Overview of Installed Software

Libraries, Programming Languages, Developer Tools

  • cmake – cross-platform free and open-source software for building, managing and testing of softwares – https://cmake.org/

  • CUDA – CUDA is a developing environment for compiling and running softwares on NVIDIA GPU-s - https://developer.nvidia.com/cuda-toolkit

  • FFTW – C subroutine for discrete Fourier transformations in one or more dimensions of arbitrary input size for more complex data. – http://www.fftw.org/

  • GCC – GNU compiler for compiling programs written in C and C++. It is also capable of compiling programs written in Objective-C, Fortran, Ada, Go and D. – https://gcc.gnu.org/

  • GMP – Arithmetic library for arbitrary precision operiations on signed integers, rational numbers, and floating-point numbers – https://gmplib.org/

  • go – Programming language developed by Google – https://golang.org/

  • HDF5 – Hierarchichal Data Format (v5) for storing and managing large and complex data. There are multiple parallel HDF5 packages installed on the Komondor supercomputer – https://www.hdfgroup.org/solutions/hdf5/

  • Intel oneAPI + HPC Toolkit – A software package developed by Intel, containing compilers (e.g.: C++, fortran), developer libraries (DAAL - Data Analytics Acceleration Library; Integrated Performance Primitives; Math Kernel Library; Message Passing Interface; Thread Building blocks), and debugger tools - https://software.intel.com/content/www/us/en/develop/tools/oneapi/commercial-base-hpc.html

  • JDK – Java Development Kit – Development platform by Oracle for creating softwares in Java. – https://www.oracle.com/java/

  • MPFR – C library for multiple-precision floating-point computations with correct rounding. – https://www.mpfr.org/

  • NetCDF – (Network Common Data Form) is a set of machine-independent software library and machine-independent data formats that support the creation, access and sharing of array-oriented scientific data.– https://www.unidata.ucar.edu/software/netcdf/

  • Open MPI – Message Passing Interface is a library and protocol that allows communication and parallel computation on multiple nodes. – https://www.open-mpi.org/

  • Intel MPI - The Intel implementation of Message Passing Interface.

  • Python – Python programming language for developing and executing programs – https://www.python.org/

  • R – Programming language for data analysis, data visualization, and statistical analyis. – https://www.r-project.org/about.html

  • Totalview - Scalable debugger tool in HPC environment, capable of debugging multithread and multi-GPU applications, provides visualizations of program data and variables.

Molecular dynamics, Quantum Chemistry

  • Amber – A suite of biomolecular simulation programs, with GPU support and low memory requirements. It provides interface for most quantum chemistry softwares, making it suitable for hybriod QM/QQ simulations – https://ambermd.org/

  • Ambertools – A free developer toolkit from from the developers of Amber. The toolkit can be used as a stand-alone software or in combination with Amber for molecular dynamics simulations – https://ambermd.org/AmberTools.php

  • Gaussian – One of the most robust software package applied in electron structure calculations. With the approximate solution of the Schrödinger equation, it is possible to investigate the electron structure of molecules starting from semi-empyric methods, through self-consistent Hartree-Fock method, to computationally demanding post-SCF methods. – https://gaussian.com

  • mopac – Software package applied for semi-empyric moecular orbital calculations. The software is suitable to calculate both solid-phase and molecular reactions. – https://www.scm.com/product/mopac/

  • Q-Chem/BrianQC - Quantum chemistry software package and GPU module, applied in chemistry to solve the Schrödinger equation for electrions, where the geometry of the system is known.

  • ORCA

Mathematical and Simulation Packages

  • Wolfram Mathematica - A computational platform to test both initial ideas and create complex solutions in HPC systems in the field of information technology, economics modelling, medical imaging, aviation engineering and industry robotics.

  • ANSYS - A multiphysic simulation software package. - https://www.ansys.com/services/ansys-learning-hub

Deep Learning and AI

  • Pytorch - A python library that provides to build deep neural networks and execute tensor computations with GPU acceleration. Pytorch is a popular package in the scientific community, and available as a stand-alone module/python environment on the Komondor supercomputer.

Software Tools for Genomic Analyses

Basic tools for processing and analyzing genomic sequencing (next-generation sequencing, NGS) data are available preinstalled in a container environment. Using the container, bioinformatics pipeline scripts can be run as scheduled slurm jobs. The container can also be used for interactive analyses.

You can find detailed information about using the genomics container in the “Software / Genomic Analyses” section.

Open-source tools that are currently available in the container:

  • Quality control of sequencing data: FastQC, MultiQC

  • Trimming and cleaning sequences: Cutadapt, Trimmomatic, Trim Galore

  • Sequence read mapping tools: BWA, Bowtie, Bowtie 2, STAR, BBMap, HISAT2, Bismark

  • Manipulation of sequences and alignment data: Samtools, Picard

  • Peak calling: MACS2

  • Motif analysis: HOMER

  • Genome arithmetics: Bedtools

  • Gene expression analysis: Salmon, DESeq2

  • Genetic variant identification and analysis: BCFtools, VCFtools, freebayes

  • Chromosome conformation capture analysis: HiCUP, HiCExplorer, HiC-Pro

  • Genome assembly: ABySS, MEGAHIT, Velvet, SPAdes, Canu, Tigmint

  • Genome analysis toolkit: GATK4

  • Data analysis and scripting: R, Python, Julia

Software Environments

  • Environment Modules - Allow you to easily load the environment required to run specific versions of installed applications. - https://modules.readthedocs.io/en/latest/

  • Singularity - Container platform to run software and complete workflows in an isolated environment. - https://sylabs.io/docs/

  • JupyterHub - Provides access to preconfigured computational environments and resources in a graphical user interface. For convenience, the most popular tools for AI, big data and genomic analysis jobs are preinstalled in containers that can be launched on our JupyterHub. - https://jupyter.hpc.kifu.hu

Licence Information

  • ANSYS - 2023r1 and 2022r2 are available for academic users

  • MATLAB - matlab/r2023a is available using Campus Licence provided by the home organization (universities)

  • Gaussian - gaussian16 is available only for users at the University of Debrecen

To use software with a commercial license, please consult the terms of the license. Proprietary software products are usually only licensed to academic users.