ARC Software: Difference between revisions

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= Software Management =
= 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
* [[Conda on ARC | Conda]] and Miniconda


= General Tools =
= General Tools =
* [[Python]]
* [[Python]]
* [[Perl]]
* [[Perl]]


= Libraries =
= File Format Libraries =
 
== File Format Libraries ==
 
* [[HDF5]]
* [[HDF5]]


= Atmospheric research =
= Atmospheric research =
* [[CESM]]


* [[CESM]]
= Biomedical research =
 
* [[Bioconda]] -- lets you install thousands of software packages related to biomedical research using the [[Conda on ARC | Conda]] package manager.


= Chemistry =
= Chemistry =
 
* [[Gaussian on ARC | Gaussian 16]] - a commercial software package for electronic structure modelling.
* [[Gaussian on ARC | Gaussian 16]]
* [[ORCA]] - an ab initio quantum chemistry program package that contains modern electronic structure methods.
* [[GROMACS]] - Classical molecular dynamics simulator.
* [[GROMACS]] - Classical molecular dynamics simulator.


= 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.
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* [[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]]


* [[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]]
= Reservoir Simulations =
= Bioinformatics =


[[Category:ARC]]
[[Category:ARC]]
[[Category:Software]]
{{Navbox ARC}}

Latest revision as of 16:36, 21 March 2024

Software Management

For some general consideration for setting up software in your home directory see Managing software on ARC.

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.

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.

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.

Statistics