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Dyngja

Introduction​

The Dyngja cluster consists of two compute nodes and is primarily designed to support computationally intensive geodetic research. Typical applications include processing large datasets from InSAR (Interferometric Synthetic Aperture Radar) and GNSS (Global Navigation Satellite System) observations, as well as performing geodetic inversions.

Users interact with Dyngja through remote login and job submission via the SLURM workload manager. Heavy computations should be submitted to SLURM instead of running directly on the login node.

Hardware Specification​

In total, the Dyngja cluster has 96 CPU cores, 192 CPU threads, and 376 GB of memory available:

CountNameCores/NodeMemory/Node (GB)Features
1Dyngja-batch48 (2x24)188Intel Gold 6248R
1Dyngja-interactive48 (2x24)188Intel Gold 6248R

More information can be found in the specs chapter and the partition chapter.

Request Access​

To obtain access to Dyngja, users should request an account from the IT Department through their supervisor or contact person. Users are assigned to the HPC-Dyngja group.

To speed up the account creation process, users can generate an SSH key in advance and send the public key together with the required account information.

Software and Modules​

A number of commonly used scientific software packages are installed on Dyngja, including:

SoftwareVersion
ROI_PAC3.0.1
StaMPS4.1.0
isce2.6.4
GMT6.5.0
GMTSAR6.5.0
LicSBAS1.17
MintPy1.6.1
GBIS202409

Software is managed through the module system. To list available software:

module avail

To load a specific software environment:

module load <software-name>

Dependencies are loaded automatically with the software where possible. The stacking processors for isce 2.6.4 are provided as separate modules and should be loaded manually when needed:

module load isce_stack/2.6.4-stamps-GCCcore-12.3.0
module load isce_stack/2.6.4-strip-GCCcore-12.3.0
module load isce_stack/2.6.4-tops-GCCcore-12.3.0

SLURM Usage​

Dyngja provides two SLURM partitions:

  • Dyngja-batch: batch processing
  • Dyngja-interactive: interactive processing, mostly for StaMPS and GBIS

Example batch job submission:

sbatch -p Dyngja-batch -o current.out -e current.err -n 4 -t 6:00:00 --mem=8000 <your-script>

Example interactive session:

srun -p Dyngja-interactive -c 4 --mem=8000 --time 1-00:00:00 --pty <your-software-or-script>

Both Dyngja-batch and Dyngja-interactive currently have a maximum time limit of two (2) days. To check submitted jobs:

squeue

To cancel a job:

scancel <jobid>

MATLAB Usage​

MATLAB is available through the container module path. To start MATLAB in an interactive SLURM session:

ml use /hpcapps/lib-containers/modules/all
ml load matlab/r2024a
srun -p Dyngja-interactive -t 24:00:00 --mem=9000 --pty matlab -nodisplay

MATLAB on HPC-Dyngja does not support the graphical interface or visualization. If you use StaMPS or GBIS from MATLAB, load the corresponding module before starting MATLAB.

Installation and Environment Notes​

Most software on Dyngja is managed using EasyBuild. Before installing software with EasyBuild:

. /hpcapps/lib-dyngja/installer/easy2install

To check an EasyBuild installation before running it:

eb <software-name>-<version>-<toolchain>-<toolchain-version>.eb --dry-run

To install after a successful dry run:

eb <software-name>-<version>-<toolchain>-<toolchain-version>.eb

Manually installed software source code should be stored under:

/hpcapps/lib-dyngja/source

Installed software should be placed under:

/hpcapps/lib-dyngja/software

Module files should be created under:

/hpcapps/lib-dyngja/modules/all

Here are recommended chapters to help you get started using Dyngja: