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Running jobs: Difference between revisions
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This page is intended for the user who is already familiar with the concepts of job scheduling and job scripts, and who wants guidance on submitting jobs to | This page is intended for the user who is already familiar with the concepts of job scheduling and job scripts, and who wants guidance on submitting jobs to our clusters. | ||
If you have not worked on a large shared computer cluster before, you should probably read [[What is a scheduler?]] first. | If you have not worked on a large shared computer cluster before, you should probably read [[What is a scheduler?]] first. | ||
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On | On our clusters, the job scheduler is the | ||
[https://en.wikipedia.org/wiki/Slurm_Workload_Manager Slurm Workload Manager]. | [https://en.wikipedia.org/wiki/Slurm_Workload_Manager Slurm Workload Manager]. | ||
Comprehensive [https://slurm.schedmd.com/documentation.html documentation for Slurm] is maintained by SchedMD. If you are coming to Slurm from PBS/Torque, SGE, LSF, or LoadLeveler, you might find this table of [https://slurm.schedmd.com/rosetta.pdf corresponding commands] useful. | Comprehensive [https://slurm.schedmd.com/documentation.html documentation for Slurm] is maintained by SchedMD. If you are coming to Slurm from PBS/Torque, SGE, LSF, or LoadLeveler, you might find this table of [https://slurm.schedmd.com/rosetta.pdf corresponding commands] useful. | ||
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On general-purpose (GP) clusters this job reserves 1 core and 256MB of memory for 15 minutes. On [[Niagara]] this job reserves the whole node with all its memory. | On general-purpose (GP) clusters this job reserves 1 core and 256MB of memory for 15 minutes. On [[Niagara]] this job reserves the whole node with all its memory. | ||
Directives (or "options") in the job script are prefixed with <code>#SBATCH</code> and must precede all executable commands. All available directives are described on the [https://slurm.schedmd.com/sbatch.html sbatch page]. | Directives (or "options") in the job script are prefixed with <code>#SBATCH</code> and must precede all executable commands. All available directives are described on the [https://slurm.schedmd.com/sbatch.html sbatch page]. Our policies require that you supply at least a time limit (<code>--time</code>) for each job. You may also need to supply an account name (<code>--account</code>). See [[#Accounts and projects|Accounts and projects]] below. | ||
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If you want to know more about the output of <code>sq</code> or <code>squeue</code>, or learn how to change the output, see the [https://slurm.schedmd.com/squeue.html online manual page for squeue]. <code>sq</code> is a | If you want to know more about the output of <code>sq</code> or <code>squeue</code>, or learn how to change the output, see the [https://slurm.schedmd.com/squeue.html online manual page for squeue]. <code>sq</code> is a local customization. | ||
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Every job must have an associated ''account name'' corresponding to a | Every job must have an associated ''account name'' corresponding to a [[Frequently_Asked_Questions_about_the_CCDB#What_is_a_RAP.3F|Resource Allocation Project]] (RAP). If you are a member of only one account, the scheduler will automatically associate your jobs with that account. | ||
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#!/bin/bash | #!/bin/bash | ||
# --------------------------------------------------------------------- | # --------------------------------------------------------------------- | ||
# SLURM script for a multi-step job on | # SLURM script for a multi-step job on our clusters. | ||
# --------------------------------------------------------------------- | # --------------------------------------------------------------------- | ||
#SBATCH --account=def-someuser | #SBATCH --account=def-someuser | ||
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#!/bin/bash | #!/bin/bash | ||
# --------------------------------------------------------------------- | # --------------------------------------------------------------------- | ||
# SLURM script for job resubmission on | # SLURM script for job resubmission on our clusters. | ||
# --------------------------------------------------------------------- | # --------------------------------------------------------------------- | ||
#SBATCH --job-name=job_chain | #SBATCH --job-name=job_chain | ||
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== Automating job submission == <!--T:174--> | == Automating job submission == <!--T:174--> | ||
As described earlier, [[#Array job|array jobs]] can be used to automate job submission. | As described earlier, [[#Array job|array jobs]] can be used to automate job submission. We provide a few other (more advanced) tools designed to facilitate running a large number of related serial, parallel, or GPU calculations. This practice is sometimes called "farming", "serial farming", or "task farming". In addition to automating the workflow, these tools can also improve computational efficiency by bundling up many short computations into fewer tasks of longer duration. | ||
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Certain software packages such as [https://github.com/alekseyzimin/masurca Masurca] operate by submitting jobs to Slurm automatically, and expect a partition to be specified for each job. This is in conflict with | Certain software packages such as [https://github.com/alekseyzimin/masurca Masurca] operate by submitting jobs to Slurm automatically, and expect a partition to be specified for each job. This is in conflict with what we recommend, which is that you should allow the scheduler to assign a partition to your job based on the resources it requests. If you are using such a piece of software, you may configure the software to use <code>--partition=default</code>, which the script treats the same as not specifying a partition. | ||
== Cluster particularities == <!--T:154--> | == Cluster particularities == <!--T:154--> | ||
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There are certain differences in the job scheduling policies from one | There are certain differences in the job scheduling policies from one our clusters to another and these are summarized by tab in the following section: | ||
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