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.