VÝPOČTOVÉ STREDISKO SLOVENSKEJ AKADÉMIE VIED

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Odbor vysokovýkonnej výpočtovej techniky: Softvérové vybavenie

Žilina:

ORCA 4: The program ORCA is a modern electronic structure program package written by F. Neese, with contributions from many current and former coworkers and several collaborating groups. The binaries of ORCA are available free of charge for academic users for a variety of platforms. (https://orcaforum.cec.mpg.de/)

ORCA je na klastri v Žiline nainštalovaný v priečinku /gpfs/home/freeware/LINUX/orca4/.
Bowtie (v2.1.0): Bowtie is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small.(http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)

Bowtie je na klastri v Žiline nainštalovaný v priečinku /gpfs/home/freeware/LINUX/bowtie/.
V priečinku /gpfs/home/freeware/LINUX/EXAMPLE_JOBS/bowtie nájdete príklad skriptu pre LoadLeveler.
diyabc (v2.0.4): diyabc software provides a user-friendly approach to Approximate Bayesian Computation for inference on population history using molecular markers. (http://www1.montpellier.inra.fr/CBGP/diyabc/)

diyabc je na klastri v Žiline nainštalovaný v priečinku /gpfs/home/freeware/LINUX/diyabc/.
GRASS GIS (v7.0.1, 7.0.2, 7.0.3, 7.3-dev): GRASS GIS, commonly referred to as GRASS (Geographic Resources Analysis Support System), is a free and open source Geographic Information System (GIS) software suite used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization. GRASS GIS is currently used in academic and commercial settings around the world, as well as by many governmental agencies and environmental consulting companies. It is a founding member of the Open Source Geospatial Foundation (OSGeo). (https://grass.osgeo.org/)

GRASS GIS je na klastri v Žiline nainštalovaný v priečinku /gpfs/home/freeware/LINUX/grass/.
V priečinku /gpfs/home/freeware/LINUX/EXAMPLE_JOBS/grass/ nájdete príklad skriptu pre LoadLeveler.
HMMER (v3.1): HMMER is a program used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. (http://hmmer.janelia.org/)

HMMER je na klastri v Žiline nainštalovaný v priečinku /gpfs/home/freeware/LINUX/hmmer-3.1/.
GAMESS (2010, 2012, 2014): GAMESS (General Atomic and Molecular Electronic Structure System) is a computational chemistry software program. It can perform a number of general computational chemistry calculations, including Hartree–Fock, density functional theory (DFT), generalized valence bond (GVB), and Multi-configurational self-consistent field (MCSCF). (http://www.msg.ameslab.gov/GAMESS/GAMESS.html)

GAMESS je na klastri v Žiline nainštalovaný v priečinku /gpfs/home/freeware/LINUX/gamess-2010/.
V priečinku /gpfs/home/freeware/LINUX/EXAMPLE_JOBS/gamess/ nájdete príklad skriptu pre LoadLeveler.
Maxent (v3.3.3k): Maxent is a software for species habitat modeling (https://www.cs.princeton.edu/~schapire/maxent/)

Maxent je na klastri v Žiline nainštalovaný v priečinku /gpfs/home/freeware/LINUX/maxent/.
NWChem (v6.5): NWChem provides many methods for computing the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density. (http://www.nwchem-sw.org/index.php/Main_Page)

NWChem je na klastri v Žiline nainštalovaný v priečinku /gpfs/home/freeware/LINUX/NWChem-6.5/.
OpenFOAM (v1.5.0): OpenFOAM is the free, open source CFD software released and developed primarily by OpenCFD Ltd since 2004. It has a large user base across most areas of engineering and science, from both commercial and academic organisations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics. (http://www.openfoam.com/)

NWChem je na klastri v Žiline nainštalovaný v priečinku /gpfs/home/freeware/LINUX/OpenFOAM/.
V priečinku /gpfs/home/freeware/LINUX/EXAMPLE_JOBS/openfoam/ nájdete príklad skriptu pre LoadLeveler.
openModeller (v1606+): openModeller provides a flexible, robust, cross-platform environment to carry out ecological niche modeling experiments. It is comprised of a single framework written in C++ allowing multipe interfaces on top of it, such as command line programs, Desktop interface, Web interface and Web Service interface. The framework includes facilities for sampling points, creating, testing, evaluating and projecting models into different environmental scenarios, reading species occurrence and environmental data in different formats. (http://openmodeller.sourceforge.net/)

NWChem je na klastri v Žiline nainštalovaný v priečinku /gpfs/home/freeware/LINUX/openmodeller/.
V priečinku /gpfs/home/freeware/LINUX/EXAMPLE_JOBS/openmodeller/ nájdete príklad skriptu pre LoadLeveler.
Structure (v2.3.4): The program structure is a software package for using multi-locus genotype data to investigate population structure. (http://pritchardlab.stanford.edu/structure.html)

Structure je na klastri v Žiline nainštalovaný v priečinku /gpfs/home/freeware/LINUX/Structure-2.3.4/.
trinity (v2.0.6): Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. (https://github.com/trinityrnaseq/trinityrnaseq/wiki)

triknity je na klastri v Žiline nainštalovaný v priečinku /gpfs/home/freeware/LINUX/trinity/.
V priečinku /gpfs/home/freeware/LINUX/EXAMPLE_JOBS/trinity/ nájdete príklad skriptu pre LoadLeveler.

Aurel:

NWChem NWChem is an ab initio computational chemistry software package which also includes quantum chemical and molecular dynamics functionality. It was designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources. (http://www.nwchem-sw.org/index.php/Main_Page)

NWCHEM je na superpočítači Aurel nainštalovaný v priečinku (/gpfs/home/freeware/nwchem/).
V priečinku /gpfs/home/freeware/EXAMPLE_JOBS/nwchem nájdete príklad skriptu pre LoadLeveler

ACES: ACES (Advanced Concepts in Electronic Structure) is a program for performing parallel calculations on both closed shell and open shell molecular systems. (http://www.qtp.ufl.edu/aces/docs.shtml)

ACES je na superpočítači Aurel nainštalovaný v priečinku /gpfs/home/freeware/aces3/.
V priečinku /gpfs/home/freeware/EXAMPLE_JOBS/aces3/ nájdete príklad skriptu pre LoadLeveler.
BEAST (v1.8.0): BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a program for Bayesian analysis of molecular sequences using MCMC. (http://beast.bio.ed.ac.uk/)

BEAST je na superpočítači Aurel nainštalovaný v priečinku /gpfs/home/freeware/BEASTv1.8.0/.
Block (v0.9.6): Block implements the density matrix renormalization group (DMRG) algorithm for quantum chemistry. The DMRG is a variational wavefunction method. (http://www.princeton.edu/chemistry/chan/software/dmrg/)

Block je na superpočítači Aurel nainštalovaný v priečinku /gpfs/home/freeware/block-0.9.6/.
V priečinku /gpfs/home/freeware/EXAMPLE_JOBS/block/ nájdete príklad skriptu pre LoadLeveler.
CP2K (v2.5.1): CP2K is a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. (http://www.cp2k.org/)

CP2K je na superpočítači Aurel nainštalovaný v priečinku /gpfs/home/freeware/cp2k-2.5.1/.
V priečinku /gpfs/home/freeware/EXAMPLE_JOBS/cp2k-2.5.1/ nájdete príklad skriptu pre LoadLeveler.
CPMD (v4.1): The CPMD code is a parallelised plane wave / pseudo-potential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. (http://www.cpmd.org/)

CPMD je na superpočítači Aurel nainštalovaný v priečinku /gpfs/home/freeware/cpmd-4.1/.
V priečinku /gpfs/home/freeware/EXAMPLE_JOBS/cpmd/ nájdete príklad skriptu pre LoadLeveler.
DL_CLASSIC (v1.9) and DL_POLY (v4.03): DL_CLASSIC and DL_POLY are molecular simulation packages designed to facilitate molecular dynamics simulations of macromolecules, polymers, ionic systems, solutions and other molecular systems on parallel computers. (http://www.ccp5.ac.uk/DL_POLY_CLASSIC/)

DL_CLASSIC a DL_POLY sú na superpočítači Aurel nainštalované v priečinkoch /gpfs/home/freeware/dl_classic_1.9/ a /gpfs/home/freeware/dl_poly_4.03/.
V priečinku /gpfs/home/freeware/EXAMPLE_JOBS/dlpoly/ nájdete príklad skriptu pre LoadLeveler.
Quantum ESPRESSO (v4.0.3, 5.0.1, 5.3.0): Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. (http://www.quantum-espresso.org/project/manifesto/)

Quantum ESPRESSO je na superpočítači Aurel nainštalovaný v priečinku /gpfs/home/freeware/espresso-4.0.3/.
V priečinku /gpfs/home/freeware/EXAMPLE_JOBS/espresso/ nájdete príklad skriptu pre LoadLeveler.
ESPResSo MD (v3.0.2): ESPResSo is a highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology. It can be used to simulate systems such as polymers, liquid crystals, colloids, ferrofluids and biological systems, for example DNA and lipid membranes. (http://espressomd.org/wordpress/)

ESPResSo MD je na superpočítači Aurel nainštalovaný v priečinku /gpfs/home/freeware/espressoMD-3.0.2/.
V priečinku /gpfs/home/freeware/EXAMPLE_JOBS/espressoMD/ nájdete príklad skriptu pre LoadLeveler.
FDS-SMV (v6): FDS (Fire Dynamics Simulator) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. SMV (Smokeview) is a visualization program used to display the output of FDS and CFAST simulations. (https://code.google.com/p/fds-smv/)

FDS-SMV je na superpočítači Aurel nainštalovaný v priečinku /gpfs/home/freeware/fds6/.
V priečinku /gpfs/home/freeware/EXAMPLE_JOBS/fds6/ nájdete príklad skriptu pre LoadLeveler.
GAMESS (2014): GAMESS (General Atomic and Molecular Electronic Structure System) is a computational chemistry software program. It can perform a number of general computational chemistry calculations, including Hartree–Fock, density functional theory (DFT), generalized valence bond (GVB), and Multi-configurational self-consistent field (MCSCF). (http://www.msg.ameslab.gov/GAMESS/GAMESS.html)

GAMESS je na superpočítači Aurel nainštalovaný v priečinku /gpfs/home/freeware/gamess-2014/.
V priečinku /gpfs/home/freeware/EXAMPLE_JOBS/gamess/ nájdete príklad skriptu pre LoadLeveler.
Gromacs (v4.6.5, 5.0.5): GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. (http://www.gromacs.org/)

Gromacs je na superpočítači Aurel nainštalovaný v priečinku /gpfs/home/freeware/gromacs/.
V priečinku /gpfs/home/freeware/EXAMPLE_JOBS/gromacs/ nájdete príklad skriptu pre LoadLeveler.
Molden (v5.1): Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS, GAUSSIAN and the Semi-Empirical packages Mopac/Ampac; it also supports a number of other programs via the Molden Format. (http://www.cmbi.ru.nl/molden/)

Molden je na superpočítači Aurel nainštalovaný v priečinku /gpfs/home/freeware/molden5.1/.
MPQC: MPQC (Massively Parallel Quantum Chemistry Program) computes properties of atoms and molecules from first principles using the time independent Schrödinger equation. (http://www.mpqc.org/)

MPQC je na superpočítači Aurel nainštalovaný v priečinku /gpfs/home/freeware/mpqc/.
V priečinku /gpfs/home/freeware/EXAMPLE_JOBS/mpqc/ nájdete príklad skriptu pre LoadLeveler.
NAMD (v2.8): NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. (http://www.ks.uiuc.edu/Research/namd/)

NAMD je na superpočítači Aurel nainštalovaný v priečinku /gpfs/home/freeware/namd-2.8/.
V priečinku /gpfs/home/freeware/EXAMPLE_JOBS/namd/ nájdete príklad skriptu pre LoadLeveler.
QWalk (v0.96.4): QWalk is a program developed to perform high accuracy quantum Monte Carlo calculations of electronic structure in molecules and solids. (https://code.google.com/p/qwalk/)

QWalk je na superpočítači Aurel nainštalovaný v priečinku /gpfs/home/freeware/qwalk/.
V priečinku /gpfs/home/freeware/EXAMPLE_JOBS/qwalk/ nájdete príklad skriptu pre LoadLeveler.