Migrating merlin6 user guide from jekyll-example1
From lsm-hpce/jekyll-example1 1eada07
This commit is contained in:
Spencer Bliven
@ -1,20 +1,11 @@
|
||||
---
|
||||
layout: default
|
||||
title: Slurm Basic Commands
|
||||
parent: Merlin6 Slurm
|
||||
grand_parent: Merlin6 User Guide
|
||||
nav_order: 1
|
||||
---
|
||||
|
||||
# Slurm Basic Commands
|
||||
{: .no_toc }
|
||||
|
||||
## Table of contents
|
||||
{: .no_toc .text-delta }
|
||||
|
||||
1. TOC
|
||||
{:toc}
|
||||
|
||||
#tags:
|
||||
#keywords:
|
||||
last_updated: 13 June 2019
|
||||
#summary: ""
|
||||
sidebar: merlin6_sidebar
|
||||
permalink: /merlin6/slurm-basics.html
|
||||
---
|
||||
|
||||
## Basic commands
|
||||
@ -42,13 +33,13 @@ sprio -l # to view the factors that comprise a job's scheduling priority
|
||||
|
||||
## Basic slurm example
|
||||
|
||||
You can copy-paste the following example in a file file called ``mySlurm.batch``.
|
||||
Some basic parameters are explained in the example.
|
||||
You can copy-paste the following example in a file file called ``mySlurm.batch``.
|
||||
Some basic parameters are explained in the example.
|
||||
Please notice that ``#`` is an enabled option while ``##`` is a commented out option (no effect).
|
||||
|
||||
```bash
|
||||
#!/bin/sh
|
||||
#SBATCH --partition=daily # name of slurm partition to submit. Can be 'general' (default if not specified), 'daily', 'hourly'.
|
||||
#SBATCH --partition=daily # name of slurm partition to submit. Can be 'general' (default if not specified), 'daily', 'hourly'.
|
||||
#SBATCH --job-name="mySlurmTest" # name of the job. Useful when submitting different types of jobs for filtering (i.e. 'squeue' command)
|
||||
#SBATCH --time=0-12:00:00 # time limit. Here is shortened to 12 hours (default and max for 'daily' is 1 day).
|
||||
#SBATCH --exclude=merlin-c-001 # exclude which nodes you don't want to submit
|
||||
@ -74,17 +65,17 @@ squeue # check its status
|
||||
|
||||
---
|
||||
|
||||
## Advanced slurm test script
|
||||
## Advanced slurm test script
|
||||
|
||||
Copy-paste the following example in a file called myAdvancedTest.batch):
|
||||
|
||||
```bash
|
||||
#!/bin/bash
|
||||
#SBATCH --partition=merlin # name of slurm partition to submit
|
||||
#SBATCH --time=2:00:00 # limit the execution of this job to 2 hours, see sinfo for the max. allowance
|
||||
#SBATCH --nodes=2 # number of nodes
|
||||
#SBATCH --time=2:00:00 # limit the execution of this job to 2 hours, see sinfo for the max. allowance
|
||||
#SBATCH --nodes=2 # number of nodes
|
||||
#SBATCH --ntasks=24 # number of tasks
|
||||
|
||||
|
||||
module load gcc/8.3.0 openmpi/3.1.3
|
||||
module list
|
||||
|
||||
@ -92,15 +83,15 @@ echo "Example no-MPI:" ; hostname # will print one hostname per node
|
||||
echo "Example MPI:" ; mpirun hostname # will print one hostname per ntask
|
||||
```
|
||||
|
||||
In the above example are specified the options ``--nodes=2`` and ``--ntasks=24``. This means that up 2 nodes are requested,
|
||||
and is expected to run 24 tasks. Hence, 24 cores are needed for running that job. Slurm will try to allocate a maximum of 2 nodes,
|
||||
In the above example are specified the options ``--nodes=2`` and ``--ntasks=24``. This means that up 2 nodes are requested,
|
||||
and is expected to run 24 tasks. Hence, 24 cores are needed for running that job. Slurm will try to allocate a maximum of 2 nodes,
|
||||
both together having at least 24 cores. Since our nodes have 44 cores / each, if nodes are empty (no other users
|
||||
have running jobs there), job will land on a single node (it has enough cores to run 24 tasks).
|
||||
|
||||
If we want to ensure that job is using at least two different nodes (i.e. for boosting CPU frequency, or because the job requires
|
||||
more memory per core) you should specify other options.
|
||||
more memory per core) you should specify other options.
|
||||
|
||||
A good example is ``--ntasks-per-node=12``. This will equally distribute 12 tasks on 2 nodes.
|
||||
A good example is ``--ntasks-per-node=12``. This will equally distribute 12 tasks on 2 nodes.
|
||||
|
||||
```bash
|
||||
#SBATCH --ntasks-per-node=12
|
||||
@ -115,9 +106,9 @@ can allow the use of at least 12 cores per node (i.e. ``28000``)
|
||||
#SBATCH --mem-per-cpu=28000
|
||||
```
|
||||
|
||||
Finally, in order to ensure exclusivity of the node, an option *--exclusive* can be used (see below). This will ensure that
|
||||
the requested nodes are exclusive for the job (no other users jobs will interact with this node, and only completely
|
||||
free nodes will be allocated).
|
||||
Finally, in order to ensure exclusivity of the node, an option *--exclusive* can be used (see below). This will ensure that
|
||||
the requested nodes are exclusive for the job (no other users jobs will interact with this node, and only completely
|
||||
free nodes will be allocated).
|
||||
|
||||
```bash
|
||||
#SBATCH --exclusive
|
||||
@ -125,7 +116,7 @@ free nodes will be allocated).
|
||||
|
||||
This can be combined with the previous examples.
|
||||
|
||||
More advanced configurations can be defined and can be combined with the previous examples. More information about advanced
|
||||
More advanced configurations can be defined and can be combined with the previous examples. More information about advanced
|
||||
options can be found in the following link: https://slurm.schedmd.com/sbatch.html (or run 'man sbatch').
|
||||
|
||||
If you have questions about how to properly execute your jobs, please contact us through merlin-admins@lists.psi.ch. Do not run
|
||||
@ -133,7 +124,7 @@ advanced configurations unless your are sure of what you are doing.
|
||||
|
||||
---
|
||||
|
||||
## Environment Modules
|
||||
## Environment Modules
|
||||
|
||||
On top of the operating system stack we provide different software using the PSI developed
|
||||
pmodule system. Useful commands:
|
||||
@ -144,9 +135,9 @@ module load gnuplot/5.2.0 # to load specific version of
|
||||
module search hdf # try it out to see which version of hdf5 package is provided and with which dependencies
|
||||
module load gcc/6.2.0 openmpi/1.10.2 hdf5/1.8.17 # load the specific version of hdf5, compiled with specific version of gcc and openmpi
|
||||
module use unstable # to get access to the packages which are not considered to be fully stable by module provider (may be very fresh version, or not yet tested by community)
|
||||
module list # to see which software is loaded in your environment
|
||||
module list # to see which software is loaded in your environment
|
||||
```
|
||||
|
||||
### Requests for New Software
|
||||
### Requests for New Software
|
||||
|
||||
If you miss some package/version, contact us
|
||||
|
||||
Reference in New Issue
Block a user