directories and a 32GB cumulative quota for space in /tmp ( or $TMP ) across all nodes combined. | + | There is a 5GB cumulative quota on all $HOME directories |
====== Accessing experiments ====== | ====== Accessing experiments ====== | ||
Experiments can be reached multiple ways: | Experiments can be reached multiple ways: | ||
- | There is an automounter that is running on each node that can mount experiments when they are accessed through it's proxy filesystem **"/ | + | There is an automounter that is running on each node that can mount experiments when they are accessed through it's proxy filesystem **"/ |
- | A call to a valid path will be intercepted by the proxy, and mounted. | + | A call to a valid path will be intercepted by the proxy, and mounted. |
If you are unsure, you can call the helper function **findexp** in various ways to return a valid path: | If you are unsure, you can call the helper function **findexp** in various ways to return a valid path: | ||
<code bash> | <code bash> | ||
- | cd /mnt/BIAC2/munin.dhe.duke.edu/ | + | cd / |
cd `findexp Dummy.01` | cd `findexp Dummy.01` | ||
ls `findexp Dummy.01` | ls `findexp Dummy.01` | ||
Line 49: | Line 49: | ||
All of those instances would mount the experiment Dummy.01 within the proxy filesystem. | All of those instances would mount the experiment Dummy.01 within the proxy filesystem. | ||
- | |||
- | |||
- | ---- | ||
- | |||
- | |||
- | < | ||
- | [deshmukh@node4 ~]$ ls ~/ | ||
- | </ | ||
- | |||
- | this will mount the entire server and therefore you can access all the experiments on that share. | ||
- | |||
- | |||
- | ---- | ||
- | |||
- | |||
- | < | ||
- | [deshmukh@node4 ~]$ ls ~/ | ||
- | </ | ||
- | this will mount a single experiment and create a symbolic link to the path in ~/ | ||
Line 88: | Line 69: | ||
matlab -nodesktop < myscript.m | matlab -nodesktop < myscript.m | ||
</ | </ | ||
+ | |||
+ | You can run matlab without the desktop and without the java-virtual-machine if you continue to have "out of memory" | ||
+ | - some functions that require java may no longer be accessible | ||
+ | <code bash> | ||
+ | matlab -nodesktop -nojvm -nosplash | ||
+ | </ | ||
+ | |||
+ | Also, if you continue having JAVA memory errors you can create a java.opts file to increase the JAVA memory that matlab uses. | ||
+ | In a directory where you launch matlab, create a file names " | ||
+ | <code bash> | ||
+ | -Xms128m | ||
+ | -Xmx1g | ||
+ | </ | ||
+ | |||
+ | This will increase the initial java-virtual-machine to 128 megabytes from the default of 64, it will also allow it to grow to 1gigabyte from the previous default of 128mb. | ||
+ | |||
+ | You can also set the heap space preference through the graphical desktop in matlab: | ||
+ | [[http:// | ||
+ | |||
+ | Just a word of cause, setting it to the max available space in the gui caused matlab to not open ( for me ) | ||
+ | |||
====== Ending a job ====== | ====== Ending a job ====== | ||
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+ | ====== OpenGL ====== | ||
+ | |||
+ | For programs that require OpenGL rendering, like fsleyes, make sure your local X11 client supports openGL and is enabled. | ||
+ | |||
+ | on mac make sure xquartz is installed: | ||
+ | < | ||
+ | Via Terminal: | ||
+ | |||
+ | defaults read org.xquartz.X11 | ||
+ | |||
+ | { | ||
+ | " | ||
+ | " | ||
+ | SUHasLaunchedBefore = 1; | ||
+ | SULastCheckTime = " | ||
+ | " | ||
+ | " | ||
+ | " | ||
+ | " | ||
+ | " | ||
+ | " | ||
+ | " | ||
+ | " | ||
+ | } | ||
+ | </ | ||
+ | |||
+ | If iglx is not 1, enable openGL. | ||
+ | < | ||
+ | defaults write org.xquartz.X11 enable_iglx -bool true | ||
+ | </ | ||
+ | Versions of Xquartz before 2.8.0 used configuration paths of : org.macosforge.xquartz.X11 | ||
biac/cluster/interactive.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1