This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
keller_and_evans_lab:cu_research_computing [2016/07/18 20:12] matthew_keller /* Getting information on jobs */ |
keller_and_evans_lab:cu_research_computing [2019/10/28 15:59] lessem ↷ Page moved from cu_research_computing to keller_and_evans_lab:cu_research_computing |
||
---|---|---|---|
Line 1: | Line 1: | ||
- | General documentation for using RC is [[[https:// | ||
+ | This document will mostly cover specific instructions for using RC in the Vrieze and Keller labs. We will try to update this, but RC is a bit of a moving target, so some of what is written below may now be outdated. | ||
- | ======= Logging in ======= | ||
+ | ======= Getting started ======= | ||
+ | |||
+ | General documentation for using RC is [[[https:// | ||
+ | Logging In <which you've already done> | ||
+ | Duo 2-factor Authentication <which you've already done> | ||
+ | Allocations | ||
+ | Node Types | ||
+ | Filesystems | ||
+ | The modules system | ||
+ | The PetaLibrary | ||
+ | Running applications with Jobs | ||
+ | Batch Jobs and Job Scripting | ||
+ | Interactive Jobs | ||
+ | Useful Slurm commands | ||
+ | Job Resource Information | ||
+ | squeue status and reason codes | ||
+ | Containerization on Summit | ||
+ | |||
+ | |||
+ | ======= Overview of best practices ======= | ||
+ | |||
+ | This was written by Richard Border on Oct 8, 2019: | ||
+ | {{file_example.jpg}} | ||
+ | |||
+ | |||
+ | ======= Logging in ======= | ||
Put these settings in your '' | Put these settings in your '' | ||
Line 25: | Line 50: | ||
These settings should work from Mac and Linux. I'm not sure how to do the equivalent from Windows with Putty. On a Mac, those settings will cause X11 to start. If you don't want that to happen, then remove the '' | These settings should work from Mac and Linux. I'm not sure how to do the equivalent from Windows with Putty. On a Mac, those settings will cause X11 to start. If you don't want that to happen, then remove the '' | ||
+ | |||
+ | For those with access to summit (ONLY!), here are the steps to using it: | ||
+ | | ||
+ | #From a login node: | ||
+ | ssh -YC < | ||
+ | | ||
+ | #In your shell script: | ||
+ | No need to include -A UCB00000442 | ||
+ | | ||
+ | | ||
+ | #To run R: | ||
+ | ml load R | ||
+ | ml load gcc | ||
+ | R | ||
+ | |||
Line 63: | Line 103: | ||
======= Slurm ======= | ======= Slurm ======= | ||
+ | |||
+ | |||
+ | |||
+ | ====== Queues ====== | ||
+ | |||
+ | |||
+ | #if you want to run on ibg himem, you need to load the right module | ||
+ | module load slurm/ | ||
+ | |||
+ | #then in your shell script | ||
+ | #SBATCH --qos=blanca-ibg | ||
+ | |||
+ | #If you want to run on normal queues, then: | ||
+ | module load slurm/slurm | ||
+ | |||
+ | #then in your shell script, one of the below, depending on what queue you want | ||
+ | #SBATCH --qos=himem | ||
+ | #SBATCH --qos=crestone | ||
+ | #SBATCH --qos=janus | ||
+ | |||
+ | |||
Line 82: | Line 143: | ||
squeue -u < | squeue -u < | ||
squeue -u < | squeue -u < | ||
+ | |||
+ | #detailed information on a queue (who is running on it, how many cpus requested, memory requested, time information, | ||
+ | squeue -q blanca-ibg -o %u, | ||
#current status of queues | #current status of queues | ||
Line 92: | Line 156: | ||
#other commands | #other commands | ||
showq-slurm -o -U -q < | showq-slurm -o -U -q < | ||
- | scontrol show jobid -dd < | + | scontrol show jobid -dd < |
pbsnodes -a #To look at the status of each node | pbsnodes -a #To look at the status of each node | ||