ILRI Research Computing

User Tools

Site Tools

You are here: start » using-slurm
using-slurm

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
Last revision Both sides next revision
using-slurm [2019/02/01 12:30]
jean-baka [Using SLURM] 		using-slurm [2020/10/08 13:06]
jean-baka [Batch jobs]
Line 8: Line 8:
   * highmem   * highmem
  
-"debug" is the default queue, which is useful for testing job parameters, program paths, etc. The run-time limit of the "debug" partition is 5 minutes, after which jobs are killed.+"debug" is the default queue, which is useful for testing job parameters, program paths, etc. The run-time limit of the "debug" partition is 5 minutes, after which jobs are killed. The other partitions have no set time limit.
  
 To see more information about the queue configuration, use ''sinfo -lNe''. To see more information about the queue configuration, use ''sinfo -lNe''.
  
-<code>[jbaka@compute03 ~]$ sinfo -lNe+<code>[jbaka@hpc ~]$ sinfo -lNe
 Fri Feb  1 15:27:44 2019 Fri Feb  1 15:27:44 2019
 NODELIST   NODES PARTITION       STATE CPUS    S:C:T MEMORY TMP_DISK WEIGHT AVAIL_FE REASON               NODELIST   NODES PARTITION       STATE CPUS    S:C:T MEMORY TMP_DISK WEIGHT AVAIL_FE REASON              
Line 24: Line 24:
 </code> </code>
  
-The above tells you, for instance, that compute04 has 8 CPUs while compute2 has 64 CPUs. And that a job sent to the "highmem" partition (a SLURM verb equivalent to "queue", as per the vocabulary in use with other schedulers e.g. Sun Grid Engine), then it will end up being run on either compute03 or mammoth. +The above tells you, for instance, that compute04 has 8 CPUs while compute2 has 64 CPUs. And that a job sent to the "highmem" partition (a SLURM verb equivalent to "queue", as per the vocabulary in use with other schedulers, e.g. Sun Grid Engine), then it will end up being run on either compute03 or mammoth. 
  
 ===== Submitting jobs ===== ===== Submitting jobs =====
 ==== Interactive jobs ==== ==== Interactive jobs ====
-How to get an interactive session, ie when you want to interact with a program (like R, etc):+How to get an interactive session, i.e. when you want to interact with a program (like R, etc) for a limited amount of time, making the scheduler aware that you are requesting/using resources on the cluster:
 <code>[aorth@hpc: ~]$ interactive  <code>[aorth@hpc: ~]$ interactive 
 salloc: Granted job allocation 1080 salloc: Granted job allocation 1080
Line 41: Line 41:
  
 ==== Batch jobs ==== ==== Batch jobs ====
-Request 4 CPUs for a NCBI BLAST+ job in the ''batch'' partition.  Create a file //blast.sbatch//:+We are writing a SLURM script below. The parameters in its header request 4 CPUs for in the ''batch'' partition, and name our job "blastn". This name is only used internally by SLURM for reporting purposes. So let's go ahead and ceate a file //blast.sbatch//:
 <code>#!/usr/bin/env bash <code>#!/usr/bin/env bash
 #SBATCH -p batch #SBATCH -p batch
Line 64: Line 64:
 <code>#!/usr/bin/env bash <code>#!/usr/bin/env bash
 #SBATCH -p batch #SBATCH -p batch
-#SBATCH -n 4 
 #SBATCH -J blastn #SBATCH -J blastn
 +#SBATCH -n 4
  
 # load the blast module # load the blast module
Line 85: Line 85:
  
 ==== Check queue status ==== ==== Check queue status ====
-''squeue'' is the command to use to get more information about the different jobs that are running on the cluster, waiting in a queue for resources to become available, or halted for some reason:+''squeue'' is the command to use in order to get information about the different jobs that are running on the cluster, waiting in a queue for resources to become available, or halted for some reason:
 <code>[jbaka@compute03 ~]$ squeue <code>[jbaka@compute03 ~]$ squeue
              JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)              JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
using-slurm.txt · Last modified: 2020/10/08 13:06 by jean-baka

Page Tools

Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 4.0 International
CC Attribution-Noncommercial-Share Alike 4.0 International Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki