Table of Contents

Cluster Kraken

Software on the Kraken cluster

Commercial programs (Ansys, Comsol,…) are accessible from the system, see Documentation below. Freely available software packages, especially compilers, are also installed in various versions in modules (Lmod). In addition to installations from source code, the extensive spack system database is used. Requests for installation of freely available software, module and queue system administration are handled by Jan Pech, 2 6605 3132.

We run jobs exclusively through the SLURM queue system.

Environment Modules

Basic procedures for working with cluster modules are described on the modules page. You can use the modules to call programs (openfoam, paraview, lammps…), see the list below, but also to set up the environment (compiler, mpi, …) to compile your own code.

The modules are tagged in the form name/version[-version_compiler] and divided into 3 sections according to the architecture they are optimized for

linux-centos7-broadwell 

 boost/1.59.0-5.5.0     gcc/10.3.0                      openmpi/4.0.5-5.5.0
 boost/1.76.0-10.3.0    intel-mpi/2019.10.317-18.0.2    openmpi/4.0.5-10.3.0
 cmake/3.20.6           mesa/21.2.1-10.3.0              paraview/5.9.0-10.3.0 
 emacs/27.1             metis/5.1.0-10.3.0              python/3.8.9-10.3.0
 ffmpeg/4.3.2-10.3.0    mpich/3.4.1-5.5.0               qt/5.15.2-10.3.0
 gcc/5.5.0              mpich/3.4.1-10.3.0              scotch/6.0.10-5.5.0
 gcc/7.5.0              nektar/5.0.0-5.5.0              zlib/1.2.11-5.5.0

linux-centos7-zen2 

 boost/1.77.0-11.2.0        openmpi/4.1.1-11.2.0          py-six/1.15.0-11.2.0
 gcc/11.2.0                 py-numpy/1.21.2-11.2.0        python/3.8.11-11.2.0
 mpich/3.4.2-11.2.0         py-scipy/1.7.1-11.2.0

linux-ubuntu22.04-zen4 

 boost/1.57.0-12.3.0    boost/1.83.0-12.3.0    fftw/3.3.10-12.3.0    metis/5.1.0-12.3.0      python/3.10.12-12.3.0    tinyxml/2.6.2-12.3.0
 boost/1.76.0-12.3.0    cmake/3.27.4           gcc/12.3.0            openmpi/4.0.7-12.3.0    scotch/7.0.3-12.3.0      zlib/1.3-12.3.0

The free_modulefiles section contains programs with specially created modules (all compiled for the broadwell architecture) 

 foam-extend/4.0-5.5.0        openfoam-org/8-10.3.0        solids4foam/4.0
 foam-extend/4.1-7.5.0        openfoam/2012-10.3.0         solids4foam/4.1 
 openfoam-org/6-10.3.0        paraview/5.6.0



Documentation


Ansys

ANSYS is currently available in version 2024 R1

The input (journal) calculation file can either be prepared locally and transferred to the cluster, or created directly on the “kraken” admin node via Ansys' remotely running graphical interface, i.e. workbench. The calculation itself must then be placed in queues.

Further information can be found at:


BDDCML

Manual


COMSOL

Comsol is actively installed in version 5.5. After logging on to the cluster (ssh with GUI enabled), the command line can be used to run the comsol command. Running a job on a queueing system is described on the following page: queues / Comsol


DL_POLY

User Manual Graphical User Interface


LAMMPS

The program is currently installed with components: diffraction, dipole, extra-dump, extra-fix, extra-pair, fep, kspace, manybody, meam, misc, molecule, phonon, replica, rigid

in modules:


Matlab

Matlab is available on all cluster nodes in version R2022b.

Queuing a job is described in queues/Matlab.

On the Matlab administrative node, simply run the matlab command.

online license status; login: matlab; password: 1dohens


Open Foam

OpenFOAM is available in several versions in modules.

The procedure to run OpenFOAM:

  1. Create a folder for OpenFOAM: mkdir -p $HOME/MyOpenFOAMFolder
  2. Move to the folder: cd $HOME/MyOpenFOAMFolder
  3. Create a task.sh script to queue the task, see SLURM script for OPENFoam
  4. Queue the job: sbatch job.sh'

User Guide Programmer's Guide


ParaView

Manual


ParMETIS

Manual