HPC/Applications

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This is the catalog for HPC applications on Carbon. Applications are often referred to as modules because they are managed using the Environment Modules package.

You, the user, must select ("load") the modules that you wish to use, possibly down to a specific version. An exception to this are a handful of basic modules that are pre-loaded when you log in.

You can access this catalog on Carbon itself using the following commands to show all available modules, one-line summaries, and longer descriptions (usually with copyrights and links), respectively: 

module avail [name]
module whatis [name]
module help name
See also



pp.x (when the property was saved into an XSF file).

The following PWscf programs are supported:
  • pw.x
  • ph.x
  • pp.x
  • projwfc.x
  • d3.x
  • ld1.x (atomic)
See also: module help quantum-espresso
Installed in $QUANTUM_ESPRESSO_GUI_HOME .
http://www.quantum-espresso.org/

python-anaconda/2.7

  • 4/2.7.11-4.0.0-2
Anaconda is a Python-based open data science analytics platform. The platform can be used for ad hoc and production deployments, for batch and interactive to real-time use. Anaconda is tuned for modern computing environments.
https://www.continuum.io/why-anaconda

python-anaconda/3.5

  • 4/3.5.1-4.0.0-2
Anaconda is a Python-based open data science analytics platform. The platform can be used for ad hoc and production deployments, for batch and interactive to real-time use. Anaconda is tuned for modern computing environments.
https://www.continuum.io/why-anaconda

python-centos/2.6

  • gcc-4.4/2.6.6
WARNING: Unable to find ModulesHelp in /opt/apps/M/el6/python-centos/2.6/gcc-4.4/2.6.6.

python-env-anaconda/2.7

  • 4/2.7.11-09
Python environment within the Anaconda suite, with selected native and external packages added:
numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 ase netCDF4 deap inspyred

python-env-anaconda/3.5

  • 4/3.5.1-09
Python environment within the Anaconda suite, with selected native and external packages added:
numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 ase netCDF4 deap inspyred

python-env-intel/2.7

  • 2017/2.7-001
Customized Python conda environment for Carbon of the Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.
The following selected native and external packages were added:
numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 ase netCDF4 deap inspyred
See 'conda list' for all packages installed.
https://software.intel.com/en-us/python-distribution
  • 2017/2.7-004
Customized Python conda environment for Carbon of the Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.
The following selected native and external packages were added:
numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 intelpython ase netCDF4 deap inspyred
See 'conda list' for all packages installed.
https://software.intel.com/en-us/python-distribution
https://software.intel.com/en-us/articles/intel-distribution-for-python-support-and-documentation
https://software.intel.com/en-us/forums/intel-distribution-for-python
  • 2017/2.7-01, 2018/2.7-01
Customized Python conda environment for Carbon of the Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.
The following selected native and external packages were added:
numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 intelpython ase netCDF4 deap inspyred pytest See 'conda list' for all packages installed.
https://software.intel.com/en-us/python-distribution
https://software.intel.com/en-us/articles/intel-distribution-for-python-support-and-documentation
https://software.intel.com/en-us/forums/intel-distribution-for-python

python-env-intel/3.5

  • 2017/3.5-01
Customized Python conda environment for Carbon of the Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.
The following selected native and external packages were added:
numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 intelpython ase netCDF4 deap inspyred pytest See 'conda list' for all packages installed.
https://software.intel.com/en-us/python-distribution
https://software.intel.com/en-us/articles/intel-distribution-for-python-support-and-documentation
https://software.intel.com/en-us/forums/intel-distribution-for-python
  • 2017/3.5-001
Customized Python conda environment for Carbon of the Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.
The following selected native and external packages were added:
numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 ase netCDF4 deap inspyred
See 'conda list' for all packages installed.
https://software.intel.com/en-us/python-distribution
  • 2017/3.5-004
Customized Python conda environment for Carbon of the Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.
The following selected native and external packages were added:
numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 intelpython ase netCDF4 deap inspyred
See 'conda list' for all packages installed.
https://software.intel.com/en-us/python-distribution
https://software.intel.com/en-us/articles/intel-distribution-for-python-support-and-documentation
https://software.intel.com/en-us/forums/intel-distribution-for-python

python-env-intel/3.6

  • 2018/3.6-01
Customized Python conda environment for Carbon of the Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.
The following selected native and external packages were added:
numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 intelpython ase netCDF4 deap inspyred pytest See 'conda list' for all packages installed.
https://software.intel.com/en-us/python-distribution
https://software.intel.com/en-us/articles/intel-distribution-for-python-support-and-documentation
https://software.intel.com/en-us/forums/intel-distribution-for-python

python-intel/2.7

  • 2015/2.7.20150803_184913, 2017/2.7.12
Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.
The following popular packages are included:
cpython cython dateutil ipython jinja2 jsonschema markupsafe matplotlib mistune mock mpmath nose numexpr numpy pandas pip pygments-main pytz pyzmq scipy setuptools six sympy tempita tornado
https://software.intel.com/en-us/python-distribution
  • 2017/2.7.13-2017.3.053-1, 2018/2.7.14-2018.1.023-1
The Intel Distribution for Python ships with many specialized packages that offer accelerated workflows and advanced functionality.
Numerical and Scientific
  • NumPy - The most popular numerical library for Python, accelerated with the Intel MKL
  • SciPy - The de-facto standard for a scientific toolset in the Python language, accelerated with the Intel MKL
  • numba - A Just-In-Time Compiler for decorated Python code that allows latest SIMD features and multi-core execution in order to fully utilize modern CPUs
  • numexpr - A Python interface to symbolic and algebraic acceleration, via the Intel MKL
Data Analytics
  • Scikit-learn – A popular machine learning Python package, now accelerated with Intel's highest performance libraries.
  • * Pre-built and accelerated with Intel MKL, Intel DAAL, and Intel Thread Building Blocks through direct source code changes to the package
  • pyDAAL - A package for Python bindings to the Intel Data Analytics Acceleration Library
  • * Delivers a Python-interfaced solution for many of the steps in a data analytics pipeline, such as pre-processing, data transformations, dimensionality reduction, data modeling, prediction, and several drivers for reading and writing in most of the common data formats.
  • * Supports many computation modes, including Batch, Distributed, and Online modes for many of the support algorithms
  • daal4py (Tech Preview) – A high-level API to the Intel DAAL Library
  • * A package providing a higher-level abstraction to the Intel DAAL Library, made to cater to the needs of Data Scientists and the rapid pace of production seen in the analytics space
https://software.intel.com/en-us/distribution-for-python
https://software.intel.com/en-us/distribution-for-python/get-started
https://software.intel.com/en-us/distribution-for-python/get-help

python-intel/3.5

  • 2017/3.5.3-2017.3.052-1
The Intel Distribution for Python ships with many specialized packages that offer accelerated workflows and advanced functionality.
Numerical and Scientific
  • NumPy - The most popular numerical library for Python, accelerated with the Intel MKL
  • SciPy - The de-facto standard for a scientific toolset in the Python language, accelerated with the Intel MKL
  • numba - A Just-In-Time Compiler for decorated Python code that allows latest SIMD features and multi-core execution in order to fully utilize modern CPUs
  • numexpr - A Python interface to symbolic and algebraic acceleration, via the Intel MKL
Data Analytics
  • Scikit-learn – A popular machine learning Python package, now accelerated with Intel's highest performance libraries.
  • * Pre-built and accelerated with Intel MKL, Intel DAAL, and Intel Thread Building Blocks through direct source code changes to the package
  • pyDAAL - A package for Python bindings to the Intel Data Analytics Acceleration Library
  • * Delivers a Python-interfaced solution for many of the steps in a data analytics pipeline, such as pre-processing, data transformations, dimensionality reduction, data modeling, prediction, and several drivers for reading and writing in most of the common data formats.
  • * Supports many computation modes, including Batch, Distributed, and Online modes for many of the support algorithms
  • daal4py (Tech Preview) – A high-level API to the Intel DAAL Library
  • * A package providing a higher-level abstraction to the Intel DAAL Library, made to cater to the needs of Data Scientists and the rapid pace of production seen in the analytics space
https://software.intel.com/en-us/distribution-for-python
https://software.intel.com/en-us/distribution-for-python/get-started
https://software.intel.com/en-us/distribution-for-python/get-help
  • 2015/3.5.20150803_185146, 2017/3.5.2
Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.
The following popular packages are included:
cpython cython dateutil ipython jinja2 jsonschema markupsafe matplotlib mistune mock mpmath nose numexpr numpy pandas pip pygments-main pytz pyzmq scipy setuptools six sympy tempita tornado
https://software.intel.com/en-us/python-distribution

python-intel/3.6

  • 2018/3.6.3-2018.1.023-1
The Intel Distribution for Python ships with many specialized packages that offer accelerated workflows and advanced functionality.
Numerical and Scientific
  • NumPy - The most popular numerical library for Python, accelerated with the Intel MKL
  • SciPy - The de-facto standard for a scientific toolset in the Python language, accelerated with the Intel MKL
  • numba - A Just-In-Time Compiler for decorated Python code that allows latest SIMD features and multi-core execution in order to fully utilize modern CPUs
  • numexpr - A Python interface to symbolic and algebraic acceleration, via the Intel MKL
Data Analytics
  • Scikit-learn – A popular machine learning Python package, now accelerated with Intel's highest performance libraries.
  • * Pre-built and accelerated with Intel MKL, Intel DAAL, and Intel Thread Building Blocks through direct source code changes to the package
  • pyDAAL - A package for Python bindings to the Intel Data Analytics Acceleration Library
  • * Delivers a Python-interfaced solution for many of the steps in a data analytics pipeline, such as pre-processing, data transformations, dimensionality reduction, data modeling, prediction, and several drivers for reading and writing in most of the common data formats.
  • * Supports many computation modes, including Batch, Distributed, and Online modes for many of the support algorithms
  • daal4py (Tech Preview) – A high-level API to the Intel DAAL Library
  • * A package providing a higher-level abstraction to the Intel DAAL Library, made to cater to the needs of Data Scientists and the rapid pace of production seen in the analytics space
https://software.intel.com/en-us/distribution-for-python
https://software.intel.com/en-us/distribution-for-python/get-started
https://software.intel.com/en-us/distribution-for-python/get-help

python/2.7

  • gcc-4.1/2.7.3-1, gcc-4.4/2.7.11-1
Python is an interpreted, interactive, object-oriented programming language often compared to Tcl, Perl, Scheme or Java. Python includes modules, classes, exceptions, very high level dynamic data types and dynamic typing. Python supports interfaces to many system calls and libraries, as well as to various windowing systems (X11, Motif, Tk, Mac and MFC).
Programmers can write new built-in modules for Python in C or C++. Python can be used as an extension language for applications that need a programmable interface. This package contains most of the standard Python modules, as well as modules for interfacing to the Tix widget set for Tk and RPM.
http://www.python.org/

python/3.5

  • gcc-4.4/3.5.1-1
Python is an interpreted, interactive, object-oriented programming language often compared to Tcl, Perl, Scheme or Java. Python includes modules, classes, exceptions, very high level dynamic data types and dynamic typing. Python supports interfaces to many system calls and libraries, as well as to various windowing systems (X11, Motif, Tk, Mac and MFC).
Programmers can write new built-in modules for Python in C or C++. Python can be used as an extension language for applications that need a programmable interface. This package contains most of the standard Python modules, as well as modules for interfacing to the Tix widget set for Tk and RPM.
http://www.python.org/

q-chem/4.1

  • 4.1.0.1-1
Q-Chem is a comprehensive ab initio quantum chemistry package. Its capabilities range from the highest performance DFT/HF calculations to high level post-HF correlation methods. Q-Chem tackles a wide range of problems including:
  • Molecular Structures
  • Chemical Reactions
  • Molecular Vibrations
  • Electronic Spectra
  • NMR Spectra
  • Solvation Effects
Q-Chem offers Fast DFT calculations with accurate linear scaling algorithms, a wide range of post-HF correlation methods that are efficient and unique, and quantum calculations extended with QM/MM and molecular dynamics.
Documentation: http://www.q-chem.com/qchem-website/technical-info4.html
http://www.q-chem.com/

quantum-espresso/4

  • openmpi-1.4/intel/4.3.2-2
Quantum ESPRESSO (opEn Source Package for Research in Electronic Structure, Simulation, and Optimization) is a suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).
Quantum ESPRESSO builds onto newly-restructured electronic-structure codes (PWscf, PHONON, CP90, FPMD, Wannier) that have been developed and tested by some of the original authors of novel electronic-structure algorithms - from Car-Parrinello molecular dynamics to density-functional perturbation theory - and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency is still our main focus.
This build contains the 'historical' QE core set, plus the WanT (Wannier transport) plugin. GPL-licensed.
See also: module help wannier90 module help pwgui module help xcrysden
Installed in $QUANTUM_ESPRESSO_HOME .
http://www.quantum-espresso.org/
http://www.wannier-transport.org/

quantum-espresso/5.4

  • openmpi-1.10/intel-16/5.4.0-1
Quantum ESPRESSO (opEn Source Package for Research in Electronic Structure, Simulation, and Optimization) is a suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).
Quantum ESPRESSO builds onto newly-restructured electronic-structure codes (PWscf, PHONON, CP90, FPMD, Wannier) that have been developed and tested by some of the original authors of novel electronic-structure algorithms - from Car-Parrinello molecular dynamics to density-functional perturbation theory - and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency is still our main focus.
This build contains the 'historical' QE core set, plus the WanT (Wannier transport) plugin. GPL-licensed.
See also: module help xcrysden
Installed in $QUANTUM_ESPRESSO_HOME .
http://www.quantum-espresso.org/users-manual/

rasmol/2.6

  • 2.6.4-foc-1
RasMol2 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on Microsoft Windows, Apple Macintosh, UNIX and VMS systems. The UNIX and VMS systems require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The program reads in a molecule co-ordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.
http://www.openrasmol.org/

rasmol/2.7

  • 2.7.5-1
RasMol2 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on Microsoft Windows, Apple Macintosh, UNIX and VMS systems. The UNIX and VMS systems require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The program reads in a molecule co-ordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.
http://www.openrasmol.org/

readline/6

  • 6.2-1
The Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
The history facilites are also placed into a separate library, the History library, as part of the build process. The History library may be used without Readline in applications which desire its capabilities.
Distributed under the terms of the (GNU) General Public License, v3.
http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html

rings/1

  • openmpi-1.4/intel/1.2.3-1
The R.I.N.G.S. code (Rigorous Investigation of Networks Generated using Simulations) analyzes the results of molecular dynamics simulations. Its main feature connectivity analysis using ring statistics.
Installed in $RINGS_HOME .
http://rings-code.sourceforge.net/

ScientificPython/2

  • intel/2.8-1
ScientificPython is a collection of Python modules useful for scientific computing. Modules cover basic geometry (vectors, tensors, transformations, vector and tensor fields), quaternions, automatic derivatives, (linear) interpolation, polynomials, elementary statistics, nonlinear least-squares fits, unit calculations, Fortran-compatible text formatting, 3D visualization via VRML, and two Tk widgets for simple line plots and 3D wireframe models. There are also interfaces to the netCDF library (portable structured binary files), to MPI (Message Passing Interface, message-based parallel programming), and to BSPlib (Bulk Synchronous Parallel programming).
http://dirac.cnrs-orleans.fr/plone/software/scientificpython/

scipy/0

  • openmpi-1.4/gcc/0.9.0-1, openmpi-1.4/intel/0.10.0-1
SciPy (pronounced 'Sigh Pie') is a library for mathematics, science, and engineering, named after a popular conference on scientific programming with Python
SciPy depends on NumPy, which provides convenient and fast N-dimensional array manipulation. SciPy works with NumPy arrays, and provides user-friendly and efficient numerical routines e.g. for integration and optimization.
Open-Source, free of charge.
http://www.scipy.org/

siesta/3

  • openmpi-1.4/intel/3.2-1
SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Its main characteristics are:
  • Kohn-Sham self-consistent density functional method in the local density (LDA-LSD) or generalized gradient (GGA) approximations.
  • norm-conserving pseudopotentials in their fully nonlocal (Kleinman-Bylander) form.
  • numeric finite-range atomic orbital basis, unlimited multiple-zeta and angular momenta, polarization and off-site orbitals.
  • Projects the electron wavefunctions and density onto a real-space grid in order to calculate the Hartree and exchange-correlation potentials and their matrix elements.
  • localized linear combinations of the occupied orbitals (valence-bond or Wannier-like functions), for O(N) time and memory scaling.
  • dynamic memory allocation
  • serial or parallel execution
Available for users with confirmed licenses.
This version has been compiled without NetCDF support.
http://www.icmab.es/siesta/

siesta/4.0

  • impi-5/intel-16/4.0-1
SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Its main characteristics are:
  • Kohn-Sham self-consistent density functional method in the local density (LDA-LSD) or generalized gradient (GGA) approximations.
  • norm-conserving pseudopotentials in their fully nonlocal (Kleinman-Bylander) form.
  • numeric finite-range atomic orbital basis, unlimited multiple-zeta and angular momenta, polarization and off-site orbitals.
  • Projects the electron wavefunctions and density onto a real-space grid in order to calculate the Hartree and exchange-correlation potentials and their matrix elements.
  • localized linear combinations of the occupied orbitals (valence-bond or Wannier-like functions), for O(N) time and memory scaling.
  • dynamic memory allocation
  • serial or parallel execution
Available for users with confirmed licenses.
This version has been compiled without NetCDF support.
http://www.icmab.es/siesta/

siesta/4.1

  • impi-5/intel-16/4.1-b2-1, impi-5/intel-16/4.1-b2-2
SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Its main characteristics are:
  • Kohn-Sham self-consistent density functional method in the local density (LDA-LSD) or generalized gradient (GGA) approximations.
  • norm-conserving pseudopotentials in their fully nonlocal (Kleinman-Bylander) form.
  • numeric finite-range atomic orbital basis, unlimited multiple-zeta and angular momenta, polarization and off-site orbitals.
  • Projects the electron wavefunctions and density onto a real-space grid in order to calculate the Hartree and exchange-correlation potentials and their matrix elements.
  • localized linear combinations of the occupied orbitals (valence-bond or Wannier-like functions), for O(N) time and memory scaling.
  • dynamic memory allocation
  • serial or parallel execution
Available for users with confirmed licenses.
This version has been compiled without NetCDF support.
http://www.icmab.es/siesta/

siesta/4.1-b2

  • impi-5/intel-16/4.1-b2-1, impi-5/intel-16/4.1-b2-2
SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Its main characteristics are:
  • Kohn-Sham self-consistent density functional method in the local density (LDA-LSD) or generalized gradient (GGA) approximations.
  • norm-conserving pseudopotentials in their fully nonlocal (Kleinman-Bylander) form.
  • numeric finite-range atomic orbital basis, unlimited multiple-zeta and angular momenta, polarization and off-site orbitals.
  • Projects the electron wavefunctions and density onto a real-space grid in order to calculate the Hartree and exchange-correlation potentials and their matrix elements.
  • localized linear combinations of the occupied orbitals (valence-bond or Wannier-like functions), for O(N) time and memory scaling.
  • dynamic memory allocation
  • serial or parallel execution
Available for users with confirmed licenses.
This version has been compiled without NetCDF support.
http://www.icmab.es/siesta/

spglib/1

  • gcc/1.6.4
Spglib is a C library for finding and handling crystal symmetries with these features:
  • Find symmetry operations
  • Identify space-group type
  • Wyckoff position assignment
  • Refine crystal structure
  • Search irreducible k-points
  • Find a primitive cell
http://spglib.sourceforge.net

stress-ng/0

  • 0.08.18-1
stress-ng will stress test a computer system in various selectable ways. It was designed to exercise various physical subsystems of a computer as well as the various operating system kernel interfaces. Stress-ng features:
  • Over 180 stress tests
  • 70 CPU specific stress tests that exercise floating point, integer, bit manipulation and control flow
  • Over 20 virtual memory stress tests
stress-ng was originally intended to make a machine work hard and trip hardware issues such as thermal overruns as well as operating system bugs that only occur when a system is being thrashed hard. Use stress-ng with caution as some of the tests can make a system run hot on poorly designed hardware and also can cause excessive system thrashing which may be difficult to stop.
stress-ng can also measure test throughput rates; this can be useful to observe performance changes across different operating system releases or types of hardware. However, it has never been intended to be used as a precise benchmark test suite, so do NOT use it in this manner.
http://kernel.ubuntu.com/~cking/stress-ng/

stress/1

  • 1.0.4-1
stress is a deliberately simple workload generator for POSIX systems. It imposes a configurable amount of CPU, memory, I/O, and disk stress on the system.
stress is a tool designed to put given subsytems under a specified load. Instances in which this is useful include those in which a system administrator wishes to perform tuning activities, a kernel or libc programmer wishes to evaluate denial of service possibilities, etc.
It is free software licensed under the GPLv2.

vasp-vtst/4

  • openmpi-1.4/intel/4.6.35-mkl-12
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
This version contains the VTST patch by Graeme Henkelman,
http://theory.cm.utexas.edu/vtsttools/downloads/
Available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/

vasp-vtstscripts/2012

  • 2012-11-11-1
Vasp TST Tools - a set of scripts to perform common tasks to help with VASP calculations, and particularly with transition state finding. The included Vasp.pm perl module contains several simple routines that are used by many of the scripts.
http://theory.cm.utexas.edu/vtsttools/scripts/

vasp-vtstscripts/926

  • 926-1
Vasp TST Tools - a set of scripts to perform common tasks to help with VASP calculations, and particularly with transition state finding. The included Vasp.pm perl module contains several simple routines that are used by many of the scripts.
http://theory.cm.utexas.edu/vtsttools/scripts/

vasp/4.6

  • openmpi-1.4/intel/4.6.35-mkl-13
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
This version provides a full set of binaries resulting from various compile-time configuration options, plus the VTST patch by Graeme Henkelman, http://theory.cm.utexas.edu/vtsttools/downloads/ .
Likewise, there are binaries to calculate the DOS projected in Bader Volumes, http://theory.cm.utexas.edu/bader/ .
Available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/
  • openmpi-1.4/intel/4.6.35-mkl-nozheevx-8
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
Available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/
  • openmpi-1.4/intel/4.6.36-mkl-4
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
This version provides binaries for various compile-time options of:
  • The original sources.
  • Schmidt's patch for a periodic Natural Bond Orbital algorithm; see 'module help periodic_NBO'.
Available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/

vasp5/5.3

  • openmpi-1.4/intel/5.3.3p3-mkl-cellz-1
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
This version provides binaries modified to constrain cell relaxations along the z-axis (N. Charles).
Available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/
  • , openmpi-1.10


  • impi-5/intel-16/5.3.5-2
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
This version provides binaries modified to constrain cell relaxations along the z-axis (user request).
All binaries support the LWANNIER90 option.
Available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/
https://wiki.anl.gov/cnm/HPC/Applications/vasp
  • openmpi-1.10/intel-16/5.3.5-1
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
This version provides binaries modified to constrain cell relaxations along the z-axis (N. Charles).
All binaries support the LWANNIER90 option.
Available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/
  • openmpi-1.4/intel/5.3.2-mkl-beef-1
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
This version provides binaries for various compile-time options of:
  • BEEF-vdW ensemble XC energies (see 'module help beef').
Available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/
  • openmpi-1.4/intel/5.3.3p3-mkl-3
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
This version provides a full set of binaries resulting from various compile-time configuration options, plus the VTST patch by Graeme Henkelman, http://theory.cm.utexas.edu/vtsttools/downloads/ .
Likewise, there are binaries to calculate the DOS projected in Bader Volumes, http://theory.cm.utexas.edu/bader/ .
All binaries support the LWANNIER90 option.
Available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/

vasp5/5.3-scan

  • openmpi-1.10/intel-16/5.3.5-scan-1
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
This version supports the 2015 Perdew Strongly Constrained and Appropriately Normed Semilocal Density Functional (SCAN), see https://doi.org/10.1103/PhysRevLett.115.036402 .
This version provides binaries modified to constrain cell relaxations along the z-axis (N. Charles).
All binaries support the LWANNIER90 option.
Available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/
  • impi-5/intel-16/5.3.5-scan-1
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
This version supports the 2015 Perdew Strongly Constrained and Appropriately Normed Semilocal Density Functional (SCAN), see https://doi.org/10.1103/PhysRevLett.115.036402 .
This version provides binaries modified to constrain cell relaxations along the z-axis (user request).
All binaries support the LWANNIER90 option.
Available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/
https://wiki.anl.gov/cnm/HPC/Applications/vasp

vasp5/5.4

  • impi-5/intel-16/5.4.1.3-10, impi-5/intel-16/5.4.1.3-11, impi-5/intel-16/5.4.1.3-9, openmpi-1.10/intel-16/5.4.1.3-10, openmpi-1.10/intel-16/5.4.1.3-11, openmpi-1.10/intel-16/5.4.1.3-9
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
This version provides the standard set of binaries for the 5.4 build system:
  • vasp_std - Multiple k-point version
  • vasp_gam - GAMMA-point only version
  • vasp_ncl - Non-collinear version
Patches applied: patch.5.4.1.14032016.gz
All binaries support the following features (some previously required third-party add-ons):
Alternate sets of binaries provide:
VASP is available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/
https://wiki.anl.gov/cnm/HPC/Applications/vasp
  • impi-5/intel-16/5.4.1.3-6, openmpi-1.10/intel-16/5.4.1.3-6
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
This version provides the standard set of binaries for the 5.4 build system:
  • vasp_std - Multiple k-point version
  • vasp_gam - GAMMA-point only version
  • vasp_ncl - Non-collinear version
Further sets of binaries are included to provide:
  • Transition state tools by Graeme Henkelman, as binaries vasp_vtst_{std,gam,ncl}, http://theory.cm.utexas.edu/vtsttools/
  • Cell relaxations constrained along the z-axis, with binaries vasp_cellz_{std,gam,ncl}
All binaries support the following features (some previously required third-party add-ons):
VASP is available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/
https://wiki.anl.gov/cnm/HPC/Applications/vasp
  • impi-5/intel-16/5.4.1.3-8, openmpi-1.10/intel-16/5.4.1.3-8
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
This version provides the standard set of binaries for the 5.4 build system:
  • vasp_std - Multiple k-point version
  • vasp_gam - GAMMA-point only version
  • vasp_ncl - Non-collinear version
The following patches are built-in to all binaries:
Alternate sets of binaries provide:
All binaries support the following features (some previously required third-party add-ons):
VASP is available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/
https://wiki.anl.gov/cnm/HPC/Applications/vasp
  • impi-5/intel-16/5.4.4.0-1
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
This version provides the standard set of binaries for the 5.4 build system:
  • vasp_std - Multiple k-point version
  • vasp_gam - GAMMA-point only version
  • vasp_ncl - Non-collinear version
Patches applied:
All binaries support the following features (some previously required third-party add-ons):
Alternate sets of binaries provide:
VASP is available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/
https://wiki.anl.gov/cnm/HPC/Applications/vasp

vasp5/5.4-z2pack

  • impi-5/intel-16/5.4.1.3-z2pack-1, impi-5/intel-16/5.4.1.3-z2pack-2, openmpi-1.10/intel-16/5.4.1.3-z2pack-1
VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.
This version provides the standard set of binaries for the 5.4 build system:
  • vasp_std - Multiple k-point version
  • vasp_gam - GAMMA-point only version
  • vasp_ncl - Non-collinear version
Patches applied: patch.5.4.1.14032016.gz
All binaries support the following features (some previously required third-party add-ons):
Alternate sets of binaries provide:
VASP is available to licensed users only.
http://cms.mpi.univie.ac.at/vasp/
https://wiki.anl.gov/cnm/HPC/Applications/vasp

vesta/3

  • 3.2.1-1
VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies. Some of the novel features of VESTA are listed below.
  • Deal with multiple structural models, volumetric data, and crystal morphologies in the same window.
  • Support multiple tabs corresponding to files.
  • Support multiple windows with more than two tabs in the same process.
  • Deal with virtually unlimited number of objects such as atoms, bonds polyhedra, and polygons on isosurfaces (theoretical limit on 32bit operating system is 1,073,741,823)
  • Support lattice transformation from conventional to non-conventional lattice by using matrix. The transformation matrix is also used to create superlattice and sublattice.
  • Visualize interatomic distances and bond angles that are restrained in Rietveld analysis with RIETAN-FP.
  • Transparent isosurfaces can be overlap with structural models.
  • Isosurface can be colored on the basis of another physical quantity.
  • Arithmetic operations among multiple volumetric data files.
  • High quality smooth rendering of isosurfaces and sections.
  • Export high-resolution graphic images exceeding Video card limitation.
  • VESTA is a successor to two 3D visualization programs, VICS and VEND, in the VENUS (Visualization of Electron/NUclear and Structures) software package.
This installation includes the PowderPlot utility.
Contributed free of charge for non-commercial users.
http://jp-minerals.org/vesta/en/

vmd/1

  • 1.9.1-2
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.
VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.
This build includes the VMD Density Profile Tool (1.1).
http://www.ks.uiuc.edu/Research/vmd/
http://multiscalelab.org/utilities/DensityProfileTool

voro++/0

  • intel/0.4.5-1
Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles.
Voro++ comprises of several C++ classes that can be built as a static library. A command-line utility is also provided that can use most features of the code. The direct cell-by-cell construction makes the library particularly well-suited to handling special boundary conditions and walls. It employs algorithms that are tolerant for numerical precision errors, it exhibits high performance, and it has been successfully employed on very large particle systems.
The directory $VOROXX_HOME/share/ contains examples and scripts.
http://math.lbl.gov/voro++/doc/
http://math.lbl.gov/voro++/

vtk/5

  • intel/5.0.4-icc-3
The Visualization ToolKit (VTK) is an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. VTK consists of a C++ class library, and several interpreted interface layers including Tcl/Tk, Java, and Python. Professional support and products for VTK are provided by Kitware, Inc. VTK supports a wide variety of visualization algorithms including scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as implicit modelling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. In addition, dozens of imaging algorithms have been directly integrated to allow the user to mix 2D imaging / 3D graphics algorithms and data. The design and implementation of the library has been strongly influenced by object-oriented principles.
http://www.vtk.org/
https://visualization.hpc.mil/wiki/VTK
https://visualization.hpc.mil/wiki/Getting_Started_with_VTK

wannier90/1

  • 1.2-1, 1.2-2
The wannier90 code obtains maximally-localised generalised Wannier functions, using them to calculate bandstructures, Fermi surfaces, dielectric properties, sparse Hamiltonians and many things besides.
The method is those of Marzari and Vanderbilt, except for entangled energy bands, where the method of Souza, Marzari and Vanderbilt is used.
See also: module help quantum-espresso
Installed in $WANNIER90_HOME .
http://www.wannier.org/

wannier90/1-z2pack

  • 1.2-z2pack-1
The wannier90 code obtains maximally-localised generalised Wannier functions, using them to calculate bandstructures, Fermi surfaces, dielectric properties, sparse Hamiltonians and many things besides.
The method is those of Marzari and Vanderbilt, except for entangled energy bands, where the method of Souza, Marzari and Vanderbilt is used.
See also: module help quantum-espresso
Installed in $WANNIER90_HOME .
http://www.wannier.org/

wannier90/2

  • impi-5/intel-16/2.0.1-3, openmpi-1.10/intel-16/2.0.1-3
The wannier90 code obtains maximally-localised generalised Wannier functions, using them to calculate bandstructures, Fermi surfaces, dielectric properties, sparse Hamiltonians and many things besides.
The method is those of Marzari and Vanderbilt, except for entangled energy bands, where the method of Souza, Marzari and Vanderbilt is used.
See also: module help quantum-espresso
Installed in $WANNIER90_HOME .
http://www.wannier.org/

wien2k/09

  • intel/09.2-1
WIEN2k allows to perform electronic structure calculations of solids using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave ((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. WIEN2k is an all-electron scheme including relativistic effects and has many features.
Available to registered users only.
http://www.wien2k.at/

wien2k/14.2

  • impi-5/intel-16/14.2-7
WIEN2k allows to perform electronic structure calculations of solids using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave ((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. WIEN2k is an all-electron scheme including relativistic effects and has many features.
Available to registered users only.
http://www.wien2k.at/

xcrysden/1

  • 1.5.21-1
XCrySDen (Crystalline Structures and Densities and X) is a crystalline and molecular visualisation program with support for superimposed isosurfaces and contours.
See also: module help quantum-espresso
Installed in $XCRYSDEN_HOME .
http://www.xcrysden.org/

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