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HPC Software

HPC Installed Software Applications

All shared cluster applications are stored on the mount point:    /cm/shared/apps 

Bio-Science

DockoMatic

module load dockomatic/gcc/64/2.1

DockoMatic is a GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions.

·         Click here for the R1 DockoMatic Run-Book

Gromacs

module load gromacs/openmpi/gcc/64/5.0.4

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.

It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

·         Click here for the R1 GROMACS Run-Book

OpenMM

OpenMM is a library which provides tools for modern molecular modeling simulation. As a library it can be hooked into any code, allowing that code to do molecular modeling with minimal extra coding.

Moreover, OpenMM has a strong emphasis on hardware acceleration, thus providing not just a consistent API, but much greater performance than what one could get from just about any other code available.


Material Science

BoltzTraP

module load BoltzTraP/gcc/64/1.2.5

Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients. The code uses a mesh of self-consistent band energies and is interfaced to the WIEN2k, AB-INIT, SIESTA, VASP and QuantumEspresso programs.

Quantum Espresso

module load espresso/intel/64/5.1.1

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. The Quantum ESPRESSO distribution consists of a “historical” core set of components, and a set of plug-ins that perform more advanced tasks, plus a number of third-party packages designed to be inter-operable with the core components.

VASP

module load vasp/intel/64/5.4.1

The Vienna Ab init io Simulation Package (VASP) is a computer program for atomic scale materials modeling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.

VASP computes an approximate solution to the many-body Schrodinger equation, either within density functional theory (DFT), solving the Kohn-Sham equations, or within the Hartree-Fock (HF) approximation, solving the Roothaan equations. Hybrid functionals that mix the Hartree-Fock approach with density functional theory are implemented as well. Furthermore, Green’s functions methods (GW quasiparticles, and ACFDT-RPA) and many-body perturbation theory (2nd-order Møller- Plesset) are available in VASP.

·    Click here for the R1 VASP Runbook

VMD

module load vmd/gcc/64/1.9.2

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. (more details…)

·    Click here for the R1 VMD User Guide


Geo-Science

Gdal

module load gdal/gcc/64/2.0.0

GDAL is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single raster abstract data model and vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.

NCL/Ncarg

module load ncarg/gcc/64/6.2.0

NCAR Graphics is a Fortran and C based software package for scientific visualization

NCAR Graphics is comprised of:

  • a library containing over two dozen Fortran/C utilities for drawing contours, maps, vectors, streamlines, weather maps, surfaces, histograms, X/Y plots, annotations, and more
  • an ANSI/ISO standard version of GKS, with both C and FORTRAN callable entries
  • a math library containing a collection of C and Fortran interpolators and approximators for one-dimensional, two-dimensional, and three-dimensional data
  • applications for displaying, editing, and manipulating graphical output
  • map databases
  • hundreds of FORTRAN and C examples
  • demo programs
  • compilation scripts

NCO

module load nco/gcc/64/4.4.4

The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. It exploits the geophysical expressivity of many CF (Climate & Forecast) metadata conventions, the flexible description of physical dimensions translated by UDUnits, the network transparency of OPeNDAP, the storage features (e.g., compression, chunking, groups) of HDF (the Hierarchical Data Format), and many powerful mathematical and statistical algorithms of GSL (the GNU Scientific Library). NCO is fast, powerful, and free.

Netcdf

module load netcdf/gcc/64/4.3.3.1

NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Parflow

module load parflow/gcc/64/r743

ParFlow is an open-source, object-oriented, parallel watershed flow model. It includes fully-integrated overland flow, the ability to simulate complex topography, geology and heterogeneity and coupled land-surface processes including the land-energy budget, biogeochemistry and snow (via CLM). It is multi-platform and runs with a common I/O structure from laptop to supercomputer. ParFlow is the result of a long, multi-institutional development history and is now a collaborative effort between CSM, LLNL, UniBonn and UCB. ParFlow has been coupled to the mesoscale, meteorological code ARPS and the NCAR code WRF.

·    Click here for the R1 ParFlow Run-Book

PROJ.4

module load proj.4/gcc/64/4.8.0

PROJ.4 is a library for performing conversions between cartographic projections. The library is based on the work of Gerald Evenden at the USGS, but is now an OSGeo project maintained by Frank Warmerdam. The library also ships with executables for performing these transformations from the command line.

WRF

The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. It features multiple dynamical cores, a 3-dimensional variational (3DVAR) data assimilation system, and a software architecture allowing for computational parallelism and system extensibility.

WRF is suitable for a broad spectrum of applications across scales ranging from meters to thousands of kilometers.

WRF allows researchers the ability to conduct simulations reflecting either real data or idealized configurations. WRF provides operational forecasting a model that is flexible and efficient computationally, while offering the advances in physics, numerics, and data assimilation contributed by the research community.

·   Click here for the R1 WRF run-book


Mathematics

Blacs

module load blacs/openmpi/gcc/64/1.1patch03

The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms.

Blas

module load blas/gcc/64/3.5.0

The BLAS (Basic Linear Algebra Subprograms) are routines that provide standard building blocks for performing basic vector and matrix operations. The Level 1 BLAS perform scalar, vector and vector-vector operations, the Level 2 BLAS perform matrix-vector operations, and the Level 3 BLAS perform matrix-matrix operations. Because the BLAS are efficient, portable, and widely available, they arecommonly used in the development of high quality linear algebra software, LAPACK for example.

MatLab

module load matlab/R2015a

MATLAB is a high-level language and interactive environment for numerical computation, visualization, and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications. The language, tools, and built-in math functions enable you to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java#.

·        Click here for the R1 Matlab run-book

Openbugs

BUGS is a software package for performing Bayesian inference Using Gibbs Sampling. The user specifies a statistical model, of (almost) arbitrary complexity, by simply stating the relationships between related variables. The software includes an `expert system’, which determines an appropriate MCMC (Markov chain Monte Carlo) scheme (based on the Gibbs sampler) for analysing the specified model. The user then controls the execution of the scheme and is free to choose from a wide range of output types.

R

module load R/gcc/64/3.2.3

R is a language and environment for statistical computing and graphics. It is a GNU project that provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, …) and graphical techniques, and is highly extensible.

One of R’s strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.

·    Click here for the standard R Manuals


Physics

Mesa

module load mesa/r6794

MESA is Modules for Experiments in Stellar Astrophysics and is capable of the following:

  • Mass loss/gain, Schwarzschild/Ledoux, double diffusion,
    gravitational settling, radiative levitation…
  • It includes the physics of rotation (in a diffusion
    approximation) and of dynamo generated magnetic fields in
    radiative zones
  • Asteroseismology : MESA is natively coupled with two
    oscillations codes: ADIPLS (J. Christensen-Dalsgaard 2008)
    and the non-adiabatic code GYRE (Townsend & Teitler 2013)
  • Giant planets, Low-mass stars, Massive Stars, Compact
    Objects, Asteroseismology, Accretion / Massloss…

LAMMPS

CPU Version- module load lammps/gcc/64/1Feb16

GPU Version- module load lammps/gcc/64/1Feb16-gpu

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. It’s a classical molecular dynamics (MD) code. As the name implies, it’s designed to run well on parallel machines, but it also runs fine on single-processor desktop machines.

·         Click here for the R1 LAMMPS run-book

Phonopy

module load phonopy/gcc/64/1.8.4.1
or
module load phono3py/gcc/64/1.10.7

Phonopy is an open source package of phonon calculations based on the supercell approach.


Visualization

VisIt

module load visit/gcc/64/2.7.2

VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. From Unix, Windows or Mac workstations, users can interactively visualize and analyze data ranging in scale from small (<101 core) desktop-sized projects to large (>105 core) leadership-class computing facility simulation campaigns. Users can quickly generate visualizations, animate them through time, manipulate them with a

variety of operators and mathematical expressions, and save the resulting images and animations for presentations. VisIt contains a rich set of visualization features to enable users to view a wide variety of data including scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured, adaptive and unstructured meshes. Owing to its customizeable plugin design, VisIt is capabable of visualizing data from over 120 different scientific data formats (see this partial list).

Paraview

module load paraview/4.0.1

ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities.

ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of petascale size as well as on laptops for smaller data, has become an integral tool in many national laboratories, universities and industry, and has won several awards related to high performance computation.


System Tools

Boost

On R1, Boost is loaded in the system by default.

Boost is a set of libraries for the C++ programming language that provide support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing. It contains over eighty individual libraries.

Most of the Boost libraries are licensed under the Boost Software License, designed to allow Boost to be used with both free and proprietary software projects. Many of Boost’s founders are on the C++ standards committee, and several Boost libraries have been accepted for incorporation into both Technical Report 1 and the C++11 standard.

Cuda

module load cuda55/gdk/352.79
module load cuda75/blas/7.5.18
module load cuda75/fft/7.5.18
module load cuda75/nsight/7.5.18
module load cuda55/profiler/7.5.18
module load cuda55/toolkit/7.5.18

CUDA refers to NVIDIA’s gpu computing “ecosystem”,  a collection of APIs, libraries and tools for getting the most out of gpus.  Cuda75 is currently installed on R1. The CUDA compute platform extends from the 1000s of general purpose compute processors featured in Nvidia’s GPU’s compute architecture, parallel computing extensions to many popular languages, powerful drop-in accelerated libraries to turn key applications and cloud based compute appliances, but CUDA extends beyond the popular CUDA Toolkit and the CUDA C/C++ programming language.

CFITSIO

module load cfitsio/gcc/64/cfitsio3.370

CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. CFITSIO provides simple high-level routines for reading and writing FITS files that insulate the programmer from the internal complexities of the FITS format. CFITSIO also provides many advanced features for manipulating and filtering the information in FITS files.

FFmpeg

module load ffmpeg/gcc/64/2.1.1

FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created. It supports the most obscure ancient formats up to the cutting edge. No matter if they were designed by some standards committee, the community or a corporation.

It contains libavcodec, libavutil, libavformat, libavfilter, libavdevice, libswscale and libswresample which can be used by applications. As well as ffmpeg, ffserver, ffplay and ffprobe which can be used by end users for transcoding, streaming and playing.]

OpenBlas

module load openblas/dynamic/0.2.14

OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.

OpenFOAM

module load openfoam/gcc/64/v3.0

OpenFOAM is first and foremost a C++ library, used primarily to create executables, known as applications. The applications fall into two categories: solvers, that are each designed to solve a specific problem in continuum mechanics; and utilities, that are designed to perform tasks that involve data manipulation.

The OpenFOAM distribution contains numerous solvers and utilities covering a wide range of problems.One of the strengths of OpenFOAM is that new solvers and utilities can be created by its users with some pre-requisite knowledge of the underlying method, physics and programming techniques involved.

Qt

module load qt/gcc/64/4.8.4

Qt is a cross-platform application and UI framework for developers using C++ or QML, a CSS & JavaScript like language. Qt Creator is the supporting Qt IDE.

VTK

module load vtk/gcc/64/6.1.0

The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python.

VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.

VTK has an extensive information visualization framework, has a suite of 3D interaction widgets, supports parallel processing, and integrates with various databases on GUI toolkits such as Qt and Tk. VTK is cross-platform and runs on Linux, Windows, Mac and Unix platforms.