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techstaff:slurm [2020/10/07 13:06] – SLURM is known as Slurm now kauffmantechstaff:slurm [2020/10/07 13:08] – [Common Issues] kauffman
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 Think of these machines as a dumping ground for discrete computing tasks that might be rude or disruptive to execute on the main (shared) shell servers (i.e., linux1, linux2, linux3). Think of these machines as a dumping ground for discrete computing tasks that might be rude or disruptive to execute on the main (shared) shell servers (i.e., linux1, linux2, linux3).
  
-For job submission we will be using a piece of software called [[http://slurm.schedmd.com|SLURM]]. Simply put, Slurm is a queue management system; it was developed at the Lawrence Livermore National Lab. It currently supports some of the largest compute clusters in the world. The best description of Slurm can be found on its homepage:+For job submission we will be using a piece of software called [[http://slurm.schedmd.com|Slurm]]. Simply put, Slurm is a queue management system; it was developed at the Lawrence Livermore National Lab. It currently supports some of the largest compute clusters in the world. The best description of Slurm can be found on its homepage:
  
 "Slurm is an open-source workload manager designed for Linux clusters of all sizes. It provides three key functions. First it allocates exclusive and/or non-exclusive access to resources (computer nodes) to users for some duration of time so they can perform work. Second, it provides a framework for starting, executing, and monitoring work (typically a parallel job) on a set of allocated nodes. Finally, it arbitrates contention for resources by managing a queue of pending work."((http://slurm.schedmd.com/)) "Slurm is an open-source workload manager designed for Linux clusters of all sizes. It provides three key functions. First it allocates exclusive and/or non-exclusive access to resources (computer nodes) to users for some duration of time so they can perform work. Second, it provides a framework for starting, executing, and monitoring work (typically a parallel job) on a set of allocated nodes. Finally, it arbitrates contention for resources by managing a queue of pending work."((http://slurm.schedmd.com/))
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 ===== Resources ===== ===== Resources =====
   * [[https://rc.fas.harvard.edu/resources/documentation/convenient-slurm-commands|Common Slurm commands]]   * [[https://rc.fas.harvard.edu/resources/documentation/convenient-slurm-commands|Common Slurm commands]]
-  * [[http://slurm.schedmd.com/|Official SLURM website]]+  * [[http://slurm.schedmd.com/|Official Slurm website]]
   * [[http://slurm.schedmd.com/documentation.html|Official Slurm documentation]]   * [[http://slurm.schedmd.com/documentation.html|Official Slurm documentation]]
-  * [[http://slurm.schedmd.com/tutorials.html|SLURM tutorial videos]]+  * [[http://slurm.schedmd.com/tutorials.html|Slurm tutorial videos]]
   * [[https://computing.llnl.gov/linux/slurm/quickstart.html|LLNL quick start user guide]]   * [[https://computing.llnl.gov/linux/slurm/quickstart.html|LLNL quick start user guide]]
   * [[http://research.computing.yale.edu/support/hpc/user-guide/slurm| Yale's User Guide]]   * [[http://research.computing.yale.edu/support/hpc/user-guide/slurm| Yale's User Guide]]
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 ===== Usage ===== ===== Usage =====
-Below are some common examples. You should consult the [[http://slurm.schedmd.com/documentation.html|documentation]] of SLURM if you need further assistance.+Below are some common examples. You should consult the [[http://slurm.schedmd.com/documentation.html|documentation]] of Slurm if you need further assistance.
  
 === Default Quotas === === Default Quotas ===
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 ==== sbatch ==== ==== sbatch ====
-The sbatch command is used for submitting jobs to the cluster. sbatch accepts a number of options either from the command line, or (more typically) from a batch script. An example of a SLURM batch script is shown below:+The sbatch command is used for submitting jobs to the cluster. sbatch accepts a number of options either from the command line, or (more typically) from a batch script. An example of a Slurm batch script is shown below:
  
 === Sample script === === Sample script ===
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 ====== Monitoring Jobs ====== ====== Monitoring Jobs ======
  
-''%%squeue%%'' and ''%%sacct%%'' are two different commands that allow you to monitor job activity in Slurm. ''%%squeue%%'' is the primary and most accurate monitoring tool since it queries the SLURM controller directly. ''%%sacct%%'' gives you similar information for running jobs, and can also report on previously finished jobs, but because it accesses the Slurm database, there are some circumstances when the information is not in sync with squeue.+''%%squeue%%'' and ''%%sacct%%'' are two different commands that allow you to monitor job activity in Slurm. ''%%squeue%%'' is the primary and most accurate monitoring tool since it queries the Slurm controller directly. ''%%sacct%%'' gives you similar information for running jobs, and can also report on previously finished jobs, but because it accesses the Slurm database, there are some circumstances when the information is not in sync with squeue.
  
 Running ''%%squeue%%'' without arguments will list all currently running jobs. It is more common, though to list jobs for a particular user (like yourself) using the ''%%-u%%'' option... Running ''%%squeue%%'' without arguments will list all currently running jobs. It is more common, though to list jobs for a particular user (like yourself) using the ''%%-u%%'' option...
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 | JOB <jobid> CANCELLED AT <time> DUE TO TIME LIMIT | You did not specify enough time for your job to run. The ''%%-t%%'' flag will allow you to set the time limit.| | JOB <jobid> CANCELLED AT <time> DUE TO TIME LIMIT | You did not specify enough time for your job to run. The ''%%-t%%'' flag will allow you to set the time limit.|
 | Job <jobid> exceeded <mem> memory limit, being killed | Your job is attempting to use more memory that you have requested for it. Either increase the amount of memory you have requested or reduce the amount of memory usage your application is trying to use.| | Job <jobid> exceeded <mem> memory limit, being killed | Your job is attempting to use more memory that you have requested for it. Either increase the amount of memory you have requested or reduce the amount of memory usage your application is trying to use.|
-| JOB <jobid> CANCELLED AT <time> DUE TO NODE FAILURE | There can be many reasons for this message, but most often it means that the node your job was set to run on can no longer be contacted by the the SLURM controller.|+| JOB <jobid> CANCELLED AT <time> DUE TO NODE FAILURE | There can be many reasons for this message, but most often it means that the node your job was set to run on can no longer be contacted by the the Slurm controller.|
 | error: Unable to allocate resources: More processors requested than permitted | It usually has **nothing** to do with priviledges you may or may not have. Rather, it usually means that you have allocated more processors than one compute node actually has. | | error: Unable to allocate resources: More processors requested than permitted | It usually has **nothing** to do with priviledges you may or may not have. Rather, it usually means that you have allocated more processors than one compute node actually has. |
  
/var/lib/dokuwiki/data/pages/techstaff/slurm.txt · Last modified: 2021/01/06 16:13 by kauffman
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