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| doku:slurm [2022/02/01 21:32] – [Node configuration - hyperthreading] goldenberg | doku:slurm [2023/02/17 16:37] – msiegel |
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| ====== Submitting batch jobs ====== | |
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| ===== Module environment ===== | |
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| In order to set environment variables needed for a specific application, the **module** environment may be used: | |
| * ''module avail'' lists the **available** Application-Software, Compilers, Parallel-Environment, and Libraries | |
| * ''module list'' shows currently loaded package of your session | |
| * ''module unload <xyz>'' unload a particular package <xyz> from your session | |
| * ''module load <xyz>'' load a particular package <xyz> into your session | |
| * ''module display <xyz>'' OR ''module show <xyz>'' show module details such as the full path of the module file and all (or most) of the environment changes the modulefile will make if loaded | |
| * ''module purge'' unloads all loaded modulefiles | |
| == Note: == | |
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| - **<xyz>** format corresponds exactly to the output of ''module avail''. Thus, in order to load or unload a selected module, copy and paste exactly the name listed by ''module avail''.\\ | |
| - a list of ''module load/unload'' directives may also be included in the top part of a job submission script\\ | |
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| When all required/intended modules have been loaded, user packages may be compiled as usual. | |
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| ===== spack ===== | |
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| On VSC-4, spack is also user to install and provide software. See [[doku:spack|SPACK - a package manager for HPC systems]] | |
| ===== SLURM (Simple Linux Utility for Resource Management) ===== | ===== SLURM (Simple Linux Utility for Resource Management) ===== |
| | Contrary to the previously on VSC-1 and VSC-2 employed SGE, the scheduler on VSC-3, VSC-4, and VSC-5 is [[http://slurm.schedmd.com|SLURM]]. |
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| Contrary to the previously on VSC 1 and VSC 2 employed SGE, the scheduler on VSC-3 and VSC-4 is [[http://slurm.schedmd.com|SLURM]]. | ==== Basic SLURM commands: ==== |
| === Basic SLURM commands: === | * ''[...]$ sinfo'' gives information on which partitions are available for job submission. Note: What SGE on VSC-2 termed a 'queue' is now called a 'partition' under SLURM. |
| * ''[...]$ sinfo'' gives information on which 'queues'='partitions' are available for job submission. Note: the under SGE termed 'queue' is called a 'partition' under SLURM. | |
| * ''[...]$ scontrol'' is used to view SLURM configuration including: job, job step, node, partition, reservation, and overall system configuration. Without a command entered on the execute line, scontrol operates in an interactive mode and prompt for input. With a command entered on the execute line, scontrol executes that command and terminates. | * ''[...]$ scontrol'' is used to view SLURM configuration including: job, job step, node, partition, reservation, and overall system configuration. Without a command entered on the execute line, scontrol operates in an interactive mode and prompt for input. With a command entered on the execute line, scontrol executes that command and terminates. |
| * ''[...]$ scontrol show job 567890'' shows information on the job with number 567890. | * ''[...]$ scontrol show job 567890'' shows information on the job with number 567890. |
| * ''[...]$ scontrol show partition'' shows information on available partitions. | * ''[...]$ scontrol show partition'' shows information on available partitions. |
| * ''[...]$ squeue'' to see the current list of submitted jobs, their state and resource allocation. [[doku:slurm_job_reason_codes|Here]] is a description of the most important **job reason codes** returned by the squeue command. | * ''[...]$ squeue'' to see the current list of submitted jobs, their state and resource allocation. [[doku:slurm_job_reason_codes|Here]] is a description of the most important **job reason codes** returned by the squeue command. |
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| | ==== Software Installations and Modules ==== |
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| | On VSC-4 and VSC-5, spack is used to install and provide modules, see [[doku:spack|SPACK - a package manager for HPC systems]]. The methods described in [[doku:modules]] can still be used for backwards compatibility, but we suggest using spack. |
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| ==== Node configuration - hyperthreading ==== | ==== Node configuration - hyperthreading ==== |
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