diff --git a/anselm.csv b/anselm.csv index 2708681673a31b453744bfeba886193c03cac5c6..6cb035546934511f258410400a240233725cc2e8 100644 --- a/anselm.csv +++ b/anselm.csv @@ -735,6 +735,7 @@ Mesa/12.0.2-intel-2017a,1 Mesa/17.0.2-intel-2017a,1 Mesa/18.1.3-GCC-6.3.0-2.27,1 Mesa/18.1.3-intel-2017a,1 +METIS/5.1.0,1 METIS/5.1.0-intel-2017a,1 MIKE/2014,1 MIKE/2016,1 diff --git a/anselm.md b/anselm.md index 5984d7f3530cd96c24457cd005978c80ec190d99..a7a0ddc2dafccd48c6f56cc4dc0f8ab8460b8c25 100644 --- a/anselm.md +++ b/anselm.md @@ -311,3 +311,319 @@ | [ISL](http://isl.gforge.inria.fr/) | isl is a library for manipulating sets and relations of integer points bounded by linear constraints. | | [Keras](https://keras.io/) | Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano. | | MATLAB | | +| [METIS](http://glaros.dtc.umn.edu/gkhome/metis/metis/overview) | METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. | +| [MLD2P4](http://www.mld2p4.it) | MLD2P4 (Multi-Level Domain Decomposition Parallel Preconditioners Package based on PSBLAS) is a package of parallel algebraic multi-level preconditioners. It implements various versions of one-level additive and of multi-level additive and hybrid Schwarz algorithms. In the multi-level case, a purely algebraic approach is applied to generate coarse-level corrections, so that no geometric background is needed concerning the matrix to be preconditioned. The matrix is assumed to be square, real or complex, with a symmetric sparsity pattern. | +| MPFR | | +| [numpy](https://github.com/jupyter/testpath) | Test utilities for code working with files and commands | +| [Octave](http://www.gnu.org/software/octave/) | GNU Octave is a high-level interpreted language, primarily intended for numerical computations. | +| [ParMETIS](http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview) | ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. | +| [PSBLAS](http://people.uniroma2.it/salvatore.filippone/psblas/) | Most computationally intensive applications work on irregular and sparse domains that complicate their implementation on parallel machines. The major goal of the Parallel Sparse Basic Linear Algebra Subroutines (PSBLAS) project is to provide a framework to enable easy, efficient and portable implementations of iterative solvers for linear systems, while shielding the user from most details of their parallelization. The interface is designed keeping in view a Single Program Multiple Data programming model on distributed memory machines. | +| [PSBLAS-ext](http://people.uniroma2.it/salvatore.filippone/psblas/) | PSBLAS - Extended formats and NVIDIA GPU support | +| [Qhull](http://www.qhull.org) | Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. | +| [ScientificPython](https://sourcesup.cru.fr/projects/scientific-py/) | ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization. | +| [scipy](https://github.com/jupyter/testpath) | Test utilities for code working with files and commands | +| [SCOTCH](http://gforge.inria.fr/projects/scotch/) | Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. | +| [Theano](http://deeplearning.net/software/theano) | Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. | + +## Mpi + +| Module | Description | +| ------ | ----------- | +| bullxmpi | | +| [impi](http://software.intel.com/en-us/intel-mpi-library/) | The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification. | +| lam | | +| [MPICH](http://www.mpich.org/) | MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). | +| mvapich2 | | +| [OpenMPI](http://www.open-mpi.org/) | The Open MPI Project is an open source MPI-3.1 implementation. | +| openmpi | | + +## Numlib + +| Module | Description | +| ------ | ----------- | +| [Armadillo](http://arma.sourceforge.net/) | Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. | +| [arpack-ng](http://forge.scilab.org/index.php/p/arpack-ng/) | ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. | +| [ATLAS](http://math-atlas.sourceforge.net) | ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library. | +| CGAL | | +| Clp | | +| [cuDNN](https://developer.nvidia.com/cudnn) | The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. | +| [FFTW](http://www.fftw.org) | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. | +| [GSL](http://www.gnu.org/software/gsl/) | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. | +| [imkl](http://software.intel.com/en-us/intel-mkl/) | Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. | +| LIBLINEAR | | +| [mkl](http://software.intel.com/en-us/intel-mkl/) | Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. | +| [MPI-LIBLINEAR](https://www.csie.ntu.edu.tw/~cjlin/libsvmtools/distributed-liblinear/mpi/) | MPI LIBLINEAR is an extension of LIBLINEAR on distributed environments. The usage and the data format are the same as LIBLINEAR. It supports L2-regularized logistic regression, L2-regularized logistic regression, L2-regularized L2-loss linear SVM (primal trust-region Newton), L2-regularized L1-loss linear SVM (dual), L2-regularized logistic regression (primal limited common directions), L2-regularized L2-loss linear SVM (primal limited common directions). Module created by the PERMON Team (http://permon.it4i.cz). | +| [NLopt](http://ab-initio.mit.edu/wiki/index.php/NLopt) | NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. | +| [OpenBLAS](http://xianyi.github.com/OpenBLAS/) | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. | +| PETSc | | +| [qrupdate](https://sourceforge.net/projects/qrupdate/) | qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. | +| [ScaLAPACK](http://www.netlib.org/scalapack/) | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. | +| [SLEPc](http://www.grycap.upv.es/slepc/) | SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. | +| [SuiteSparse](http://faculty.cse.tamu.edu/davis/suitesparse.html) | SuiteSparse is a collection of libraries manipulate sparse matrices. | +| [Trilinos](http://trilinos.sandia.gov/) | The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. | + +## Omics + +| Module | Description | +| ------ | ----------- | +| fastqc | | +| gatk | | +| hpg-aligner | | +| hpg-fastq | | +| hpg-variant | | +| ngsPipeline | | +| picard | | +| samtools | | +| snpEff | | + +## Perf + +| Module | Description | +| ------ | ----------- | +| [Advisor](https://software.intel.com/intel-advisor-xe) | Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies†- Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain | +| [Cube](http://www.scalasca.org/software/cube-4.x/download.html) | Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. | +| [OPARI2](http://www.score-p.org) | OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface. | +| [OTF2](http://www.score-p.org) | The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It is the new standard trace format for Scalasca, Vampir, and TAU and is open for other tools. | +| [PAPI](http://icl.cs.utk.edu/projects/papi/) | PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. | +| [PDT](http://www.cs.uoregon.edu/research/pdt/) | Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations. | +| [Scalasca](http://www.scalasca.org/) | Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks -- in particular those concerning communication and synchronization -- and offers guidance in exploring their causes. | +| [Score-P](http://www.score-p.org) | The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications. | +| [Vampir](http://www.vampir.eu) | The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data. | + +## Phys + +| Module | Description | +| ------ | ----------- | +| [ALAMODE](http://alamode.readthedocs.io/) | ALAMODE is an open source software designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice thermal conductivity, phonon linewidth, and other anharmonic phonon properties from first principles. | +| [ALPScore](http://alps.comp-phys.org/) | The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as C++ libraries for simplifying the development of such code. | +| [DynaPhoPy](https://github.com/abelcarreras/DynaPhoPy) | Software to calculate crystal microscopic anharmonic properties from molecular dynamics (MD) using the normal-mode-decomposition technique. These properties include the phonon frequency shifts and linewidths, as well as the renormalized force constanst and thermal properties by using quasiparticle theory. This code includes interfaces for MD outputs from VASP and LAMMPS .PHONOPY code is used to obtain harmonic phonon modes. | +| [MotionCor2](http://msg.ucsf.edu/em/software/motioncor2.html) | This program corrects anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. | +| [phono3py](http://phonopy.sourceforge.net/phono3py/index.html) | This software calculates phonon-phonon interaction related properties | +| [phonopy](http://phonopy.sourceforge.net/) | Phonopy is an open source package of phonon calculations based on the supercell approach. | +| [Siesta](http://departments.icmab.es/leem/siesta) | SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. This version si compiled with OpenMP and MPI support. | +| [VASP](http://www.vasp.at) | The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment. | + +## Prace + +| Module | Description | +| ------ | ----------- | +| GLOBUS | | +| PRACE | | + +## Python + +| Module | Description | +| ------ | ----------- | +| [absl-py](https://pypi.python.org/pypi/absl-py) | Abseil Python Common Libraries, see https://github.com/abseil/abseil-py. | +| [ASE](https://wiki.fysik.dtu.dk/ase/) | ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. | +| [BoltzTraP2](https://www.imc.tuwien.ac.at/index.php?id=21094) | BoltzTraP2 is a modern implementation of the smoothed Fourier interpolation algorithm for electronic bands that formed the base of the original and widely used BoltzTraP code. | +| [certifi](https://pypi.python.org/pypi/certifi) | Python package for providing Mozillas CA Bundle. | +| [click](https://pypi.python.org/pypi/click) | A simple wrapper around optparse for powerful command line utilities. | +| [dask](https://pypi.python.org/pypi/dask) | Parallel PyData with Task Scheduling. | +| [decorator](https://pypi.python.org/pypi/decorator) | Better living through Python with decorators. | +| [DynaPhoPy](https://pypi.python.org/pypi/dynaphopy) | oftware to calculate crystal microscopic anharmonic properties from molecular dynamics (MD) using the normal-mode-decomposition technique. | +| [h5py](https://github.com/jupyter/testpath) | Test utilities for code working with files and commands | +| [horovod](https://pypi.python.org/pypi/horovod) | Distributed training framework for TensorFlow. | +| [Keras](https://keras.io/) | Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano. | +| [latexcodec](https://pypi.python.org/pypi/latexcodec) | A lexer and codec to work with LaTeX code in Python. | +| [lxml](http://lxml.de/) | The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. | +| [matplotlib](http://matplotlib.org) | Matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits. | +| [monty](https://pypi.python.org/pypi/monty) | Monty is the missing complement to Python. | +| [mpi4py](http://mpi4py.scipy.org/docs) | MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. | +| [mpmath](https://pypi.python.org/pypi/mpmath) | Python library for arbitrary-precision floating-point arithmetic. | +| [networkx](https://pypi.python.org/pypi/networkx) | NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | +| [numpy](http://www.numpy.org) | NumPy is the fundamental package needed for scientific computing with Python. | +| [packaging](https://pypi.python.org/pypi/packaging) | Core utilities for Python packages. | +| [palettable](https://pypi.python.org/pypi/palettable) | Color palettes for Python. | +| [pandas](https://pypi.python.org/pypi/pandas) | Powerful data structures for data analysis, time series,and statistics. | +| [phonopy](https://atztogo.github.io/phonopy) | Phonopy is an open source package of phonon calculations based on the supercell approach. | +| [Pillow](http://pillow.readthedocs.org/) | Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. | +| [pybtex](https://pypi.python.org/pypi/pybtex) | A BibTeX-compatible bibliography processor in Python. | +| [PyDispatcher](https://pypi.python.org/pypi/PyDispatcher) | Multi-producer-multi-consumer signal dispatching mechanism. | +| [pyFFTW](https://pypi.python.org/pypi/pyFFTW) | A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms. | +| [pymatgen](https://pypi.python.org/pypi/pymatgen) | Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes. It is currently the core analysis code powering the Materials Project (https://www.materialsproject.org). | +| [pyparsing](http://pyparsing.wikispaces.com) | The pyparsing module provides a library of classes that client code uses to construct the grammar directly in Python code. | +| [PyQt5](http://www.riverbankcomputing.co.uk/software/pyqt) | PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. | +| [python-dateutil](https://github.com/dateutil/dateutil) | Useful extensions to the standard Python datetime features. | +| [pytz](http://pytz.sourceforge.net/) | pytz brings the Olson tz database into Python. This library allows accurate and cross platform timezone calculations using Python 2.4 or higher. | +| [PyWavelets](https://pypi.python.org/pypi/PyWavelets) | PyWavelets, wavelet transform module. | +| [PyYAML](https://pypi.python.org/pypi/PyYAML/) | PyYAML is a YAML parser and emitter for the Python programming language. | +| [requests](https://pypi.python.org/pypi/requests) | Python HTTP for Humans. | +| [ruamel.yaml](https://pypi.python.org/pypi/ruamel.yaml) | ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order | +| [scikit-image](http://scikit-learn.org/stable/index.html) | Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. | +| [scikit-learn](http://scikit-learn.org/stable/index.html) | Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. | +| [scipy](http://scipy.org) | SciPy (pronounced 'Sigh Pie') is open-source software for mathematics, science, and engineering. It includes modules for statistics, optimization, integration, linear algebra, Fourier transforms, signal and image processing, ODE solvers, and more. | +| [seaborn](https://pypi.python.org/pypi/seaborn) | Seaborn: statistical data visualization | +| [SIP](http://www.riverbankcomputing.com/software/sip/) | SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. | +| [six](https://github.com/benjaminp/six) | Python 2 and 3 compatibility library. | +| [spglib-python](https://pypi.python.org/pypi/spglib) | Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C. | +| [sympy](https://pypi.python.org/pypi/sympy) | Computer algebra system (CAS) in Python | +| [tabulate](https://pypi.python.org/pypi/tabulate) | Pretty-print tabular data. | +| [toolz](https://pypi.python.org/pypi/toolz) | List processing tools and functional utilities. | +| [urllib3](https://pypi.python.org/pypi/urllib3) | HTTP library with thread-safe connection pooling, file post, and more. | + +## System + +| Module | Description | +| ------ | ----------- | +| [CUDA](https://developer.nvidia.com/cuda-toolkit) | CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. | +| [hwloc](http://www.open-mpi.org/projects/hwloc/) | The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. | +| [libpciaccess](http://cgit.freedesktop.org/xorg/lib/libpciaccess/) | Generic PCI access library. | +| [OpenSSL](http://www.openssl.org/) | The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. | + +## Toolchain + +| Module | Description | +| ------ | ----------- | +| [foss]((none)) | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. | +| [gimkl]((none)) | GNU Compiler Collection (GCC) based compiler toolchain, next to Intel MPI and Intel MKL (BLAS, (Sca)LAPACK, FFTW). | +| [gimpi]((none)) | GNU Compiler Collection (GCC) based compiler toolchain, next to Intel MPI. | +| [GNU](http://www.gnu.org/software/) | Compiler-only toolchain with GCC and binutils. | +| [gompi]((none)) | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. | +| [iccifort](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel C, C++ and Fortran compilers | +| [iimpi](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel C/C++ and Fortran compilers, alongside Intel MPI. | +| intel | | +| [iomkl](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI. | +| [iompi](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel C/C++ and Fortran compilers, alongside Open MPI. | +| [Py](https://www.python.org) | Python 3.6 toolchain | + +## Tools + +| Module | Description | +| ------ | ----------- | +| advisor_xe | | +| [ANSYS](http://www.ansys.com) | ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. | +| [APR](http://apr.apache.org/) | Apache Portable Runtime (APR) libraries. | +| [APR-util](http://apr.apache.org/) | Apache Portable Runtime (APR) util libraries. | +| [Bash](http://www.gnu.org/software/bash) | Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh). | +| [binutils](http://directory.fsf.org/project/binutils/) | binutils: GNU binary utilities | +| [bzip2](http://www.bzip.org/) | bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. | +| cmake | | +| cube | | +| [cURL](http://curl.haxx.se) | libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. | +| [DMTCP](http://dmtcp.sourceforge.net/index.html) | DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints a single-host or distributed computation in user-space -- with no modifications to user code or to the O/S. | +| [EasyBuild](https://easybuilders.github.io/easybuild) | EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. | +| elmer | | +| [expat](http://expat.sourceforge.net/) | Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) | +| [gettext](http://www.gnu.org/software/gettext/) | GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation | +| [Ghostscript](http://ghostscript.com) | Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that. | +| [git](http://git-scm.com/) | Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. | +| [GLPK](https://www.gnu.org/software/glpk/) | The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. | +| gnuplot | | +| [gperftools](http://github.com/gperftools/gperftools) | gperftools are for use by developers so that they can create more robust applications. Especially of use to those developing multi-threaded applications in C++ with templates. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. | +| grace | | +| [Graph500](http://graph500.org/) | Reference code of the Graph500 benchmark. | +| [gzip](http://www.gnu.org/software/gzip/) | gzip (GNU zip) is a popular data compression program as a replacement for compress | +| help2man | | +| inspector_xe | | +| intelpcm | | +| ipm | | +| itac | | +| [JOE](http://joe-editor.sourceforge.net) | JOE is a full featured terminal-based screen editor which is distributed under the GNU General Public License (GPL) | +| likwid | | +| Lmod | | +| MATLAB | | +| memoryscape | | +| [Mercurial](http://mercurial.selenic.com/) | Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. | +| mercurial | | +| MIKE | | +| mono | | +| mpi.net | | +| [nano](http://www.nano-editor.org/) | Small and friendly text editor | +| [networkx](https://pypi.python.org/pypi/networkx) | NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | +| [numactl](http://oss.sgi.com/projects/libnuma/) | The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program. | +| octave | | +| opari2 | | +| openssh-x509 | | +| oscar-modules | | +| otf2 | | +| papi | | +| parallel | | +| [PatchELF](https://nixos.org/patchelf.html) | PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. | +| [pigz](http://zlib.net/pigz/) | pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. | +| python | | +| R | | +| racket | | +| relion | | +| [RStudio](https://www.rstudio.com) | RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. | +| ruby | | +| scite | | +| [Serf](http://serf.apache.org/) | The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library | +| [Singularity](http://gmkurtzer.github.io/singularity) | Singularity is a container platform focused on supporting "Mobility of Compute" | +| [Subversion](http://subversion.apache.org/) | Subversion is an open source version control system. | +| Szip | | +| tcl | | +| [tcsh](http://www.tcsh.org) | Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. | +| tk | | +| tmux | | +| totalview | | +| turbovnc | | +| [util-linux](http://www.kernel.org/pub/linux/utils/util-linux) | Set of Linux utilities | +| valgrind | | +| vampir | | +| virtualgl | | +| [VTune](http://software.intel.com/en-us/intel-vtune-amplifier-xe) | Intel VTune Amplifier XE 2016 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. | +| [XZ](http://tukaani.org/xz/) | xz: XZ utilities | + +## Virtualization + +| Module | Description | +| ------ | ----------- | +| qemu | | +| vde2 | | +| wine | | + +## Vis + +| Module | Description | +| ------ | ----------- | +| [ATK](https://developer.gnome.org/ATK/stable/) | ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. | +| [cairo](http://cairographics.org) | Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB | +| [ffmpeg](https://www.ffmpeg.org/) | A complete, cross-platform solution to record, convert and stream audio and video. | +| [FFmpeg](https://www.ffmpeg.org/) | A complete, cross-platform solution to record, convert and stream audio and video. | +| [fixesproto](http://www.freedesktop.org/wiki/Software/xlibs) | X.org FixesProto protocol headers. | +| [FLTK](http://www.fltk.org) | FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. | +| [fontconfig](http://www.freedesktop.org/software/fontconfig) | Fontconfig is a library designed to provide system-wide font configuration, customization and application access. | +| [freetype](http://freetype.org) | FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. | +| [Gdk-Pixbuf](https://developer.gnome.org/gdk-pixbuf/stable/) | The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. | +| gettext | | +| [GL2PS](http://www.geuz.org/gl2ps/) | GL2PS: an OpenGL to PostScript printing library | +| [GLib](http://www.gtk.org/) | GLib is one of the base libraries of the GTK+ project | +| [gnuplot](http://gnuplot.sourceforge.net/) | Portable interactive, function plotting utility | +| [grace](http://freecode.com/projects/grace) | Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. | +| [GraphicsMagick](http://www.graphicsmagick.org/) | GraphicsMagick is the swiss army knife of image processing. | +| [GST-plugins-base](http://gstreamer.freedesktop.org/) | GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. | +| [GStreamer](http://gstreamer.freedesktop.org/) | GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. | +| [GTK+](https://developer.gnome.org/gtk+/stable/) | The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. | +| [HarfBuzz](http://www.freedesktop.org/wiki/Software/HarfBuzz) | HarfBuzz is an OpenType text shaping engine. | +| [inputproto](http://www.freedesktop.org/wiki/Software/xlibs) | X.org InputProto protocol headers. | +| [JasPer](http://www.ece.uvic.ca/~frodo/jasper/) | The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. | +| [kbproto](http://www.freedesktop.org/wiki/Software/xlibs) | X.org KBProto protocol headers. | +| libGLU | | +| [libICE](http://www.freedesktop.org/wiki/Software/xlibs) | X Inter-Client Exchange library for freedesktop.org | +| [libX11](http://www.freedesktop.org/wiki/Software/xlibs) | X11 client-side library | +| [libXau](http://www.freedesktop.org/wiki/Software/xlibs) | The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display. | +| [libXdmcp](http://www.freedesktop.org/wiki/Software/xlibs) | The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager. | +| [libXext](http://www.freedesktop.org/wiki/Software/xlibs) | Common X Extensions library | +| [libXfixes](http://www.freedesktop.org/wiki/Software/xlibs) | X Fixes extension library | +| [libXfont](http://www.freedesktop.org/wiki/Software/xlibs) | X font libary | +| libXinerama | | +| [libXrender](http://www.freedesktop.org/wiki/Software/xlibs) | X11 client-side library | +| [libXt](http://www.freedesktop.org/wiki/Software/xlibs) | libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation). | +| [matplotlib](http://matplotlib.org) | matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits. | +| Mesa | | +| [motif](http://motif.ics.com/) | Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix. | +| [OpenCV](http://opencv.org/) | OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. | +| [opencv-python](http://deeplearning.net/software/theano) | Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. | +| [OSPRay](http://www.ospray.org) | A Ray Tracing Based Rendering Engine for High-Fidelity Visualization | +| [Pango](http://www.pango.org/) | Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x. | +| [ParaView](http://www.paraview.org) | ParaView is a scientific parallel visualizer. | +| [Pillow](http://pillow.readthedocs.org/) | Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. | +| [pixman](http://www.pixman.org/) | Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server. | +| [PyQt](http://www.riverbankcomputing.co.uk/software/pyqt) | PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework. | +| [scikit-image](http://scikit-learn.org/stable/index.html) | Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. | +| [seekpath](https://github.com/giovannipizzi/seekpath) | SeeK-path is a python module to obtain and visualize band paths in the Brillouin zone of crystal structures. The definition of k-point labels follows crystallographic convention, as defined and discussed in the HPKOT paper. Moreover, the Bravais lattice is detected properly using the spacegroup symmetry. Also the suggested band path provided in the HPKOT paper is returned. Systems without time-reversal and inversion-symmetry are also properly taken into account. | +| [Tk](http://www.tcl.tk/) | Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages. | +| [VTK](http://www.vtk.org) | 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. | +| [X11](https://www.x.org) | The X Window System (X11) is a windowing system for bitmap displays | +| [x264](http://www.videolan.org/developers/x264.html) | x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL. |