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This article is for mox.hyak (hyak nextgen). If you are using ikt.hyak (hyak classic) then go to Hyak_scheduler .

Mox uses a scheduler called slurm. It is similar to but different from the PBS based scheduler used on hyak classic.

Below xyz is your hyak group name and abc is your UW netid.

To logon:

ssh abc@mox.hyak.uw.edu

The above command gives you access to the login node of mox. The login node is only for logging in and submitting jobs. The computational work is  done on a compute node. As shown below, you can get either an interactive compute node or submit a batch job. The build node is a special compute node which can connect to the internet.

To see the various partitions (aka allocations):

sinfo

To see the usage of your group's nodes:

squeue -p xyz

Below mox specific command  shows  the number of nodes etc. of all allocations.

hyakalloc

Interactive Single Node Usage:

The build node can connect to outside mox. It is useful for using git, transferring files to outside mox or getting files from outside mox, installing packages in R or Python etc.

To get an interactive build node for 2 hours:

srun -p build --time=2:00:00 --pty /bin/bash

An interactive node in your own group cannot connect to outside mox.

To get an interactive node in your own group for 2 hours:

srun -p xyz -A xyz --time=2:00:00 --pty /bin/bash

Issue below comand at an interactive node prompt to find the list of SLURM environment variables:

export | grep SLURM

scancel

Use scancel to cancel jobs. For example to cancel a job with job id 1234:

scancel 1234

If your userid is abc then you can cancel all your jobs by using below command:

scancel -u abc


Batch usage:

To submit a batch job:

sbatch -p xyz -A xyz myscript.slurm

The script myscript.slurm is similar to myscript.pbs used in hyak classic. Below is an example slurm script.

#!/bin/bash

## Job Name

#SBATCH --job-name=myjob

## Allocation Definition
#SBATCH --account=xyz
#SBATCH --partition=xyz

## Resources

## Nodes

#SBATCH --nodes=1   

## Walltime (3 hours)

#SBATCH --time=3:00:00

## Memory per node

#SBATCH --mem=30G

## Specify the working directory for this job

#SBATCH --workdir=/gscratch/xyz/abc/myjobdir

myprogram

 

 

More details are here:

Hyak mox Overview

https://slurm.schedmd.com/quickstart.html

https://slurm.schedmd.com/documentation.html

 

===== Below is for Advanced users only ====

Interactive Multiple Node Usage with srun:

If you are setting up an application which uses multiple nodes (e.g. Apache Spark), you will need interactive access to multiple nodes .

To get 2 nodes for interactive use:

srun -N 2 -p xyz -A xyz  --time=2:00:00 --pty /bin/bash

When the above command runs, then you will have been allocated 2 nodes but will be on one of the two allocated node.

scontrol show nodes

Once you know the node names, then you can use them for your work (e.g. Apache Spark, Hadoop etc.)

Below command will tell you about other SLURM environment variables.

export | grep SLURM

Interactive Multiple Node Usage with salloc:

If you are setting up an application which uses multiple nodes (e.g. Apache Spark), you will need interactive access to multiple nodes .

To get 2 nodes for interactive use:

salloc -N 2 -p xyz -A xyz  --time=2:00:00

When the above command runs, then you will have been allocated 2 nodes but will still be on the mox login node.

If you issue a command like below then srun will run the command hostname on each node:

srun hostname

In order to find the names of the nodes that you have been allocated, issue below command:

scontrol show nodes

Once you know the node names, then you can use them for your work (e.g. Apache Spark, Hadoop etc.)

Below command will tell you about other SLURM environment variables.

export | grep SLURM

 

srun vs salloc

If no nodes have been allocated then (1) and (2) are equivalent.

(1) srun -p xyz -A xyz --time=4:00:00  --pty /bin/bash

(2) salloc -p xyz -A xyz --time=4:00:00    This allocates the node.

     srun --pty /bin/bash            This uses the same node.

If nodes have already been allocated by using salloc then srun just uses those nodes.

Alternative to srun is to allocate a node and then ssh to it e.g.

Allocate a node:

salloc -p xyz -A xyz --time=4:00:00

Find the name of the allocated node:

export | grep LIST

If above command gives a hostname of n1234 then you can ssh to n1234 and use it for your work.

 

 

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