BRC Cluster Workshop

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 </code> </code>
  
-"--exclusive" requests a whole node. Use it only when you need to. "-c" specifies how many cores your job will use. (Use only one of "-c" and "--exclusive".) "scriptname" must be the name of a shell script (but see the "--wrap" option.)+"--exclusive" requests all cores on a node. Use it only when you need to. "-c" specifies how many cores your job will use. (Use only one of "-c" and "--exclusive".) "scriptname" must be the name of a shell script (but see the "--wrap" option.) "--mem=0" requests all memory on a node.
  
 For submitting many jobs look at using the "--array" option.  For submitting many jobs look at using the "--array" option. 
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 Will run 100 copies of **scriptname** in total, but only allow 5 to be running at any one time. The script itself must sort out how to do something different for each instance (using the SLURM_ARRAY_TASK_ID environment variable). Will run 100 copies of **scriptname** in total, but only allow 5 to be running at any one time. The script itself must sort out how to do something different for each instance (using the SLURM_ARRAY_TASK_ID environment variable).
  
-On the new cluster you may need to use the "--mem" option to make sure that sufficient memory is allocated to your task.+On the new cluster you may need to use the "--mem" or "--mem-per-cpu" options to make sure that sufficient memory is allocated to your task. The default is 8GB per cpu/core.
  
 === Check the queue === === Check the queue ===
  
 <code> <code>
 +squeue
 squeue -u USERNAME squeue -u USERNAME
 squeue -w NODENAME squeue -w NODENAME
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 **Not "skill" - which does exist, but isn't part of SLURM.** **Not "skill" - which does exist, but isn't part of SLURM.**
  
-The second of these commands would kill all of your jobs.+The second of these commands would kill **all** of your slurm jobs.
  
 === Report Job Details === === Report Job Details ===
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 The second command above will get you a command line on a node. You can use the "-w" option to target a specific node. (Note that you will only get the command line if there is a free core on the node in question.) You could use this to check on your job's status - e.g. amount of memory it is using, number of cores it is using. This can also be done more programmatically in your scripts, or using sstat (for memory use), but this command line technique can be useful sometimes. The second command above will get you a command line on a node. You can use the "-w" option to target a specific node. (Note that you will only get the command line if there is a free core on the node in question.) You could use this to check on your job's status - e.g. amount of memory it is using, number of cores it is using. This can also be done more programmatically in your scripts, or using sstat (for memory use), but this command line technique can be useful sometimes.
 +
 +As a matter of etiquette, please don't start up a shell on a node and just leave it running when you aren't using it. This tends to reduce the number of nodes available for exclusive use for users who need one.
  
 === Checking Disk Space === === Checking Disk Space ===
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 </code> </code>
  
-You should check this before you add a lot more data to your home directory. If you need more space than is available on your home volume please talk to the system administrators: we may be able to give you space on a different volume.+**You should check this before you add a lot more data to your home directory, or run jobs that generate a lot of output.** If you need more space than is available on your home volume please talk to the system administrators: we may be able to give you space on a different volume. Consider using /scratch for data that can easily be replaced (e.g. data download from NCBI).
  
 See space remaining on all home volumes: See space remaining on all home volumes:
cheat_sheet.1625001799.txt.gz ยท Last modified: 2021/06/29 17:23 by root

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