Getting Started
Logging onto Boreal
To log on Boreal remotely, use:
ssh –X your_userid@boreal.emsl.pnl.gov
The -X option allows remote users to access X Windows functionality across
the internet.
Key fingerprints
MSC may occasionally update the host keys on the major systems. Check here to confirm the current fingerprint for Tahoma. If you see an alert about that indicates the fingerprints are different and they don’t match the following, contact support at mscf-consulting@emsl.pnl.gov
256 SHA256:4ROdyHeFOgFo4FLYwgIPSrFJayGd5I9DBdm1rE+dqKE no comment (ED25519)
256 SHA256:eOIgmn2o4rAP+UZXynYvoBbN52RxEjKi05FQZBBbbhI no comment (ECDSA)
2048 SHA256:uGIa1Zj5HaZPkAVJYoUiLE2DW8tAk32ovPMOHmYMp8c no comment (RSA)
Running Jobs on Boreal
Boreal is a batch scheduled environment managed by Slurm. For commonly used software we have pre-formed submission scripts that either interactively query you for the required input fields or take a prescribed set of arguments. These scripts then build the submission script and submit it for you.
To list the available submit scripts type:
ls /home/scicons/boreal/bin/submit*
Most of these scripts accept a -h or --help as an argument to give a
description of how to use them. When using the preformed submit scripts,
please be sure to run them from your /dtemp project directory. This is so
that output files land in the lustre file system which has much higher
bandwidth and lower latency than the /home file system. It is also a good
idea to have the input files (if needed) in the /dtemp file system.
Running jobs are subject to the limits set within our Job Policy.
Project Account Names on Boreal
All of the above pre-formed scripts and when you build your own you need to specify which project account is to be used. To see which project accounts you are permitted to run under, type:
gbalance
This will produce a list of the projects you may run under as well as the node hours used and remaining in the project. In the non-header lines of the output, the characters up to the first blank are the project name. If you are building your own submission scripts you will need to define the project in your scheduler directives:
#SLURM --account 'project'
Writing a Batch Script
If you are creating your own submission script, you submit them with the
sbatch command:
sbatch 'my_submission_script'
The scheduler will return the SLURM job ID or some error message if your
account is incorrect or the scheduler is not accepting jobs. When submitting
jobs, please run them from your /dtemp project directory.
More information is available at Job Scripts.