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biac:cluster:interactive [2013/12/04 19:29] cmp12 [Job restrictions] |
biac:cluster:interactive [2023/03/26 20:39] cmp12 [Accessing experiments] |
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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 187GB on any node, so if you request more than that, the job will just sit in the queue waiting indefinitely. | 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. | ||
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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/BIAC/munin.dhe.duke.edu/ | + | cd / |
cd `findexp Dummy.01` | cd `findexp Dummy.01` | ||
ls `findexp Dummy.01` | ls `findexp Dummy.01` | ||
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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 a single experiment and create a symbolic link to the path in ~/ | ||
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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. | 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 | ||