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:
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: