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Software packages#

Software on our systems is installed in the following ways:

  1. as packages from the Linux distribution (free open-source software when available and recent enough) -- no modules needed

  2. through the SPACK package manager (free open-source software when available in SPACK) - load the *-spack modules by command:

    Bash
    module load rocky8-spack

  3. manually (mostly non-free software (not GPL/BSD license) - load the */all modules by command:

    Bash
    module load rocky8/all

Here is a list of important software for special purpose:

  • CAD & Meshing software --- FreeCAD, Salome, BRL-CAD, Gmsh and netgen; see CAD-Mesh
  • Finite element software for multiphysical problems --- ElmerFEM, CalculiX, Abaqus
  • Computational Fluid Dynamics -- OpenFOAM, SU2
  • Conformational search --- xtb-CREST
  • General purpose computational chemistry, biology and physics software packages --- Gaussian, ORCA, NWChem, xTB, CP2K
  • Wavefunction analysis --- Multiwfn
  • Visualization software for computational chemistry, biology and physics --- Molden, Avogadro, JMol, VMD, RasMol
  • Interactive and non-interactive Jupyter notebooks for Julia, Python, Octave
  • Matlab-compatible computation environment --- Octave
  • Data analysis --- R, Matlab, Octave, Julia, awk, Python, GNUplot
  • Visualization software --- MayaVi2, ParaView, VisIt, COVISE, OpenDX, GNUplot

A more detailed description of available softwares, as well as a division by area of use, is given below.

If software you want to use is missing in the list above, it means that it is not installed, but can be installed by your request to hpcsupport@taltech.ee or create a ticket in Helpdesk Portal. In the case of licensed software, the user must provide the license himself and the corresponding program will be installed.

Engineering#

CAD & Mesh-Tools#

Computer-aided design (CAD) is software for building models in a virtual space, that allows to visualize various properties of an object, such as height, width, distance, material, etc. This category contains software that is essential for the pre-processing of many simulations: CAD and mesh generation. More about CAD and meshing options on our HPC can be found here.

FreeCAD#

FreeCAD is a CAD software, which uses Gmsh or Netgen for meshing. It can also serve as a frontend for CalculiX and ElmerFEM, thus providing similar functionality as SolidWorks. More about FreeCAD on our HPC can be found here.

Salome#

Salome is a CAD program with interfaces to meshing software. It can be used by a GUI or python scripts. More about Salome on our HPC can be found here.

BRL-CAD#

BRL-CAD is a CAD software that has been in development since 1979 and is open-source since 2004. It is based on CSG modeling. BRL-CAD does not provide volume meshing, however, the CSG geometry can be exported to BREP (boundary representation, like STL, OBJ, STEP, IGES, PLY), the g- tools are for this, while the -g tools are for importing. More about BRL-CAD on our HPC can be found here.

Blender#

Blender is a 3D modeling software developed for computer animation (movie production).

Gmsh#

Gmsh is an open source 3D finite element mesh generator with a built-in CAD engine and post-processor. More about Gmsh on our HPC can be found here.

Netgen#

Netgen is a part of the NGsolve suite. Netgen is a automatic 3d tetrahedral mesh generator containing modules for mesh optimization and hierarchical mesh refinement. More about Netgen on our HPC can be found here.

Cubit (non-commercial, affiliate)#

Coreform Cubit is a commercial preprocessing software with the ability to create high quality hex and hex-dominant meshes. Our affilialte license is limited to exporting 50000 cells and is for non-commercial use only! Go to https://coreform.com/account/login and select "Activate a limited-use associate license", enter the affiliate code from cat /gpfs/mariana/software/green/Coreform/affiliate.txt.

Finite Element Analysis (FEA)#

The Finite Element Method (FEM) is an general numerical method for solving partial differential equations in two or three space variables perfommed by dividing a large system into smaller parts (finite elements). The method is used for numerically solving differential equations in engineering and mathematical modeling.

See also under computational-fluid-dynamics-CFD.

ElmerFEM#

Elmer is a multi-physics simulation software developed by CSC. It can perform coupled mechanical, thermal, fluid, electro-magnetic simulations and can be extended by own equations. Elmer manuals and tutorials can be found here and for more details and example job scripts go here.

CalculiX#

CalculiX is a finite-element analysis application. The two programs that form CalculiX are cgx and ccx, where cgx is a graphical frontend (pre- and post-processing) and ccx is the solver doing the actual numerics. CalculiX can be used for grid data generation or mech data generation. It can be applied in such areas as mechanical analysis, heat transfer, electromagnetic calculations, computational fluid dynamics, etc. For more detais see overview of the finite element capabilities of CalculiX Version 2.18. Solver makes use of the Abaqus input format.

FreeFEM#

FreeFEM is a software focused on solving partial differential equations using the finite element method. Can be used for linear, non-linear elasticity, thermal diffusion/convection/radiation, magnetostatics, electrostatics, CFD, fluid structure interaction; continuous and discontinuous Galerkin method. Allows to implement own physics modules using the FreeFEM language.

deal.II#

deal.II - an open source finite element library

MFEM#

MFEM is a free, lightweight, scalable C++ library for finite element methods.

code-aster and Salome-meca#

Code-Aster is a free finite element analysis software, which is developed by EDF. It is used for planning power plants. Salome-meca is a version of code-aster integrated into the CAD software Salome. Modules for both are in the rocky8 module list. They are currently to be considered experimental. For use with a GUI, the OnDemand login to the cluster is recommended (please note the runtime limitation).

code-aster

Bash
module load rocky8 code_aster

Salome-meca

Bash
module load rocky8 salome-meca
and start with

Bash
salome-meca

Abaqus#

Abaqus is a commercial software suite for finite element analysis and computer-aided engineering. The Abaqus products use Python for scripting and customization. User modules can be written in Fortran or C/C++, our installation is configured to use gcc-10.3.0. Abaqus versions 2018 and 2021 are installed. The number of concurrent processes is limited and managed by flexlm.

Bash
    module load rocky8
    module load abaqus

To use Abaqus' PlatformMPI, SLURM's Global Task ID needs to be cleared

Bash
    unset SLURM_GTIDS

Currently submitting abaqus.slurm scripts directly with sbatch or srun does not work!

The current workaround is to use an interactive session on a node, this means either an OnDemand desktop session (limited to 4 hours, please reserve enough CPUs and RAM for the job) or srun -N 1 -n XXX --mem YYGB -p common --pty bash and run the abaqus manually or the abaqus.slurm script as a regular shell script (XXXX is number of ntasks, YY is needed memory in GB): sh abaqus.slurm The disadvantage is that the ssh connection must stay open (or use screen on base.

Comsol#

Commercial multi-physics finite element simulation software. License belongs to a research group.

LSDyna#

License belongs to a research group.

Bash
    module load rocky8
    module load LSDyna/SMP-13.0.0-D

Star-CCM+#

Commercial software. System wide installation, bring your own license. Star-CCM+ can be used with PowerOnDemand (PoD) keys. Power on demand (PoD) licensing for STAR-CCM+ is essentially cloud licensing. To use PoD licensing, a PoD key must be copied from the Star-CCM+ support center and put into the STAR-CCM+ interface.

More information about licenses:

Bash
    module load rocky8
    module load star-ccm+/18.04.009-R8
    starccm+

OpenRadioss#

Altair OpenRadioss is an explicit FEA software for highly dynamic simulations, like impact and blasts.

Computational Fluid Dynamics (CFD)#

See also under FEA.

OpenFOAM#

OpenFOAM is an open source software for computational fluid dynamics (CFD). There are two major flavours of OpenFOAM, the OpenFOAM.com (ESI/Keysight) version and the OpenFOAM.org (Foundation) verion. OpenFOAM has a wide range of tools for modelling complex fluid flows and can be used for solving such problems as chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics. More about OpenFOAM on our HPC can be found here.

SU2#

SU2 is a computational analysis and design package that has been developed to solve multiphysics analysis and optimization tasks using unstructured mesh topologies. SU2 is intalled through SPACK.

Water Wave Modelling#

WAM#

WAM is a third generation wave model, developed and maintained by GKSS. It describes the evolution of the wave spectrum by solving the wave energy transfer equation. WAM predicts directional spectra and wave properties (such as wave height, direction and frequency, swell height and mean direction), wind stress fields etc. WAM can be coupled to a range of other models (NEMO, RegCM, SEAOM, etc.). More info how to use it on HPC see here.

Swan#

SWAN is a third generation wave model for obtaining realistic estimates of wave parameters in coastal areas, lakes and estuaries from given wind, bottom and current conditions, developed and maintained by TU Delft. The model is based on the wave action balance equation with sources and sinks. SWAN allows to use two types of grids (structured and unstructured) and nesting approach. More info how to use it on HPC see here.

Chemistry, biology and physics#

Conformational search & sampling#

xtb-CREST#

Conformer–Rotamer Ensemble Sampling Tool (xtb-CREST) is designed as conformer sampling program by Grimme's group. CREST uses meta-dynamics, regular MD simulations and Genetic Z-matrix crossing (GC) algorithms with molecular mechanics or semiempirical methods (GFNn-xTB). Conformational search can be done in gas or solvent (using several continuum models). More about xtb-CREST on our HPC can be found here.

General purpose computational chemistry, biology and physics#

Gaussian#

Gaussian is a general purpose package for calculation of electronic structures. It can calculate properties of molecules (structures, energies, spectroscopic and thermochemical properties, atomic charges, electron affinities and ionization potentials, electrostatic potentials and electron densities etc.) and reactions properties (such as reaction pathways, IRC)sing different methods (such as Molecular mechanics, Semi-empirical methods, Hartree-Fock, Density functional, Møller-Plesset perturbation theory, coupled cluster). More about Gaussian on HPC can be found here.

ORCA#

ORCA is a multi-purpose quantum-chemical software package developed in the research group of Frank Neese. ORCA includes a wide variety of methods (semi-empirical, density functional theory, many-body perturbation, coupled cluster, multireference, nudged elastic band (NEB) methods). In ORCA, molecules' and spectroscopic properties calculations are available, and environmental (MD (including ab initio), QM/MM, Crystal-QMMM) as well as relativistic effects can be taken into account. ORCA is parallelized, and uses the resolution of the identity (RI) approximation and domain based local pair natural orbital (DLPNO) methods, which significantly speed calculations. More about ORCA on HPC can be found here

xtb#

Extended tight binding - xTB program developed in the research group of Stefan Grimme for solutions of common chemical problems. The workhorses of xTB are the GFN methods, both semi-empirical and force-field. The program contains several implicit solvent models: GBSA, ALPB, ddCOSMO, and CPCM-X. xTB functionality covers single-point energy calculations, geometry optimization, frequency calculations, reaction path methods. Also allows to perform molecular dynamics, meta-dynamics, and ONIOM calculations. More about xTB on HPC can be found here

NWChem#

The North West computational chemistry (NWChem) is an ab initio computational chemistry software package which includes quantum chemical ( HF, DFT, MP2, MCSCF, and CC, including the tensor contraction engine (TCE)) and molecular dynamics (using either force fields (AMBER or CHARMM) or DFT) functionality. In NWChem, ab initio methods can be coupled with the classical MD to perform mixed quantum-mechanics and molecular-mechanics simulations (QM/MM). Various molecular response properties, solvent models, nudged elastic band (NEB) method, relativistic and resolution of the identity (RI) approaches are also available.

NWChem was developed to enable large scale calculations by using many CPUs and has parallel scalability and performance. Additionally, python programs may be embedded into the NWChem input and used to control the execution of NWChem.

Wavefunction analysis#

Multiwfn#

Multiwfn it is an interactive program that performs almost all important wavefunction analyzes. In addition, Multiwfn is able to display plots of the predicted spectra. More about Multiwfn on HPC can be found here.

Visualization software for computational chemistry, biology and physics#

Electronics (EDA CAD)#

NGSpice#

ngspice is the open source spice simulator for electric and electronic circuits.

Bash
module load rocky8-spack
module load ngspice

Qucs#

Quite Universal Circuit Simulator (Qucs) is a free-software electronics circuit simulator software

Bash
module load rocky8-spack
module load qucs

The recommended way is now to use a desktop session in OnDemand, see also the visualization page on how to start these and on GPU acceleration.