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 For mox.hyak (hyak nextgen) or ikt.hyak please go to  Mox_scheduler .

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Ignore below article. Below article is for historical interest.

Hyak classic (ikt) used a PBS based scheduler.

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

To logon:

ssh abc@hyak.washington.edu

The above command gives you access to the login node of ikt.hyak. 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 usage of your group's nodes:

nodestate xyz

To get information about your nodes:

mdiagn -t xyz

Interactive Single Node Usage:

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

To get an interactive build node for 2 hours:

qsub -q build -I -l walltime=2:00:00

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

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

qsub -I -l walltime=2:00:00

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

export | grep PBS


Interactive Multiple Node Usage:

To get 2 nodes for interactive use for 2 hours:

qsub -I -l nodes=2:ppn=16,feature=16core,walltime=2:00:00

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

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

cat $PBS_NODEFILE | uniq

Once you know the node names, then you can use them for your work.

Below command will tell you about other PBS environment variables.

export | grep PBS


Batch usage:

To submit a batch job:

qsub myscript.pbs

Below is an example PBS script myscript.pbs.

#!/bin/bash

#PBS -N "single_word_logical_job_name"

#PBS -d /gscratch/xyz/abc/mydirectory

#PBS -l nodes=1:ppn=16,feature=16core,mem=40gb,walltime=24:00:00

#PBS -M user@u.washington.edu

#PBS -m abe

myprogram

 

qdel

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

qdel 1234

 

More details are here:

 Hyak Job Scheduler

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