diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 0d7a43087e02114088f2cb7d1425e9e9dfbae9cc..5e5b51274661790f3fb235678e328323b7e75b8f 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -47,7 +47,8 @@ ext_links: script: - wget -V - echo https://docs.it4i.cz/devel/$CI_BUILD_REF_NAME/ - - wget --spider -o /tmp/wget.log -e robots=off -r -p https://docs.it4i.cz/devel/$CI_BUILD_REF_NAME/ + #- wget --spider -o /tmp/wget.log -e robots=off -r -p https://docs.it4i.cz/devel/$CI_BUILD_REF_NAME/ + - curl https://docs.it4i.cz/devel/$CI_BUILD_REF_NAME/ - sed -n '/^Found .* broken links.$/,$p' /tmp/wget.log mkdocs: diff --git a/docs.it4i/modules-salomon-uv.md b/docs.it4i/modules-salomon-uv.md index ea701e5caa17d1aeab555304f85cdc09b82c4429..b76ee3910e2e1c9a3686d5ee6d0f16c195fbffad 100644 --- a/docs.it4i/modules-salomon-uv.md +++ b/docs.it4i/modules-salomon-uv.md @@ -164,3 +164,43 @@ | ------ | ----------- | | [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 | +| [BLCR](http://crd.lbl.gov/departments/computer-science/CLaSS/research/BLCR/) | Future Technologies Group researchers are developing a hybrid kernel/user implementation of checkpoint/restart. Their goal is to provide a robust, production quality implementation that checkpoints a wide range of applications, without requiring changes to be made to application code. This work focuses on checkpointing parallel applications that communicate through MPI, and on compatibility with the software suite produced by the SciDAC Scalable Systems Software ISIC. | +| [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. | +| [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 | | +| [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) | +| [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. | +| [gzip](http://www.gnu.org/software/gzip/) | gzip (GNU zip) is a popular data compression program as a replacement for compress | +| MATLAB | | +| [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. | +| [moreutils](https://joeyh.name/code/moreutils/) | Moreutils is a growing collection of the unix tools that nobody thought to write long ago when unix was young. | +| [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. | +| pigz | | +| [QEMU](http://wiki.qemu.org/Main_Page) | QEMU is a generic and open source machine emulator and virtualizer. | +| [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. | +| Singularity | | +| [Szip](http://www.hdfgroup.org/doc_resource/SZIP/) | Szip compression software, providing lossless compression of scientific data | +| [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. | +| [util-linux](http://www.kernel.org/pub/linux/utils/util-linux) | Set of Linux utilities | +| [VDE2](http://vde.sourceforge.net) | VDE is an ethernet compliant virtual network that can be spawned over a set of physical computer over the Internet. VDE is part of virtualsquare project. | +| [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 | + +## Vis + +| Module | Description | +| ------ | ----------- | +| [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 | +| [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. | +| [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 | +| [GLib](http://www.gtk.org/) | GLib is one of the base libraries of the GTK+ project | +| [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. | +| [libGLU](ftp://ftp.freedesktop.org/pub/mesa/glu/) | The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. | +| [Mesa](http://www.mesa3d.org/) | Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. | +| [ParaView](http://www.paraview.org) | ParaView is a scientific parallel visualizer. | +| [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. | +| [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. | +| [VisIt](https://wci.llnl.gov/simulation/computer-codes/visit) | VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool | +| [X11](https://www.x.org) | The X Window System (X11) is a windowing system for bitmap displays | diff --git a/docs.it4i/modules-salomon.md b/docs.it4i/modules-salomon.md index b181c5e0c0db0b691608aeb86bd2bc02a1cc9766..12b5328421e69c7c7ad59a184162eb97d69d0535 100644 --- a/docs.it4i/modules-salomon.md +++ b/docs.it4i/modules-salomon.md @@ -5,7 +5,7 @@ | Module | Description | | ------ | ----------- | | [CentOS](https://www.centos.org/) | The CentOS Project is a community-driven free software effort focused on delivering a robust open source ecosystem. For users, we offer a consistent manageable platform that suits a wide variety of deployments. For open source communities, we offer a solid, predictable base to build upon, along with extensive resources to build, test, release, and maintain their code. We’re also expanding the availability of CentOS images across a number of vendors, providing official images for Amazon, Google, and more. For self-hosted cloud, we also provide a generic cloud-init enabled image. For more information about updates and improvements in CentOS 7, please check out the release notes or the release announcement in the mailing list archive. | -| [Debian](https://www.ubuntu.com/) | Ubuntu is a Debian-based Linux operating system for personal computers, tablets and smartphones, where Ubuntu Touch edition is used. It also runs network servers. That is usually with the Ubuntu Server edition, either on physical or virtual servers (such as on mainframes) or with containers, that is with enterprise-class features. It runs on the most popular architectures, including server-class ARM-based. Ubuntu is published by Canonical Ltd, who offer commercial support. It is based on free software and named after the Southern African philosophy of ubuntu (literally, 'human-ness'), which Canonical Ltd. suggests can be loosely translated as "humanity to others" or "I am what I am because of who we all are". Since Ubuntu 11.04 Natty Narwhal Ubuntu has used Unity as its default user interface for the desktop, but following the release of Ubuntu 17.10 it will move to the GNOME 3 desktop instead, as work on Unity ends. Ubuntu is the most popular operating system running in hosted environments, so–called "clouds", as it is the most popular server Linux distribution. Development of Ubuntu is led by UK-based Canonical Ltd., a company of South African entrepreneur Mark Shuttleworth. Canonical generates revenue through the sale of technical support and other services related to Ubuntu. The Ubuntu project is publicly committed to the principles of open-source software development; people are encouraged to use free software, study how it works, improve upon it, and distribute it. | +| [Debian](https://www.debian.org/) | Debian is a Unix-like operating system composed entirely of free software packaged by a team of volunteers. The Debian Project was started by Ian Murdock on August 16, 1993, Debian 0.01 was released on September 15, 1993, and the first stable version, 1.1, was released on June 17, 1996. The Debian stable branch is the most popular edition for personal computers and network servers, and is used as a base for many other distributions. The project's work is carried out over the Internet, guided by the Debian Project Leader and three foundational documents: the Debian Social Contract, the Debian Constitution, and the Debian Free Software Guidelines. New distributions are updated continually, and the next candidate is released after a time-based freeze. One of the earliest operating systems based on the Linux kernel, Debian has been developed openly and distributed freely in the spirit of the GNU Project. This decision drew the support of the Free Software Foundation, which sponsored the project for one year from November 1994 to November 1995. When the sponsorship ended, the Debian Project formed Software in the Public Interest to continue supporting development. While all Debian releases are based on the GNU userland and GNU C Library (glibc), kernels other than Linux are also available, including FreeBSD and the GNU Hurd microkernel. | | Singularity-wrappers | | | [Ubuntu](https://www.ubuntu.com/) | Ubuntu is a Debian-based Linux operating system for personal computers, tablets and smartphones, where Ubuntu Touch edition is used. It also runs network servers. That is usually with the Ubuntu Server edition, either on physical or virtual servers (such as on mainframes) or with containers, that is with enterprise-class features. It runs on the most popular architectures, including server-class ARM-based. Ubuntu is published by Canonical Ltd, who offer commercial support. It is based on free software and named after the Southern African philosophy of ubuntu (literally, 'human-ness'), which Canonical Ltd. suggests can be loosely translated as "humanity to others" or "I am what I am because of who we all are". Since Ubuntu 11.04 Natty Narwhal Ubuntu has used Unity as its default user interface for the desktop, but following the release of Ubuntu 17.10 it will move to the GNOME 3 desktop instead, as work on Unity ends. Ubuntu is the most popular operating system running in hosted environments, so–called "clouds", as it is the most popular server Linux distribution. Development of Ubuntu is led by UK-based Canonical Ltd., a company of South African entrepreneur Mark Shuttleworth. Canonical generates revenue through the sale of technical support and other services related to Ubuntu. The Ubuntu project is publicly committed to the principles of open-source software development; people are encouraged to use free software, study how it works, improve upon it, and distribute it. | @@ -38,7 +38,7 @@ | [deMonNano](http://www.demon-software.com) | deMonNano is a software package for density functional theory based tight binding calculations. It is part of the deMon (density of Montréal) suite of programs. The present version of the code of deMon for DFT is now known as deMon2k. This code and general information about deMon are available at http://www.demon-software.com | | [Digimat](http://www.mscsoftware.com/product/digimat) | The Nonlinear Multi-scale Material and Structure Modeling Platform - Todays' major challenge is the shift from metal to composite in order to bring significant weight saving in the design. This paradigm however requires a dedicated tool for composite design in order to take into account the specific composite behavior. Classical design tools are not able to describe accurately the local composite material behavior, leading to introduction of safety factors and lack of confidence in the design. | | [FreeFem++](http://www.freefem.org) | FreeFem++ is a partial differential equation solver. It has its own language. freefem scripts can solve multiphysics non linear systems in 2D and 3D. Problems involving PDE (2d, 3d) from several branches of physics such as fluid-structure interactions require interpolations of data on several meshes and their manipulation within one program. FreeFem++ includes a fast 2^d-tree-based interpolation algorithm and a language for the manipulation of data on multiple meshes (as a follow up of bamg (now a part of FreeFem++ ). FreeFem++ is written in C++ and the FreeFem++ language is a C++ idiom. It runs on Macs, Windows, Unix machines. FreeFem++ replaces the older freefem and freefem+. | -| [HyperWorks](pavel.marsalek@vsb.cz) | Altair HyperMesh is a high-performance finite element pre-processor to prepare even the largest models, starting from import of CAD geometry to exporting an analysis run for various disciplines. This module is licensed for specified users only. For more informations please contact Pavel Marsalek <pavel.marsalek@vsb.cz>. | +| [HyperWorks](https://altairhyperworks.com/) | Altair HyperMesh is a high-performance finite element pre-processor to prepare even the largest models, starting from import of CAD geometry to exporting an analysis run for various disciplines. This module is licensed for specified users only. For more informations please contact Pavel Marsalek <pavel.marsalek@vsb.cz>. | | [Marc](http://www.mscsoftware.com/product/marc) | Advanced Nonlinear Simulation Solution. Simulate products more accurately with the industry’s leading nonlinear FEA solver technology. | | [OpenFOAM](http://www.openfoam.com/) | OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. | @@ -64,7 +64,6 @@ | [ORCA](http://cec.mpg.de/forum/) | ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. | | [PLUMED](http://www.plumed-code.org) | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. | | [pWord2Vec](https://github.com/IntelLabs/pWord2Vec) | This tool provides an efficient implementation of the continuous bag-of-words and skip-gram architectures for computing vector representations of words. These representations can be subsequently used in many natural language processing applications and for further research. | -| [PYXAID](oprezhdo@chem.rochester.edu) | PYthon eXtension for Ab Inition Dynamics version 1.0, Contact info alexvakimov@gmail.com, oprezhdo@chem.rochester.edu | | [QuantumESPRESSO](http://www.pwscf.org/) | Quantum ESPRESSO is an integrated 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). | | [S4MPLE](http://infochim.u-strasbg.fr/spip.php?rubrique152) | S4MPLE (Sampler For Multiple Protein-Ligand Entities) is a flexible molecular modeling tool, supporting empirical force field-driven conformational sampling and geometry optimization heuristics using a hybrid genetic algorithm (GA). | | [Scipion](https://github.com/I2PC/scipion/wiki) | Scipion is an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents a unified interface for both biologists and developers. Scipion allows you to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. | @@ -449,7 +448,7 @@ | [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). | | [PyNaCl](https://pypi.python.org/pypi/PyNaCl) | Python binding to the Networking and Cryptography (NaCl) library | | [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. | -| PyQt | | +| [PyQt](http://www.riverbankcomputing.co.uk/software/pyqt) | PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework. | | [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. | | [pyspark](https://pypi.python.org/pypi/pyspark) | Apache Spark Python API | | [pytest](http://pytest.org) | Simple powerful testing with Python |