ARC Software: Difference between revisions
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= | = Software Management = | ||
For some general consideration for setting up software in your home directory see [[Managing software on ARC]]. | |||
* [[Conda on ARC | Conda]] and Miniconda | |||
[[ | |||
= | = Containers = | ||
* [[ | * [[Apptainer]] -- former '''Singularity''' container engine. | ||
= General Tools = | = General Tools = | ||
* [[Python]] | * [[Python]] | ||
* [[Perl]] | * [[Perl]] | ||
= Libraries = | = File Format Libraries = | ||
* [[HDF5]] | |||
== | = Atmospheric research = | ||
* [[CESM]] | |||
= Biomedical research = | |||
* [[Bioconda]] -- lets you install thousands of software packages related to biomedical research using the [[Conda on ARC | Conda]] package manager. | |||
* [[ | * [[SignalP]] -- Prediction of Signal Peptides and their cleavage sites in all domains of life | ||
= Chemistry = | = Chemistry = | ||
* [[Gaussian on ARC | Gaussian 16]] - a commercial software package for electronic structure modelling. | |||
* [[ORCA]] - an ab initio quantum chemistry program package that contains modern electronic structure methods. | |||
* [[GROMACS]] - Classical molecular dynamics simulator. | |||
* [[Quantum ESPRESSO]] - 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. | |||
* [[ | * [[CPMD]] -- | ||
= Computational Fluid Dynamics = | = Computational Fluid Dynamics = | ||
* [[ANSYS]] - Fluent and CFX - commercial CFD software. | * [[ANSYS]] - Fluent and CFX - commercial CFD software. | ||
* [[OpenFOAM]] - Open-source toolkit for creating CFD applications. | * [[OpenFOAM]] - Open-source toolkit for creating CFD applications. | ||
| Line 36: | Line 40: | ||
* [[ANSYS]] - ANSYS Fluent - commercial software for finite element-based structural analysis. | * [[ANSYS]] - ANSYS Fluent - commercial software for finite element-based structural analysis. | ||
* [[Abaqus]] - Commercial software for finite element-based analysis. | * [[Abaqus]] - Commercial software for finite element-based analysis. | ||
* [[Nektar++]] -- a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers. | |||
= Geospatial Analysis = | = Geospatial Analysis = | ||
* [[GDAL on ARC | GDAL]] | * [[GDAL on ARC | GDAL]] | ||
* [[Geopandas on ARC | Geopandas]] | * [[Geopandas on ARC | Geopandas]] | ||
= Machine Learning = | = Machine Learning = | ||
* [[Tensorflow on ARC | Tensorflow]] | * [[Tensorflow on ARC | Tensorflow]] | ||
* [[Torch on ARC | PyTorch]] | * [[Torch on ARC | PyTorch]] | ||
= Mathematical Libaries and Applications = | = Mathematical Libaries and Applications = | ||
* [[MATLAB]] - Commercial general-purpose high-level programming environment for linear algebra, statistics, image processing and a wide range of other calculations. | * [[MATLAB]] - Commercial general-purpose high-level programming environment for linear algebra, statistics, image processing and a wide range of other calculations. | ||
* [[Mathematica]] - Commercial general-purpose high-level programming package for both symbolic and numerical calculations. | * [[Mathematica]] - Commercial general-purpose high-level programming package for both symbolic and numerical calculations. | ||
= Microscopy = | = Microscopy = | ||
* [[Relion on ARC | Relion]] | * [[Relion on ARC | Relion]] | ||
* [[Cellprofiler on ARC | Cellprofiler]] | * [[Cellprofiler on ARC | Cellprofiler]] | ||
= Neuroimaging = | = Neuroimaging = | ||
* [[AFNI on ARC | AFNI]] | |||
* [[Freesurfer on ARC | Freesurfer]] | * [[Freesurfer on ARC | Freesurfer]] | ||
* [[FSL on ARC | FSL]] | * [[FSL on ARC | FSL]] | ||
* [[fmriprep on ARC | fmriprep]] | * [[fmriprep on ARC | fmriprep]] | ||
* [[Statistical Parametric Mapping on ARC | SPM 12]] | |||
* [[ | = Physics = | ||
* [[ROOT]] - An open-source data analysis framework used by high energy physics and others. | |||
= Statistics = | = Statistics = | ||
* [[R on ARC | R]] | * [[R on ARC | R]] | ||
* [[Stan on ARC | rstan]] | * [[Stan on ARC | rstan]] | ||
[[Category:ARC]] | [[Category:ARC]] | ||
{{Navbox ARC}} | |||
Latest revision as of 19:54, 22 November 2024
Software Management
For some general consideration for setting up software in your home directory see Managing software on ARC.
- Conda and Miniconda
Containers
- Apptainer -- former Singularity container engine.
General Tools
File Format Libraries
Atmospheric research
Biomedical research
- Bioconda -- lets you install thousands of software packages related to biomedical research using the Conda package manager.
- SignalP -- Prediction of Signal Peptides and their cleavage sites in all domains of life
Chemistry
- Gaussian 16 - a commercial software package for electronic structure modelling.
- ORCA - an ab initio quantum chemistry program package that contains modern electronic structure methods.
- GROMACS - Classical molecular dynamics simulator.
- Quantum ESPRESSO - 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.
- CPMD --
Computational Fluid Dynamics
- ANSYS - Fluent and CFX - commercial CFD software.
- OpenFOAM - Open-source toolkit for creating CFD applications.
Finite Element Modelling
- ANSYS - ANSYS Fluent - commercial software for finite element-based structural analysis.
- Abaqus - Commercial software for finite element-based analysis.
- Nektar++ -- a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers.
Geospatial Analysis
Machine Learning
Mathematical Libaries and Applications
- MATLAB - Commercial general-purpose high-level programming environment for linear algebra, statistics, image processing and a wide range of other calculations.
- Mathematica - Commercial general-purpose high-level programming package for both symbolic and numerical calculations.
Microscopy
Neuroimaging
Physics
- ROOT - An open-source data analysis framework used by high energy physics and others.