diff --git a/docs.it4i/anselm/resources-allocation-policy.md b/docs.it4i/anselm/resources-allocation-policy.md
index 34f1ee4186e532b7ee26ef93a30bed7f4229d452..40edd72bcbb93e64ae171423ee9ad73d1bcb36c4 100644
--- a/docs.it4i/anselm/resources-allocation-policy.md
+++ b/docs.it4i/anselm/resources-allocation-policy.md
@@ -24,7 +24,7 @@ The resources are allocated to the job in a fair-share fashion, subject to const
* **qexp**, the Express queue: This queue is dedicated for testing and running very small jobs. It is not required to specify a project to enter the qexp. There are 2 nodes always reserved for this queue (w/o accelerator), maximum 8 nodes are available via the qexp for a particular user, from a pool of nodes containing Nvidia accelerated nodes (cn181-203), MIC accelerated nodes (cn204-207) and Fat nodes with 512GB RAM (cn208-209). This enables to test and tune also accelerated code or code with higher RAM requirements. The nodes may be allocated on per core basis. No special authorization is required to use it. The maximum runtime in qexp is 1 hour.
* **qprod**, the Production queue: This queue is intended for normal production runs. It is required that active project with nonzero remaining resources is specified to enter the qprod. All nodes may be accessed via the qprod queue, except the reserved ones. 178 nodes without accelerator are included. Full nodes, 16 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprod is 48 hours.
* **qlong**, the Long queue: This queue is intended for long production runs. It is required that active project with nonzero remaining resources is specified to enter the qlong. Only 60 nodes without acceleration may be accessed via the qlong queue. Full nodes, 16 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qlong is 144 hours (three times of the standard qprod time - 3 x 48 h).
-* **qnvidia**, qmic, qfat, the Dedicated queues: The queue qnvidia is dedicated to access the Nvidia accelerated nodes, the qmic to access MIC nodes and qfat the Fat nodes. It is required that active project with nonzero remaining resources is specified to enter these queues. 23 nvidia, 4 mic and 2 fat nodes are included. Full nodes, 16 cores per node are allocated. The queues run with very high priority, the jobs will be scheduled before the jobs coming from the qexp queue. An PI needs explicitly ask [support](https://support.it4i.cz/rt/) for authorization to enter the dedicated queues for all users associated to her/his Project.
+* **qnvidia**, **qmic**, **qfat**, the Dedicated queues: The queue qnvidia is dedicated to access the Nvidia accelerated nodes, the qmic to access MIC nodes and qfat the Fat nodes. It is required that active project with nonzero remaining resources is specified to enter these queues. 23 nvidia, 4 mic and 2 fat nodes are included. Full nodes, 16 cores per node are allocated. The queues run with very high priority, the jobs will be scheduled before the jobs coming from the qexp queue. An PI needs explicitly ask [support](https://support.it4i.cz/rt/) for authorization to enter the dedicated queues for all users associated to her/his Project.
* **qfree**, The Free resource queue: The queue qfree is intended for utilization of free resources, after a Project exhausted all its allocated computational resources (Does not apply to DD projects by default. DD projects have to request for persmission on qfree after exhaustion of computational resources.). It is required that active project is specified to enter the queue, however no remaining resources are required. Consumed resources will be accounted to the Project. Only 178 nodes without accelerator may be accessed from this queue. Full nodes, 16 cores per node are allocated. The queue runs with very low priority and no special authorization is required to use it. The maximum runtime in qfree is 12 hours.
## Queue Notes
diff --git a/docs.it4i/index.md b/docs.it4i/index.md
index f16bff16e2c7735f30e673d1d6d9ab7d288a38b7..1d095539fe07ef804b16c63539173cbf9625fc6c 100644
--- a/docs.it4i/index.md
+++ b/docs.it4i/index.md
@@ -62,4 +62,6 @@ local $
Although we have taken every care to ensure the accuracy of the content, mistakes do happen.
If you find an inconsistency or error, please report it by visiting <http://support.it4i.cz/rt>, creating a new ticket, and entering the details.
By doing so, you can save other readers from frustration and help us improve.
-We will fix the problem as soon as possible.
+
+!!! tip
+ We will fix the problem as soon as possible.
diff --git a/docs.it4i/modules-anselm.md b/docs.it4i/modules-anselm.md
index a7087cf121dbae35054dfdded2b18d695253d05a..0cb167fb850e995b522485fb7ae3a7114dbb8fc5 100644
--- a/docs.it4i/modules-anselm.md
+++ b/docs.it4i/modules-anselm.md
@@ -1,11 +1,13 @@
# Available Modules
-## Core
+## Os
| Module | Description |
| ------ | ----------- |
-| lmod | |
-| settarg | |
+| [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. |
+| [Fedora](https://fedoraproject.org) | The Fedora Project is a global partnership of free software community members. The Fedora Project is sponsored by Red Hat, which invests in our infrastructure and resources to encourage collaboration and incubate innovative new technologies. Some of these technologies may later be integrated into Red Hat products. They are developed in Fedora and produced under a free and open source license from inception, so other free software communities and projects are free to study, adopt, and modify them. Read an overview to learn more about our mission, our community, our governance, and what makes Fedora unique. You can also learn about our vision and core values — the foundations upon which the project is built. We also have information relating to our user base, and the objectives for our technical work. |
+| [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. |
## Bio
@@ -16,28 +18,26 @@
| [GROMACS](http://www.gromacs.org) | GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. |
| [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. |
-## Bullxde
+## Cae
| Module | Description |
| ------ | ----------- |
-| bullxde | |
-
-## Bullxmpi
-
-| Module | Description |
-| ------ | ----------- |
-| bullxmpi | |
+| COMSOL | |
+| [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 |
+| OpenFOAM | |
## Chem
| Module | Description |
| ------ | ----------- |
-| abinit | |
+| ABINIT | |
| cp2k-mpi | |
| lammps | |
+| libxc | |
| molpro | |
| namd | |
-| nwchem | |
+| [NWChem](http://www.nwchem-sw.org) | NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. |
+| [OpenBabel](http://openbabel.org) | Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. |
| [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. |
| [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). |
@@ -45,27 +45,22 @@
## Compiler
-| Module | Description |
-| ------ | ----------- |
-| GCC | |
-| GCCcore | |
-| icc | |
-| ifort | |
-
-## Compilers
-
| Module | Description |
| ------ | ----------- |
| bupc | |
| chicken | |
+| [Clang](http://clang.llvm.org/) | C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. |
| gcc | |
| [GCC](http://gcc.gnu.org/) | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). |
-| [GCCcore](http://gcc.gnu.org/) | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). |
+| [GCCcore](http://gcc.gnu.org/) | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). [NOTE: This module does not include Objective-C, Java or Ada] |
| gupc | |
| [icc](http://software.intel.com/en-us/intel-compilers/) | C and C++ compiler from Intel |
| [ifort](http://software.intel.com/en-us/intel-compilers/) | Fortran compiler from Intel |
+| ispc | |
| java | |
-| llvm | |
+| LLVM | |
+| [OpenCoarrays](http://www.opencoarrays.org/) | A transport layer for coarray Fortran compilers. |
+| [PGI](http://www.pgroup.com/) | C, C++ and Fortran compilers from The Portland Group - PGI |
## Data
@@ -73,6 +68,9 @@
| ------ | ----------- |
| [GDAL](http://www.gdal.org/) | GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. |
| [HDF5](http://www.hdfgroup.org/HDF5/) | HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. |
+| netCDF | |
+| netCDF-Fortran | |
+| [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. |
## Debugger
@@ -85,32 +83,52 @@
| Module | Description |
| ------ | ----------- |
+| [ant](http://ant.apache.org/) | Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. |
| [Autoconf](http://www.gnu.org/software/autoconf/) | Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. |
| [Automake](http://www.gnu.org/software/automake/automake.html) | Automake: GNU Standards-compliant Makefile generator |
| [Autotools](http://autotools.io) | This bundle collect the standard GNU build tools: Autoconf, Automake and libtool |
+| Bazel | |
| [Boost](http://www.boost.org/) | Boost provides free peer-reviewed portable C++ source libraries. |
+| [Caffe](https://github.com/BVLC/caffe) | Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors. |
| [CMake](http://www.cmake.org) | CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. |
-| [Doxygen](http://www.doxygen.org) | Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. |
+| Doxygen | |
| [fontsproto](http://www.freedesktop.org/wiki/Software/xlibs) | X11 font extension wire protocol |
+| [gflags](https://github.com/gflags/gflags) | The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used. |
+| [glog](https://github.com/google/glog) | A C++ implementation of the Google logging module. |
+| [GObject-Introspection](https://wiki.gnome.org/GObjectIntrospection/) | GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library. |
+| [gperf](http://www.gnu.org/software/gperf/) | GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only. |
| [guile](http://www.gnu.org/software/guile) | Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system. |
+| [JUnit](http://sourceforge.net/projects/junit) | A programmer-oriented testing framework for Java. |
+| [LevelDB](https://github.com/google/leveldb) | LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values. |
| [libSM](http://www.freedesktop.org/wiki/Software/xlibs) | X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use. |
+| [LMDB](https://github.com/LMDB/lmdb) | OpenLDAP's Lightning Memory-Mapped Database (LMDB) library. |
| [M4](http://www.gnu.org/software/m4/m4.html) | GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. |
| [make](http://www.gnu.org/software/make/make.html) | make-3.82: GNU version of make utility |
-| makedepend | The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. |
+| [makedepend](http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html) | The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. |
+| Mako | |
| Maven | |
| [ncurses](http://www.gnu.org/software/ncurses/) | The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. |
| [PCRE](http://www.pcre.org/) | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. |
| [pkg-config](http://www.freedesktop.org/wiki/Software/pkg-config/) | pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). |
+| [protobuf](https://github.com/google/protobuf/) | Google Protocol Buffers |
| [Qt](http://qt-project.org/) | Qt is a comprehensive cross-platform C++ application framework. |
+| Qt5 | |
| [renderproto](http://www.freedesktop.org/wiki/Software/xlibs) | Xrender protocol and ancillary headers |
| [SCons](http://www.scons.org/) | SCons is a software construction tool. |
+| [Spack](https://spack.io/) | Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine. |
| [SQLite](http://www.sqlite.org/) | SQLite: SQL Database Engine in a C Library |
+| [SWIG](http://www.swig.org/) | SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. |
| [xbitmaps](http://www.freedesktop.org/wiki/Software/xlibs) | provides bitmaps for x |
| [xcb-proto](http://xcb.freedesktop.org/) | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
+| xcb-util | |
+| xcb-util-image | |
+| xcb-util-keysyms | |
+| xcb-util-renderutil | |
+| xcb-util-wm | |
| [xextproto](http://www.freedesktop.org/wiki/Software/xlibs) | XExtProto protocol headers. |
| [xineramaproto](http://www.freedesktop.org/wiki/Software/xlibs) | X protocol and ancillary headers for xinerama |
| [xorg-macros](http://cgit.freedesktop.org/xorg/util/macros) | X.org macros utilities. |
-| [xproto](http://www.freedesktop.org/wiki/Software/xlibs) | X protocol and ancillary headers |
+| xproto | |
| [xtrans](http://www.freedesktop.org/wiki/Software/xlibs) | xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. |
## Engineering
@@ -150,44 +168,80 @@
| PrgEnv-gnu | |
| PrgEnv-intel | |
+## Geo
+
+| Module | Description |
+| ------ | ----------- |
+| [Doris](http://doris.tudelft.nl/) | Delft object-oriented radar interferometric software |
+| [PHREEQC](https://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/) | A Computer Program for Speciation, Batch-Reaction, One-Dimensional Transport, and Inverse Geochemical Calculations |
+
+## Init
+
+| Module | Description |
+| ------ | ----------- |
+
## Lang
| Module | Description |
| ------ | ----------- |
+| [Anaconda2](https://www.continuum.io/anaconda-overview) | Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. |
+| [Anaconda3](https://www.continuum.io/anaconda-overview) | Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. |
| [Bison](http://www.gnu.org/software/bison) | Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. |
| [byacc](http://invisible-island.net/byacc/byacc.html) | Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler. |
| [flex](http://flex.sourceforge.net/) | Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. |
| [Java](http://java.com/) | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. |
| [libgdiplus](https://github.com/mono/libgdiplus) | An Open Source implementation of the GDI+ API. |
| [Lua](http://www.lua.org/) | Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. |
-| Mono | |
+| [Mono](http://mono-framework.com) | An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. |
| [NASM](http://www.nasm.us/) | NASM: General-purpose x86 assembler |
-| Perl | |
+| [OpenCL-runtime](https://software.intel.com/en-us/intel-opencl) | OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software. |
+| [Perl](http://www.perl.org/) | Larry Wall's Practical Extraction and Report Language |
| [Python](http://python.org/) | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
+| [R](http://www.r-project.org/) | R is a free software environment for statistical computing and graphics. |
| [Ruby](https://www.ruby-lang.org) | Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. |
-| [Tcl](http://www.tcl.tk/) | Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. |
+| Tcl | |
+| [Yasm](http://www.tortall.net/projects/yasm/) | Yasm: Complete rewrite of the NASM assembler with BSD license |
## Lib
| Module | Description |
| ------ | ----------- |
-| [libdrm](http://dri.freedesktop.org) | Direct Rendering Manager runtime library. |
+| [astroid](https://github.com/PyCQA/astroid) | The aim of this module is to provide a common base representation of python source code for projects such as pychecker, pyreverse, pylint… Well, actually the development of this library is essentially governed by pylint’s needs. It used to be called logilab-astng. |
+| [Embree](https://embree.github.io/index.html) | Embree is a collection of high-performance ray tracing kernels, developed at Intel. |
+| [freeglut](http://freeglut.sourceforge.net/) | freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. |
+| [GLM](https://github.com/g-truc/glm) | OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. |
+| [isort](https://github.com/timothycrosley/isort) | isort is a Python utility / library to sort imports alphabetically, and automatically separated into sections. It provides a command line utility, Python library and plugins for various editors to quickly sort all your imports. |
+| libdrm | |
| libevent | |
| [libffi](http://sourceware.org/libffi/) | The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. |
| [libfontenc](http://www.freedesktop.org/wiki/Software/xlibs/) | X11 font encoding library |
+| [libgd](https://libgd.github.io/) | GD is an open source code library for the dynamic creation of images by programmers. |
| [libjpeg-turbo](http://sourceforge.net/projects/libjpeg-turbo/) | libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. |
| [libmatheval](http://www.gnu.org/software/libmatheval/) | GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. |
| [libpng](http://www.libpng.org/pub/png/libpng.html) | libpng is the official PNG reference library |
| [libpthread-stubs](http://xcb.freedesktop.org/) | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
| [libreadline](http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html) | The GNU 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. |
+| [libsndfile](http://www.mega-nerd.com/libsndfile) | Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface. |
+| LIBSVM | |
| [LibTIFF](http://www.remotesensing.org/libtiff/) | tiff: Library and tools for reading and writing TIFF data files |
| libtool | |
| [libunistring](http://www.gnu.org/software/libunistring/) | This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. |
-| [libxcb](http://xcb.freedesktop.org/) | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
-| [libxml2](http://xmlsoft.org/) | Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). |
+| libxcb | |
+| libxml2 | |
+| [libxslt](http://xmlsoft.org/) | Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). |
+| [libyaml](http://pyyaml.org/wiki/LibYAML) | LibYAML is a YAML 1.1 parser and emitter written in C. |
+| [lxml](http://lxml.de/) | The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. |
+| [MATIO](http://sourceforge.net/projects/matio/) | matio is an C library for reading and writing Matlab MAT files. |
+| [mpi4py](https://bitbucket.org/mpi4py/mpi4py) | 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. |
+| [nettle](http://www.lysator.liu.se/~nisse/nettle/) | Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. |
+| [PROJ](http://trac.osgeo.org/proj/) | Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates |
+| [pylint](https://github.com/PyCQA/pylint) | Pylint is a Python source code analyzer which looks for programming errors, helps enforcing a coding standard and sniffs for some code smells (as defined in Martin Fowler's Refactoring book). |
+| [PyYAML](https://pypi.python.org/pypi/PyYAML/) | PyYAML is a YAML parser and emitter for the Python programming language. |
| [SIONlib](http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html) | SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version. |
+| [snappy](https://github.com/google/snappy) | Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression. |
| [spGPU](https://github.com/davidebarbieri/spgpu) | spGPU is a set of custom matrix storages and CUDA kernels for sparse linear algebra computing on GPU. It isn't a replacement for cuBLAS/cuSPARSE that should be used for a full featured linear algebra environment on GPU. |
-| tbb | |
+| [tbb](http://software.intel.com/en-us/articles/intel-tbb/) | Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms. |
+| Tensorflow | |
| zlib | |
## Libraries
@@ -195,7 +249,6 @@
| Module | Description |
| ------ | ----------- |
| adios | |
-| boost | |
| dataspaces | |
| fftw2 | |
| fftw2-mpi | |
@@ -206,7 +259,6 @@
| hdf5 | |
| hdf5-parallel | |
| ipp | |
-| libmesh | |
| magma | |
| mkl | |
| mxml | |
@@ -218,31 +270,42 @@
| opencl-sdk | |
| petsc | |
| plasma | |
-| slepc | |
| szip | |
| tbb | |
| trilinos | |
-| zlib | |
## Math
| Module | Description |
| ------ | ----------- |
+| Eigen | |
+| [GEOS](http://trac.osgeo.org/geos) | GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) |
| [GMP](http://gmplib.org/) | GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. |
+| [h5py](https://github.com/jupyter/testpath) | Test utilities for code working with files and commands |
| [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. |
+| [libcerf](http://gnuplot.sourceforge.net/) | libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions. |
+| [MATLAB](http://www.mathworks.com/products/matlab) | MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. |
+| METIS | |
| [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. |
-| [numpy](http://www.numpy.org) | NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. |
+| 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 | |
+| [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 | |
+| [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 | |
@@ -256,18 +319,22 @@
| [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 | |
| [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 | |
+| [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. |
-
-## Nvidia
-
-| Module | Description |
-| ------ | ----------- |
-| cuda | |
+| [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
@@ -283,33 +350,30 @@
| samtools | |
| snpEff | |
-## Oscar-Modulefiles
-
-| Module | Description |
-| ------ | ----------- |
-
-## Oscar-Modules
-
-| Module | Description |
-| ------ | ----------- |
-| oscar-modules | |
-
## 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 |
| ------ | ----------- |
-| [phono3py](http://python.org/) | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
-| [phonopy](http://python.org/) | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
-| VASP | |
+| [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. |
+| [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. |
+| [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
@@ -322,7 +386,7 @@
| Module | Description |
| ------ | ----------- |
-| CUDA | |
+| [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. |
@@ -338,13 +402,15 @@
| [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. |
## Tools
| Module | Description |
| ------ | ----------- |
| advisor_xe | |
-| ANSYS | |
+| [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). |
@@ -353,11 +419,13 @@
| 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. |
-| dhi-mike | |
+| [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](http://hpcugent.github.com/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) |
+| [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 | |
+| [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 | |
| grace | |
| [gzip](http://www.gnu.org/software/gzip/) | gzip (GNU zip) is a popular data compression program as a replacement for compress |
@@ -371,11 +439,12 @@
| Lmod | |
| MATLAB | |
| memoryscape | |
-| [Mercurial](https://www.mercurial-scm.org/) | Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. |
+| [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 | |
+| [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 | |
@@ -388,17 +457,15 @@
| R | |
| racket | |
| relion | |
-| Rstudio | |
+| [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 | |
-| scalasca2 | |
| scite | |
-| scorep | |
| [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 | |
+| [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](http://www.hdfgroup.org/doc_resource/SZIP/) | Szip compression software, providing lossless compression of scientific data |
+| Szip | |
| tcl | |
-| tcsh | 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. |
+| [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 | |
@@ -407,7 +474,7 @@
| valgrind | |
| vampir | |
| virtualgl | |
-| VTune | |
+| [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. |
| vtune_xe | |
| [XZ](http://tukaani.org/xz/) | xz: XZ utilities |
@@ -423,16 +490,29 @@
| 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. |
@@ -440,6 +520,21 @@
| [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 | |
| [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. |
+| [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 | |
+| [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. |
diff --git a/docs.it4i/modules-salomon-phi.md b/docs.it4i/modules-salomon-phi.md
new file mode 100644
index 0000000000000000000000000000000000000000..0eb79e5a8cb916d7571f8e81a198516166ecdb96
--- /dev/null
+++ b/docs.it4i/modules-salomon-phi.md
@@ -0,0 +1,63 @@
+# Available Modules
+
+## Compiler
+
+| Module | Description |
+| ------ | ----------- |
+| [icc](http://software.intel.com/en-us/intel-compilers/) | Intel C and C++ compilers |
+
+## Devel
+
+| Module | Description |
+| ------ | ----------- |
+| devel_environment | |
+| M4 | |
+| ncurses | |
+
+## Lang
+
+| Module | Description |
+| ------ | ----------- |
+| [Bison](http://www.gnu.org/software/bison) | Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. |
+| [flex](http://flex.sourceforge.net/) | Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. |
+| [Tcl](http://www.tcl.tk/) | Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. |
+
+## Lib
+
+| Module | Description |
+| ------ | ----------- |
+| [libreadline](http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html) | The GNU 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. |
+| [zlib](http://www.zlib.net/) | zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. |
+
+## Math
+
+| Module | Description |
+| ------ | ----------- |
+| [Octave](http://www.gnu.org/software/octave/) | GNU Octave is a high-level interpreted language, primarily intended for numerical computations. |
+
+## Mpi
+
+| Module | Description |
+| ------ | ----------- |
+| [impi](http://software.intel.com/en-us/intel-mpi-library/) | Intel MPI Library, compatible with MPICH ABI |
+
+## Toolchain
+
+| Module | Description |
+| ------ | ----------- |
+| [iccifort](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel C, C++ & Fortran compilers |
+| [ifort](http://software.intel.com/en-us/intel-compilers/) | Intel Fortran compiler |
+
+## Tools
+
+| Module | Description |
+| ------ | ----------- |
+| bzip2 | |
+| cURL | |
+| [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) |
+
+## Vis
+
+| Module | Description |
+| ------ | ----------- |
+| gettext | |
diff --git a/docs.it4i/modules-salomon-uv.md b/docs.it4i/modules-salomon-uv.md
index 8771b6431ed0dff37de965e2bbdb3d2b68ec32ad..92bd1ea8a1079718b50f5e6116d6c57aa5404215 100644
--- a/docs.it4i/modules-salomon-uv.md
+++ b/docs.it4i/modules-salomon-uv.md
@@ -3,7 +3,7 @@
## Bio
| Module | Description |
-| -------| ----------- |
+| ------ | ----------- |
| [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/download.html) | A quality control application for high throughput sequence data |
| [GATK](http://www.broadinstitute.org/gatk/) | The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. |
| [SnpEff](http://snpeff.sourceforge.net/) | Genetic variant annotation and effect prediction toolbox. |
@@ -11,40 +11,41 @@
## Cae
| Module | Description |
-| -------| ----------- |
-| ANSYS | |
+| ------ | ----------- |
+| COMSOL | |
| [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. |
## Chem
| Module | Description |
-| -------| ----------- |
-| [ABINIT](https://www.abinit.org/) | Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT. |
+| ------ | ----------- |
+| [ABINIT](http://www.abinit.org/) | Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT. |
| [Libint](https://sourceforge.net/p/libint/) | Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. |
| [libxc](http://www.tddft.org/programs/octopus/wiki/index.php/Libxc) | Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. |
## Compiler
| Module | Description |
-| -------| ----------- |
+| ------ | ----------- |
| [GCC](http://gcc.gnu.org/) | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). |
| GCCcore | |
-| [icc](http://software.intel.com/en-us/intel-compilers/) | C and C++ compiler from Intel |
+| icc | |
| [ifort](http://software.intel.com/en-us/intel-compilers/) | Fortran compiler from Intel |
-| LLVM | |
+| [LLVM](http://llvm.org/) | The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. |
## Data
| Module | Description |
-| -------| ----------- |
+| ------ | ----------- |
| [GDAL](http://www.gdal.org/) | GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. |
| [HDF5](http://www.hdfgroup.org/HDF5/) | HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. |
| [netCDF](http://www.unidata.ucar.edu/software/netcdf/) | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. |
+| [netCDF-Fortran](http://www.unidata.ucar.edu/software/netcdf/) | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. |
## Devel
| Module | Description |
-| -------| ----------- |
+| ------ | ----------- |
| [Autoconf](http://www.gnu.org/software/autoconf/) | Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. |
| [Automake](http://www.gnu.org/software/automake/automake.html) | Automake: GNU Standards-compliant Makefile generator |
| [Autotools](http://autotools.io) | This bundle collect the standard GNU build tools: Autoconf, Automake and libtool |
@@ -53,19 +54,28 @@
| [Doxygen](http://www.doxygen.org) | Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. |
| [M4](http://www.gnu.org/software/m4/m4.html) | GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. |
| [make](http://www.gnu.org/software/make/make.html) | make-3.82: GNU version of make utility |
+| [Mako](http://www.makotemplates.org) | A super-fast templating language that borrows the best ideas from the existing templating languages |
| [Maven](http://maven.apache.org/index.html) | Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. |
| [ncurses](http://www.gnu.org/software/ncurses/) | The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. |
+| [PCRE](http://www.pcre.org/) | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. |
+| [pkg-config](http://www.freedesktop.org/wiki/Software/pkg-config/) | pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). |
+| [Qt](http://qt-project.org/) | Qt is a comprehensive cross-platform C++ application framework. |
+| [Qt5](http://qt.io/) | Qt is a comprehensive cross-platform C++ application framework. |
| [SQLite](http://www.sqlite.org/) | SQLite: SQL Database Engine in a C Library |
+| [SWIG](http://www.swig.org/) | SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. |
+| [xorg-macros](http://cgit.freedesktop.org/xorg/util/macros) | X.org macros utilities. |
## Lang
| Module | Description |
-| -------| ----------- |
+| ------ | ----------- |
| [Bison](http://www.gnu.org/software/bison) | Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. |
-| [flex](http://flex.sourceforge.net/) | Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. |
+| flex | |
| [Java](http://java.com/) | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. |
| [Lua](http://www.lua.org/) | Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. |
+| [Mono](http://mono-framework.com) | An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. |
| [NASM](http://www.nasm.us/) | NASM: General-purpose x86 assembler |
+| [OpenCL-runtime](https://software.intel.com/en-us/intel-opencl) | OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software. |
| [Perl](http://www.perl.org/) | Larry Wall's Practical Extraction and Report Language |
| [Python](http://python.org/) | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
| [R](http://www.r-project.org/) | R is a free software environment for statistical computing and graphics. |
@@ -74,13 +84,18 @@
## Lib
| Module | Description |
-| -------| ----------- |
+| ------ | ----------- |
+| [libdrm](http://dri.freedesktop.org) | Direct Rendering Manager runtime library. |
| [libffi](http://sourceware.org/libffi/) | The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. |
| [libjpeg-turbo](http://sourceforge.net/libjpeg-turbo/) | libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. |
| [libpng](http://www.libpng.org/pub/png/libpng.html) | libpng is the official PNG reference library |
+| [libpthread-stubs](http://xcb.freedesktop.org/) | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
| [libreadline](http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html) | The GNU 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. |
-| [libtool](http://www.gnu.org/software/libtool) | GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. |
+| [libsndfile](http://www.mega-nerd.com/libsndfile) | Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface. |
+| [LibTIFF](http://www.remotesensing.org/libtiff/) | tiff: Library and tools for reading and writing TIFF data files |
+| libtool | |
| [libxml2](http://xmlsoft.org/) | Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). |
+| [nettle](http://www.lysator.liu.se/~nisse/nettle/) | Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. |
| [PROJ](http://trac.osgeo.org/proj/) | Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates |
| [tbb](http://software.intel.com/en-us/articles/intel-tbb/) | Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms. |
| [zlib](http://www.zlib.net/) | zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. |
@@ -88,42 +103,51 @@
## Math
| Module | Description |
-| -------| ----------- |
+| ------ | ----------- |
+| [Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) | Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. |
+| [GEOS](http://trac.osgeo.org/geos) | GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) |
| GMP | |
+| [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. |
+| [MPFR](http://www.mpfr.org) | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. |
| [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. |
## Mpi
| Module | Description |
-| -------| ----------- |
+| ------ | ----------- |
| [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. |
| [OpenMPI](http://www.open-mpi.org/) | The Open MPI Project is an open source MPI-2 implementation. |
## Numlib
| Module | Description |
-| -------| ----------- |
+| ------ | ----------- |
+| [CGAL](http://www.cgal.org/) | The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. |
+| [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. |
| [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. |
+| [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. |
| [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. |
## Phys
| Module | Description |
-| -------| ----------- |
+| ------ | ----------- |
| [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. |
## System
| Module | Description |
-| -------| ----------- |
+| ------ | ----------- |
+| CUDA | |
| [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. |
## 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. |
| [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. |
@@ -135,32 +159,44 @@
## Tools
| Module | Description |
-| -------| ----------- |
+| ------ | ----------- |
| [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. |
| [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. |
-| [EasyBuild](http://hpcugent.github.com/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. |
+| [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 | |
+| [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 |
-| help2man | |
| MATLAB | |
-| [Mercurial](https://www.mercurial-scm.org/) | Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. |
+| [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. |
| [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](https://en.wikipedia.org/wiki/Tcsh) | 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. |
+| [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 | |
+| [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 5f2c3dbc23f48373b36c12527be54e2aceedd7a7..9cff5aa271d2fed8f6e3d6cc9978303008069f9e 100644
--- a/docs.it4i/modules-salomon.md
+++ b/docs.it4i/modules-salomon.md
@@ -1,393 +1,19 @@
# Available Modules
-## Core
-
-| Module | Description |
-| ------ | ----------- |
-| lmod | |
-| settarg | |
-
-## Bio
-
-| Module | Description |
-| ------ | ----------- |
-| [almost](http://www-almost.ch.cam.ac.uk/site) | all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations. |
-| [Amber](http://ambermd.org) | A set of molecular mechanical force fields for the simulation of biomolecules |
-| [BCFtools](http://www.htslib.org/) | Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants |
-| [BWA](http://bio-bwa.sourceforge.net/) | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. |
-| [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline. |
-| [GATK](http://www.broadinstitute.org/gatk/) | The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. |
-| [GROMACS](http://www.gromacs.org) | GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. |
-| [HTSlib](http://www.htslib.org/) | A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix |
-| [picard](http://sourceforge.net/projects/picard) | A set of tools (in Java) for working with next generation sequencing data in the BAM format. |
-| [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. |
-| [RELION](http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page) | RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). |
-| [SAMtools](http://www.htslib.org/) | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
-| [SnpEff](http://snpeff.sourceforge.net/) | Genetic variant annotation and effect prediction toolbox. |
-| [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic) | Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. |
-
-## Cae
-
-| Module | Description |
-| ------ | ----------- |
-| Adams | |
-| COMSOL | |
-| Digimat | |
-| [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 | |
-| Marc | |
-| [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. |
-
-## Chem
-
-| Module | Description |
-| ------ | ----------- |
-| [ABINIT](https://www.abinit.org/) | Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT. |
-| [CP2K](http://www.cp2k.org/) | CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. |
-| [LAMMPS](http://lammps.sandia.gov) | LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. Has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. |
-| [libctl](http://ab-initio.mit.edu/libctl) | libctl is a free Guile-based library implementing flexible control files for scientific simulations. |
-| [Libint](https://sourceforge.net/p/libint/) | Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. |
-| [libxc](http://www.tddft.org/programs/octopus/wiki/index.php/Libxc) | Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. |
-| Molpro | |
-| [NAMD](http://www.ks.uiuc.edu/Research/namd/) | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. |
-| [NWChem](http://www.nwchem-sw.org) | NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. |
-| [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. |
-| [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 | 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 | |
-| [xdrfile](http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library) | XTC library |
-
-## Compiler
-
-| Module | Description |
-| ------ | ----------- |
-| [BerkeleyUPC](http://upc.lbl.gov) | The goal of the Berkeley UPC compiler group is to develop a portable, high performance implementation of UPC for large-scale multiprocessors, PC clusters, and clusters of shared memory multiprocessors. |
-| [Clang](http://clang.llvm.org/) | C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. |
-| [GCC](http://gcc.gnu.org/) | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). |
-| [GCCcore](http://gcc.gnu.org/) | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). |
-| [icc](http://software.intel.com/en-us/intel-compilers/) | C and C++ compiler from Intel |
-| [ifort](http://software.intel.com/en-us/intel-compilers/) | Fortran compiler from Intel |
-| [LLVM](http://llvm.org/) | The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. |
-| [OpenCoarrays](http://www.opencoarrays.org/) | A transport layer for coarray Fortran compilers. |
-| PGI | |
-
-## Data
-
-| Module | Description |
-| ------ | ----------- |
-| [GDAL](http://www.gdal.org/) | GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. |
-| [h5py](http://www.h5py.org/) | HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data. |
-| [HDF5](http://www.hdfgroup.org/HDF5/) | HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. |
-| [netCDF](http://www.unidata.ucar.edu/software/netcdf/) | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. |
-| [netCDF-Fortran](http://www.unidata.ucar.edu/software/netcdf/) | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. |
-
-## Debugger
-
-| Module | Description |
-| ------ | ----------- |
-| aislinn | |
-| DDT | |
-| [Forge](http://www.allinea.com/products/develop-allinea-forge) | Allinea Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and FORTRAN applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA. |
-| [PerformanceReports](http://www.allinea.com/products/allinea-performance-reports) | Allinea Performance Reports are the most effective way to characterize and understand the performance of HPC application runs. One single-page HTML report elegantly answers a range of vital questions for any HPC site. - Is this application well-optimized for the system and the processors it is running on? - Does it benefit from running at this scale? - Are there I/O, networking or threading bottlenecks affecting performance? - Which hardware, software or configuration changes can we make to improve performance further. - How much energy did this application use? |
-| TotalView | |
-| [Valgrind](http://valgrind.org/downloads/) | Valgrind: Debugging and profiling tools |
-
-## Devel
-
-| Module | Description |
-| ------ | ----------- |
-| [ant](http://ant.apache.org/) | Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. |
-| [Autoconf](http://www.gnu.org/software/autoconf/) | Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. |
-| [Automake](http://www.gnu.org/software/automake/automake.html) | Automake: GNU Standards-compliant Makefile generator |
-| [Autotools](http://autotools.io) | This bundle collect the standard GNU build tools: Autoconf, Automake and libtool |
-| [Boost](http://www.boost.org/) | Boost provides free peer-reviewed portable C++ source libraries. |
-| [CMake](http://www.cmake.org) | CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. |
-| [Doxygen](http://www.doxygen.org) | Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. |
-| [fontsproto](http://www.freedesktop.org/wiki/Software/xlibs) | X11 font extension wire protocol |
-| [glproto](http://www.freedesktop.org/wiki/Software/xlibs) | X protocol and ancillary headers |
-| [gperf](http://www.gnu.org/software/gperf/) | GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only. |
-| [guile](http://www.gnu.org/software/guile) | Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system. |
-| [JUnit](http://sourceforge.net/projects/junit) | A programmer-oriented testing framework for Java. |
-| [libSM](http://www.freedesktop.org/wiki/Software/xlibs) | X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use. |
-| [M4](http://www.gnu.org/software/m4/m4.html) | GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. |
-| [make](http://www.gnu.org/software/make/make.html) | make-3.82: GNU version of make utility |
-| makedepend | The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. |
-| [Maven](http://maven.apache.org/index.html) | Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. |
-| [ncurses](http://www.gnu.org/software/ncurses/) | The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. |
-| [PCRE](http://www.pcre.org/) | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. |
-| [PCRE2](http://www.pcre.org/) | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. |
-| [pkg-config](http://www.freedesktop.org/wiki/Software/pkg-config/) | pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). |
-| [python-meep](https://code.launchpad.net/python-meep) | Python wrapper for the Meep FDTD solver. |
-| [Qt](http://qt-project.org/) | Qt is a comprehensive cross-platform C++ application framework. |
-| [renderproto](http://www.freedesktop.org/wiki/Software/xlibs) | Xrender protocol and ancillary headers |
-| [SCons](http://www.scons.org/) | SCons is a software construction tool. |
-| [Spark](http://spark.apache.org) | Spark is Hadoop MapReduce done in memory |
-| [SQLite](http://www.sqlite.org/) | SQLite: SQL Database Engine in a C Library |
-| [SWIG](http://www.swig.org/) | SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. |
-| [xbitmaps](http://www.freedesktop.org/wiki/Software/xlibs) | provides bitmaps for x |
-| [xcb-proto](http://xcb.freedesktop.org/) | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
-| [xextproto](http://www.freedesktop.org/wiki/Software/xlibs) | XExtProto protocol headers. |
-| [xineramaproto](http://www.freedesktop.org/wiki/Software/xlibs) | X protocol and ancillary headers for xinerama |
-| [xorg-macros](http://cgit.freedesktop.org/xorg/util/macros) | X.org macros utilities. |
-| [xproto](http://www.freedesktop.org/wiki/Software/xlibs) | X protocol and ancillary headers |
-| [xtrans](http://www.freedesktop.org/wiki/Software/xlibs) | xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. |
-
-## Geo
-
-| Module | Description |
-| ------ | ----------- |
-| [DCW](http://gmt.soest.hawaii.edu/projects/gmt) | country polygons for GMT |
-| [GMT](http://gmt.soest.hawaii.edu/) | GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools. |
-| [PROJ_4](http://proj.osgeo.org) | PROJ.4 - Cartographic Projections Library originally written by Gerald Evenden then of the USGS. |
-
-## Lang
-
-| Module | Description |
-| ------ | ----------- |
-| [Bison](http://www.gnu.org/software/bison) | Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. |
-| [byacc](http://invisible-island.net/byacc/byacc.html) | Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler. |
-| [flex](http://flex.sourceforge.net/) | Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. |
-| [Java](http://java.com/) | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. |
-| [libgdiplus](https://github.com/mono/libgdiplus) | An Open Source implementation of the GDI+ API. |
-| [Lua](http://www.lua.org/) | Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. |
-| [Mono](http://www.mono-project.com) | Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime. |
-| [NASM](http://www.nasm.us/) | NASM: General-purpose x86 assembler |
-| [OpenCL-builder](https://software.intel.com/en-us/intel-opencl) | OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software. This is builder (formerly runtime) package. |
-| [OpenCL-runtime](https://software.intel.com/en-us/intel-opencl) | OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software. |
-| [Perl](http://www.perl.org/) | Larry Wall's Practical Extraction and Report Language |
-| [Python](http://python.org/) | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
-| [R](http://www.r-project.org/) | R is a free software environment for statistical computing and graphics. |
-| [Racket](http://racket-lang.org) | Racket is a full-spectrum programming language. It goes beyond Lisp and Scheme with dialects that support objects, types, laziness, and more. |
-| [Ruby](https://www.ruby-lang.org) | Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. |
-| [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. |
-| [SnuCL](http://snucl.snu.ac.kr) | An OpenCL Framework for Heterogeneous Clusters |
-| [Tcl](http://www.tcl.tk/) | Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. |
-
-## Lib
-
-| Module | Description |
-| ------ | ----------- |
-| [FOX](http://fox-toolkit.org) | FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and effectively. It offers a wide, and growing, collection of Controls, and provides state of the art facilities such as drag and drop, selection, as well as OpenGL widgets for 3D graphical manipulation. |
-| GLM | |
-| [libdrm](http://dri.freedesktop.org) | Direct Rendering Manager runtime library. |
-| libevent | |
-| [libffi](http://sourceware.org/libffi/) | The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. |
-| [libfontenc](http://www.freedesktop.org/wiki/Software/xlibs/) | X11 font encoding library |
-| [libjpeg-turbo](http://sourceforge.net/libjpeg-turbo/) | libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. |
-| [libmatheval](http://www.gnu.org/software/libmatheval/) | GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. |
-| [libMesh](http://libmesh.github.io/) | The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist to focus on the physics they are modeling. |
-| [libpng](http://www.libpng.org/pub/png/libpng.html) | libpng is the official PNG reference library |
-| [libpthread-stubs](http://xcb.freedesktop.org/) | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
-| [libreadline](http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html) | The GNU 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. |
-| [LibTIFF](http://www.remotesensing.org/libtiff/) | tiff: Library and tools for reading and writing TIFF data files |
-| [libtool](http://www.gnu.org/software/libtool) | GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. |
-| [libunistring](http://www.gnu.org/software/libunistring/) | This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. |
-| [libunwind](http://www.nongnu.org/libunwind/) | The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications |
-| [libxcb](http://xcb.freedesktop.org/) | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
-| [libxml2](http://xmlsoft.org/) | Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). |
-| libxslt | |
-| libyaml | |
-| lxml | |
-| MATIO | |
-| [OpenCoarrays](http://www.opencoarrays.org) | OpenCoarrays is an open-source software project for developing, porting and tuning transport layers that support coarray Fortran compilers. |
-| [PROJ](http://trac.osgeo.org/proj/) | Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates |
-| PyYAML | |
-| [QCA](http://delta.affinix.com/qca/) | QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers |
-| [QGIS](http://www.qgis.org) | A Free and Open Source Geographic Information System |
-| [Qwt](http://qwt.sourceforge.net/index.html) | The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Beside a framework for 2D plots it provides scales, sliders, dials, compasses, thermometers, wheels and knobs to control or display values, arrays, or ranges of type double. |
-| [SIONlib](http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html) | SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version. |
-| [spatialindex](https://libspatialindex.github.io/index.html) | The purpose of this library is to provide: * An extensible framework that will support robust spatial indexing methods. * Support for sophisticated spatial queries. Range, point location, nearest neighbor and k-nearest neighbor as well as parametric queries (defined by spatial constraints) should be easy to deploy and run. * Easy to use interfaces for inserting, deleting and updating information. |
-| [SpatiaLite](https://www.gaia-gis.it/fossil/libspatialite/index) | SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities. |
-| [tbb](http://software.intel.com/en-us/articles/intel-tbb/) | Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms. |
-| [zlib](http://www.zlib.net/) | zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. |
-
-## Math
-
-| Module | Description |
-| ------ | ----------- |
-| [FIAT](https://bitbucket.org/fenics-project/fiat) | The FInite element Automatic Tabulator FIAT supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes. |
-| [GEOS](http://trac.osgeo.org/geos) | GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) |
-| [GMP](http://gmplib.org/) | GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. |
-| [Harminv](http://ab-initio.mit.edu/wiki/index.php/Harminv) | Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids. |
-| [ISL](http://isl.gforge.inria.fr/) | isl is a library for manipulating sets and relations of integer points bounded by linear constraints. |
-| [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. |
-| MPC | |
-| [MPFR](http://www.mpfr.org) | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. |
-| MUMPS | |
-| [numpy](http://www.numpy.org) | NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. |
-| [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. |
-| [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. |
-| [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. |
-| [sympy](http://sympy.org/) | SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries. |
-
-## Mpi
-
-| Module | Description |
-| ------ | ----------- |
-| [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. |
-| [MPI_NET](http://www.osl.iu.edu/research/mpi.net/) | MPI.NET is a high-performance, easy-to-use implementation of the Message Passing Interface (MPI) for Microsoft's .NET environment |
-| [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). |
-| mpt | |
-| [MVAPICH2](http://mvapich.cse.ohio-state.edu/overview/mvapich2/) | This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH. |
-| [OpenMPI](http://www.open-mpi.org/) | The Open MPI Project is an open source MPI-2 implementation. |
-
-## 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. |
-| [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. |
-| [Hypre](https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html) | Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. |
-| [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. |
-| [LAPACKE](http://www.netlib.org/lapack/lapacke.html) | LAPACKE C Interface to LAPACK header files and library |
-| [OpenBLAS](http://xianyi.github.com/OpenBLAS/) | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. |
-| [PETSc](http://www.mcs.anl.gov/petsc) | PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. |
-| [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. |
-| [SuiteSparse](http://www.cise.ufl.edu/research/sparse/SuiteSparse/) | SuiteSparse is a collection of libraries manipulate sparse matrices. |
-
-## 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. |
-| [ipp](http://software.intel.com/en-us/articles/intel-ipp/) | Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms. |
-| MAP | |
-| [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 will become 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. |
-| perfboost | |
-| perfcatcher | |
-| PerfReports | |
-| perfsuite | |
-| [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. |
-| [VampirServer](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 |
-| ------ | ----------- |
-| [Meep](http://ab-initio.mit.edu/wiki/index.php/Meep) | Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. |
-| [phono3py](http://python.org/) | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
-| [phonopy](http://python.org/) | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
-| Siesta | |
-| VASP | |
-
-## System
-
-| Module | Description |
-| ------ | ----------- |
-| [eudev](https://wiki.gentoo.org/wiki/Project:Eudev) | eudev is a fork of systemd-udev with the goal of obtaining better compatibility with existing software such as OpenRC and Upstart, older kernels, various toolchains and anything else required by users and various distributions. |
-| [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. |
-
-## 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. |
-| [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 |
-| [ictce](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL. |
-| [iimpi](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel C/C++ and Fortran compilers, alongside Intel MPI. |
-| [intel](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL. |
-| iompi | |
-| [PRACE](http://www.prace-ri.eu/PRACE-Common-Production) | The PRACE Common Production Environment (PCPE) is a set of software tools and libraries that are planned to be available on all PRACE execution sites. The PCPE also defines a set of environment variables that try to make compilation on all sites as homogeneous and simple as possible. |
-| [prace](http://www.prace-ri.eu/PRACE-Common-Production) | PRACE Common Production Environment (PCPE) Initialisation of the PRACE common production environment. This allows you to assume that the following tools/libraries are available by default in your PATH/environment. * Fortran, C, C++ Compilers * MPI * BLAS, LAPACK, BLACS, ScaLAPACK * FFTW * HDF5, NetCDF The compiler commands on are: * mpif90 - Fortran compiler * mpicc - C compiler * mpicxx - C++ compiler For more information on the PCPE please see the documentation at: http://www.prace-ri.eu/PRACE-Common-Production For help using this system, please see Local User Guide available at: http://prace-ri.eu/Best-Practice-Guide-Anselm-HTML |
-
-## Tools
-
-| Module | Description |
-| ------ | ----------- |
-| ANSYS | |
-| [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. |
-| [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. |
-| [EasyBuild](http://hpcugent.github.com/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. |
-| [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. |
-| globus | |
-| [gzip](http://www.gnu.org/software/gzip/) | gzip (GNU zip) is a popular data compression program as a replacement for compress |
-| help2man | |
-| [HPL](http://www.netlib.org/benchmark/hpl/) | HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark. |
-| [Inspector](http://software.intel.com/en-us/intel-inspector-xe) | Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and parallel applications |
-| [itac](http://software.intel.com/en-us/intel-trace-analyzer/) | The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. |
-| [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](https://github.com/RRZE-HPC/likwid) | Toolsuite of command line applications for performance oriented programmers |
-| [Lmod](http://sourceforge.net/projects/lmod/) | Lmod is a Lua based module system. Modules allow for dynamic modification of a user's environment under Unix systems. See www.tacc.utexas.edu/tacc-projects/lmod for a complete description. Lmod is a new implementation that easily handles the MODULEPATH Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly. |
-| MATLAB | |
-| [Mercurial](https://www.mercurial-scm.org/) | Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. |
-| [MIKE](http://www.mikepoweredbydhi.com) | MIKE Powered by DHI is a part of DHI, the global organisation dedicated to solving challenges in water environments worldwide. |
-| [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. |
-| [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. |
-| [parallel](http://savannah.gnu.org/projects/parallel/) | parallel: Build and execute shell commands in parallel |
-| 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. |
-| Scalasca | |
-| Score-P | |
-| [SDE](https://software.intel.com/en-us/articles/intel-software-development-emulator) | Intel Software Development Emulator is a pintool that enables the development of applications using instruction set extensions that are not currently implemented in hardware. |
-| [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 | |
-| [Subversion](http://subversion.apache.org/) | Subversion is an open source version control system. |
-| [Szip](http://www.hdfgroup.org/doc_resource/SZIP/) | Szip compression software, providing lossless compression of scientific data |
-| tcsh | 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. |
-| tmux | |
-| [turbovnc](http://www.turbovnc.org) | TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide peak performance for 3D and video workloads. |
-| [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. |
-| [VirtualGL](http://www.virtualgl.org) | VirtualGL is an open source toolkit that gives any Unix or Linux remote display software the ability to run OpenGL applications with full 3D hardware acceleration. |
-| [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. |
-| [Wine](https://www.winehq.org) | Wine (originally an acronym for "Wine Is Not an Emulator") is a compatibility layer capable of running Windows applications on several POSIX-compliant operating systems, such as Linux, Mac OSX, & BSD. |
-| [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 |
-| [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. |
| [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 |
-| [GPI-2](http://www.gpi-site.com/gpi2/) | GPI-2 is an API for the development of scalable, asynchronous and fault tolerant parallel applications. |
-| [grace](http://freecode.com/projects/grace) | Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. |
-| [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](ftp://ftp.freedesktop.org/pub/mesa/glu/) | The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. |
-| [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. |
-| [libXdamage](http://www.freedesktop.org/wiki/Software/xlibs) | X Damage extension library |
-| [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 |
-| [libXft](http://www.freedesktop.org/wiki/Software/xlibs) | X11 client-side library |
-| [libXinerama](http://www.freedesktop.org/wiki/Software/xlibs) | Xinerama multiple monitor library |
-| [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 | |
| [Mesa](http://www.mesa3d.org/) | Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. |
-| [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. |
-| [OpenDX](http://www.opendx.org) | Open source visualization software package based on IBM's Visualization Data Explorer. |
-| [OSPRay](http://www.ospray.org) | A Ray Tracing Based Rendering Engine for High-Fidelity Visualization |
-| [p4vasp](http://www.p4vasp.at) | p4vasp is a visualization suite for the Vienna Ab-initio Simulation Package (VASP). It contains an extensible GUI framework, that can be used to view material structure, density of states, band-structure and more. |
| [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. |
-| [PyQt](http://www.riverbankcomputing.co.uk/software/pyqt) | PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework. |
-| [SUMO](http://www.sumo.dlr.de/wiki/Main_Page) | Simulation of Urban MObility (SUMO) is an open source, highly portable, microscopic and continuous road traffic simulation package designed to handle large road networks. |
| [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/salomon/job-submission-and-execution.md b/docs.it4i/salomon/job-submission-and-execution.md
index 96c47abd5a62b9a46f6062ac900204880545e595..20fc147e7c43be7a344302dbce663218b65870d1 100644
--- a/docs.it4i/salomon/job-submission-and-execution.md
+++ b/docs.it4i/salomon/job-submission-and-execution.md
@@ -69,6 +69,32 @@ $ qsub -A OPEN-0-0 -I -q qlong -l select=4:ncpus=24:accelerator=True:naccelerat
In this example, we allocate 4 nodes, with 24 cores per node (totalling 96 cores), with 2 Xeon Phi 7120p cards per node (totalling 8 Phi cards), running interactive job for 56 hours. The accelerator model name was omitted.
+#### Intel Xeon Phi - Queue QMIC
+
+Examples executions
+
+```console
+-l select=1
+exec_vnode = (r21u05n581-mic0:naccelerators=1:ncpus=0)
+
+-l select=4
+(r21u05n581-mic0:naccelerators=1:ncpus=0)+(r21u05n581-mic1:naccelerators=1:ncpus=0)+(r21u06n582-mic0:naccelerators=1:ncpus=0)+(r21u06n582-mic1:naccelerators=1:ncpus=0)
+-l select=4:naccelerators=1
+(r21u05n581-mic0:naccelerators=1:ncpus=0)+(r21u05n581-mic1:naccelerators=1:ncpus=0)+(r21u06n582-mic0:naccelerators=1:ncpus=0)+(r21u06n582-mic1:naccelerators=1:ncpus=0)
+
+-l select=1:naccelerators=2
+(r21u05n581-mic0:naccelerators=1+r21u05n581-mic1:naccelerators=1)
+
+-l select=2:naccelerators=2
+(r21u05n581-mic0:naccelerators=1+r21u05n581-mic1:naccelerators=1)+(r21u06n582-mic0:naccelerators=1+r21u06n582-mic1:naccelerators=1)
+
+-l select=1:ncpus=24:naccelerators=2
+(r22u32n610:ncpus=24+r22u32n610-mic0:naccelerators=1+r22u32n610-mic1:naccelerators=1)
+
+-l select=1:ncpus=24:naccelerators=0+4
+(r33u17n878:ncpus=24:naccelerators=0)+(r33u13n874-mic0:naccelerators=1:ncpus=0)+(r33u13n874-mic1:naccelerators=1:ncpus=0)+(r33u16n877-mic0:naccelerators=1:ncpus=0)+(r33u16n877-mic1:naccelerators=1:ncpus=0)
+```
+
### UV2000 SMP
!!! note
diff --git a/docs.it4i/salomon/resource-allocation-and-job-execution.md b/docs.it4i/salomon/resource-allocation-and-job-execution.md
index c960f3871cc94efbaa070eadae51775b00689405..b1ab38d58d926f817537a986d3d912a27f5752ca 100644
--- a/docs.it4i/salomon/resource-allocation-and-job-execution.md
+++ b/docs.it4i/salomon/resource-allocation-and-job-execution.md
@@ -10,6 +10,7 @@ The resources are allocated to the job in a fair-share fashion, subject to const
* **qprod**, the Production queue
* **qlong**, the Long queue
* **qmpp**, the Massively parallel queue
+* **qmic**, the 864 MIC nodes queue
* **qfat**, the queue to access SMP UV2000 machine
* **qfree**, the Free resource utilization queue
diff --git a/docs.it4i/salomon/resources-allocation-policy.md b/docs.it4i/salomon/resources-allocation-policy.md
index b92e2c13071025ba0bd1036949dc906cdc781c7b..9f35d15d069186075ae007daf42d5c3815305552 100644
--- a/docs.it4i/salomon/resources-allocation-policy.md
+++ b/docs.it4i/salomon/resources-allocation-policy.md
@@ -14,8 +14,9 @@ The resources are allocated to the job in a fair-share fashion, subject to const
| **qlong** Long queue | yes | > 0 | 256 nodes, max 40 per job, only non-accelerated nodes allowed | 24 | 0 | no | 72 / 144h |
| **qmpp** Massive parallel queue | yes | > 0 | 1006 nodes | 24 | 0 | yes | 2 / 4h |
| **qfat** UV2000 queue | yes | > 0 | 1 (uv1) | 8 | 0 | yes | 24 / 48h |
-| **qfree** Free resource queue | yes | none required | 752 nodes, max 86 per job | 24 | -1024 | no | 12 / 12h |
+| **qfree** Free resource queue | yes | none required | 752 nodes, max 86 per job | 24 | -1024 | no | 12 / 12h |
| **qviz** Visualization queue | yes | none required | 2 (with NVIDIA Quadro K5000) | 4 | 150 | no | 1 / 8h |
+| **qmic** Intel Xeon Phi cards | yes | > 0 | 864 Intel Xeon Phi cards, max 8 mic per job | 0 | 0 | no | 24 / 48h |
!!! note
**The qfree queue is not free of charge**. [Normal accounting](#resource-accounting-policy) applies. However, it allows for utilization of free resources, once a Project exhausted all its allocated computational resources. This does not apply to Directors Discretion (DD projects) but may be allowed upon request.
@@ -27,6 +28,7 @@ The resources are allocated to the job in a fair-share fashion, subject to const
* **qfat**, the UV2000 queue. This queue is dedicated to access the fat SGI UV2000 SMP machine. The machine (uv1) has 112 Intel IvyBridge cores at 3.3GHz and 3.25TB RAM (8 cores and 128GB RAM are dedicated for system). An PI needs explicitly ask support for authorization to enter the queue for all users associated to her/his Project.
* **qfree**, the Free resource queue: The queue qfree is intended for utilization of free resources, after a Project exhausted all its allocated computational resources (Does not apply to DD projects by default. DD projects have to request for persmission on qfree after exhaustion of computational resources.). It is required that active project is specified to enter the queue, however no remaining resources are required. Consumed resources will be accounted to the Project. Only 178 nodes without accelerator may be accessed from this queue. Full nodes, 24 cores per node are allocated. The queue runs with very low priority and no special authorization is required to use it. The maximum runtime in qfree is 12 hours.
* **qviz**, the Visualization queue: Intended for pre-/post-processing using OpenGL accelerated graphics. Currently when accessing the node, each user gets 4 cores of a CPU allocated, thus approximately 73 GB of RAM and 1/7 of the GPU capacity (default "chunk"). If more GPU power or RAM is required, it is recommended to allocate more chunks (with 4 cores each) up to one whole node per user, so that all 28 cores, 512 GB RAM and whole GPU is exclusive. This is currently also the maximum allowed allocation per one user. One hour of work is allocated by default, the user may ask for 2 hours maximum.
+* **qmic**, the queue qmic to access MIC nodes. It is required that active project with nonzero remaining resources is specified to enter the qmic. All 846 MICs are included.
!!! note
To access node with Xeon Phi co-processor user needs to specify that in [job submission select statement](job-submission-and-execution/).
diff --git a/docs.it4i/software/intel/intel-xeon-phi.anselm.md b/docs.it4i/software/intel/intel-xeon-phi-anselm.md
similarity index 100%
rename from docs.it4i/software/intel/intel-xeon-phi.anselm.md
rename to docs.it4i/software/intel/intel-xeon-phi-anselm.md
diff --git a/docs.it4i/software/intel/intel-xeon-phi.md b/docs.it4i/software/intel/intel-xeon-phi-salomon.md
similarity index 98%
rename from docs.it4i/software/intel/intel-xeon-phi.md
rename to docs.it4i/software/intel/intel-xeon-phi-salomon.md
index 0fc5ccec49d0d52e874f7878993ab05605552f2c..8d6c9c61903b9aaf6d93073a6d338efd2a7c013a 100644
--- a/docs.it4i/software/intel/intel-xeon-phi.md
+++ b/docs.it4i/software/intel/intel-xeon-phi-salomon.md
@@ -551,12 +551,6 @@ First example "CapsBasic" detects OpenCL compatible hardware, here CPU and MIC,
To compile and run the example copy it to your home directory, get a PBS interactive session on of the nodes with MIC and run make for compilation. Make files are very basic and shows how the OpenCL code can be compiled on Salomon.
-```console
-$ cp /apps/intel/opencl-examples/CapsBasic/* .
-$ qsub -I -q qmic -A NONE-0-0
-$ make
-```
-
The compilation command for this example is:
```console
@@ -594,21 +588,6 @@ CL_DEVICE_TYPE_ACCELERATOR[0]
!!! note
More information about this example can be found on Intel website: <http://software.intel.com/en-us/vcsource/samples/caps-basic/>
-The second example that can be found in "/apps/intel/opencl-examples" directory is General Matrix Multiply. You can follow the the same procedure to download the example to your directory and compile it.
-
-```console
-$ cp -r /apps/intel/opencl-examples/* .
-$ qsub -I -q qmic -A NONE-0-0
-$ cd GEMM
-$ make
-```
-
-The compilation command for this example is:
-
-```console
-$ g++ cmdoptions.cpp gemm.cpp ../common/basic.cpp ../common/cmdparser.cpp ../common/oclobject.cpp -I../common -lOpenCL -o gemm -I/apps/intel/opencl/include/
-```
-
To see the performance of Intel Xeon Phi performing the DGEMM run the example as follows:
```console
diff --git a/docs.it4i/software/mic/mic_environment.md b/docs.it4i/software/mic/mic_environment.md
new file mode 100644
index 0000000000000000000000000000000000000000..a3343ca17b08586422c63f95e63864dcbc308309
--- /dev/null
+++ b/docs.it4i/software/mic/mic_environment.md
@@ -0,0 +1,437 @@
+# Intel Xeon Phi Environment
+
+Intel Xeon Phi (so-called MIC) accelerator can be used in several modes ([Offload](../intel/intel-xeon-phi-salomon/#offload-mode) and [Native](#native-mode)). The default mode on the cluster is offload mode, but all modes described in this document are supported.
+
+See sections below for more details.
+
+## Intel Utilities for Xeon Phi
+
+Continue [here](../intel/intel-xeon-phi-salomon/)
+
+## GCC With [KNC](https://en.wikipedia.org/wiki/Xeon_Phi) Support
+
+On Salomon cluster we have module `GCC/5.1.1-knc` with cross-compiled (offload) support. (gcc, g++ and gfortran)
+
+!!! warning
+ Only Salomon cluster.
+
+To compile a code using GCC compiler run following commands
+
+* Create `reduce_mul.c`
+
+```console
+$ vim reduce_mul.c
+```
+
+```c
+#include <immintrin.h>
+
+double reduce(double* values)
+{
+ __m512d val = _mm512_load_pd(values);
+ return _mm512_reduce_mul_pd(val);
+}
+```
+
+* A create `main.c`
+
+```console
+vim main.c
+```
+
+```c
+#include <immintrin.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+double reduce(double* values);
+
+int main(int argc, char* argv[])
+{
+ // Generate random input vector of [-1, 1] values.
+ double values[8] __attribute__((aligned(64)));
+ for (int i = 0; i < 8; i++)
+ values[i] = 2 * (0.5 - rand() / (double)RAND_MAX);
+
+ double vector = reduce(values);
+ double scalar = values[0];
+ for (int i = 1; i < 8; i++)
+ scalar *= values[i];
+
+ printf("%f vs %f\n", vector, scalar);
+
+ fflush(stdout);
+
+ return 0;
+}
+```
+
+* Compile
+
+```console
+$ ml GCC/5.1.1-knc
+$ gcc -mavx512f -O3 -c reduce_mul.c -o reduce_mul.s -S
+$ gcc -O3 -c reduce_mul.s -o reduce_mul.o
+$ gcc -std=c99 -O3 -c main.c -o main_gcc.o
+$ gcc -O3 reduce_mul.o main_gcc.o -o reduce_mul
+```
+
+* To execute the code, run the following command on the host
+
+```console
+$ micnativeloadex ./reduce_mul
+-0.004276 vs -0.004276
+```
+
+## Native Mode
+
+In the native mode a program is executed directly on Intel Xeon Phi without involvement of the host machine. Similarly to offload mode, the code is compiled on the host computer with Intel compilers.
+
+To compile a code user has to be connected to a compute with MIC and load Intel compilers module. To get an interactive session on a compute node with an Intel Xeon Phi and load the module use following commands
+
+```console
+$ qsub -I -q qprod -l select=1:ncpus=24:accelerator=True -A NONE-0-0
+$ ml intel/2017b
+```
+
+To produce a binary compatible with Intel Xeon Phi architecture user has to specify `-mmic` compiler flag. Two compilation examples are shown below. The first example shows how to compile OpenMP parallel code `vect-add.c` for host only
+
+```c
+#include <stdio.h>
+
+typedef int T;
+
+#define SIZE 1000
+
+#pragma offload_attribute(push, target(mic))
+T in1[SIZE];
+T in2[SIZE];
+T res[SIZE];
+#pragma offload_attribute(pop)
+
+// MIC function to add two vectors
+__attribute__((target(mic))) add_mic(T *a, T *b, T *c, int size) {
+ int i = 0;
+ #pragma omp parallel for
+ for (i = 0; i < size; i++)
+ c[i] = a[i] + b[i];
+}
+
+// CPU function to add two vectors
+void add_cpu (T *a, T *b, T *c, int size) {
+ int i;
+ for (i = 0; i < size; i++)
+ c[i] = a[i] + b[i];
+}
+
+// CPU function to generate a vector of random numbers
+void random_T (T *a, int size) {
+ int i;
+ for (i = 0; i < size; i++)
+ a[i] = rand() % 10000; // random number between 0 and 9999
+}
+
+// CPU function to compare two vectors
+int compare(T *a, T *b, T size ){
+ int pass = 0;
+ int i;
+ for (i = 0; i < size; i++){
+ if (a[i] != b[i]) {
+ printf("Value mismatch at location %d, values %d and %dn",i, a[i], b[i]);
+ pass = 1;
+ }
+ }
+ if (pass == 0) printf ("Test passedn"); else printf ("Test Failedn");
+ return pass;
+}
+
+int main()
+{
+ int i;
+ random_T(in1, SIZE);
+ random_T(in2, SIZE);
+
+ #pragma offload target(mic) in(in1,in2) inout(res)
+ {
+
+ // Parallel loop from main function
+ #pragma omp parallel for
+ for (i=0; i<SIZE; i++)
+ res[i] = in1[i] + in2[i];
+
+ // or parallel loop is called inside the function
+ add_mic(in1, in2, res, SIZE);
+
+ }
+
+ //Check the results with CPU implementation
+ T res_cpu[SIZE];
+ add_cpu(in1, in2, res_cpu, SIZE);
+ compare(res, res_cpu, SIZE);
+
+}
+```
+
+```console
+$ icc -xhost -no-offload -fopenmp vect-add.c -o vect-add-host
+```
+
+* To run this code on host, use
+
+```console
+$ ./vect-add-host
+Test passed
+```
+
+* The second example shows how to compile the same code for Intel Xeon Phi
+
+```console
+$ icc -mmic -fopenmp vect-add.c -o vect-add-mic
+```
+
+* Execution of the Program in Native Mode on Intel Xeon Phi
+
+The user access to the Intel Xeon Phi is through the SSH. Since user home directories are mounted using NFS on the accelerator, users do not have to copy binary files or libraries between the host and accelerator. Get the PATH of MIC enabled libraries for currently used Intel Compiler.
+
+* To run this code on Intel Xeon Phi
+
+```console
+$ ssh mic0
+$ ./vect-add-mic
+./vect-add-mic: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory
+$ export LD_LIBRARY_PATH=LD_LIBRARY_PATH:/apps/all/icc/2017.4.196-GCC-6.4.0-2.28/compilers_and_libraries/linux/lib/mic
+$ ./vect-add-mic
+Test passed
+```
+
+!!! tip
+ Or use the procedure from the chapter [Devel Environment](#devel-environment).
+
+## Only Intel Xeon Phi Cards
+
+Execute native job
+
+```console
+$ qsub -A NONE-0-0 -q qmic -l select=1 -l walltime=10:00:00 -I
+r21u01n577-mic1:~$
+```
+
+## Devel Environment
+
+To get an overview of the currently loaded modules, use `module list` or `ml` (without specifying extra arguments).
+
+```console
+r21u02n578-mic0:~$ ml
+No modules loaded
+```
+
+To get an overview of all available modules, you can use `ml avail` or simply `ml av`
+
+```console
+r21u02n578-mic0:~$ ml av
+
+-------------- /apps/phi/system/devel --------------------------
+ devel_environment/1.0 (S)
+
+ Where:
+ S: Module is Sticky, requires --force to unload or purge
+
+```
+
+Activate devel environment
+
+```console
+r21u02n578-mic0:~$ ml devel_environment
+```
+
+And again to get an overview of all available modules, you can use `ml avail` or simply `ml av`
+
+```console
+r21u02n578-mic0:~$ ml av
+
+-------------- /apps/phi/modules/compiler --------------------------
+ icc/2017.4.196-GCC-6.4.0-2.28
+
+-------------- /apps/phi/modules/devel --------------------------
+ M4/1.4.18 devel_environment/1.0 (S) ncurses/6.0
+
+-------------- /apps/phi/modules/lang --------------------------
+ Bison/3.0.4 Tcl/8.6.6 flex/2.6.4
+
+-------------- /apps/phi/modules/lib --------------------------
+ libreadline/7.0 zlib/1.2.11
+
+-------------- /apps/phi/modules/math --------------------------
+ Octave/3.8.2
+
+-------------- /apps/phi/modules/mpi --------------------------
+ impi/2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28
+
+-------------- /apps/phi/modules/toolchain --------------------------
+ iccifort/2017.4.196-GCC-6.4.0-2.28 ifort/2017.4.196-GCC-6.4.0-2.28
+
+-------------- /apps/phi/modules/tools --------------------------
+ bzip2/1.0.6 cURL/7.53.1 expat/2.2.5
+
+-------------- /apps/phi/modules/vis --------------------------
+ gettext/0.19.8
+
+ Where:
+ S: Module is Sticky, requires --force to unload or purge
+
+```
+
+After load module `devel_environment` are available modules for architecture k1om-mpss-linux and now exists systems software (gcc, cmake, make, git, htop, vim, ...).
+
+* Example
+
+```console
+r21u02n578-mic0:~$ gcc --version
+gcc (GCC) 5.1.1
+Copyright (C) 2015 Free Software Foundation, Inc.
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+@r21u02n578-mic0:~$ cmake --version
+cmake version 2.8.7
+
+r21u02n578-mic0:~$ git --version
+git version 1.7.7
+
+r21u02n578-mic0:~$ make --version
+GNU Make 3.82
+Built for k1om-mpss-linux-gnu
+Copyright (C) 2010 Free Software Foundation, Inc.
+License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
+This is free software: you are free to change and redistribute it.
+There is NO WARRANTY, to the extent permitted by law.
+
+r21u02n578-mic0:~$ perl --version
+
+This is perl 5, version 14, subversion 2 (v5.14.2) built for k1om-linux
+
+Copyright 1987-2011, Larry Wall
+
+Perl may be copied only under the terms of either the Artistic License or the
+GNU General Public License, which may be found in the Perl 5 source kit.
+
+Complete documentation for Perl, including FAQ lists, should be found on
+this system using "man perl" or "perldoc perl". If you have access to the
+Internet, point your browser at http://www.perl.org/, the Perl Home Page.
+
+...
+```
+
+* Execute previous cross-compiled code `vect-add-mic`
+
+```console
+r21u01n577-mic1:~$ ml devel_environment
+r21u01n577-mic1:~$ ml icc
+r21u01n577-mic1:~$ ./vect-add-mic
+Test passed
+```
+
+!!! tip
+ PATH of MIC libraries for Intel Compiler set automatically.
+
+## Modules
+
+Examples for modules.
+
+### MPI
+
+Load module for devel environment `devel_environment` and load mpi module `impi/2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28` (intel/2017b)
+
+Execute test
+
+```console
+$ qsub -A SERVICE -q qmic -l select=4 -l walltime=01:00:00 -I
+r21u01n577-mic0:~$ ml devel_environment
+r21u01n577-mic0:~$ ml impi
+r21u01n577-mic0:~$ ml
+
+Currently Loaded Modules:
+ 1) devel_environment/1.0 (S) 3) ifort/2017.4.196-GCC-6.4.0-2.28 5) impi/2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28
+ 2) icc/2017.4.196-GCC-6.4.0-2.28 4) iccifort/2017.4.196-GCC-6.4.0-2.28
+
+ Where:
+ S: Module is Sticky, requires --force to unload or purge
+r21u01n577-mic0:~$ mpirun -n 244 hostname | sort | uniq -c | sort -n
+ 61 r21u01n577-mic0
+ 61 r21u01n577-mic1
+ 61 r21u02n578-mic0
+ 61 r21u02n578-mic1
+r21u01n577-mic0:~$ mpirun -n 976 hostname | sort | uniq -c | sort -n
+ 244 r21u01n577-mic0
+ 244 r21u01n577-mic1
+ 244 r21u02n578-mic0
+ 244 r21u02n578-mic1
+r21u01n577-mic0:~$ mpirun hostname | sort | uniq -c | sort -n
+ 1 r21u01n577-mic0
+ 1 r21u01n577-mic1
+ 1 r21u02n578-mic0
+ 1 r21u02n578-mic1
+```
+
+!!! warning
+ Modules icc, ifort and iccifort are only libraries and headers, not compilers... For compile use the procedure from the chapter [Native Mode](#native-mode)
+
+### Octave/3.8.2
+
+Load module for devel environment `devel_environment`, load module `Octave/3.8.2` and run test
+
+```console
+r21u01n577-mic0:~$ ml devel_environment
+r21u01n577-mic0:~$ ml Octave/3.8.2
+r21u01n577-mic0:~$ octave -q /apps/phi/software/Octave/3.8.2/example/test0.m
+warning: docstring file '/apps/phi/software/Octave/3.8.2/share/octave/3.8.2/etc/built-in-docstrings' not found
+warning: readline is not linked, so history control is not available
+Use some basic operators ...
+Work with some small matrixes ...
+Save matrix to file ...
+Load matrix from file ...
+Display matrix ...
+m3 =
+
+ 39.200 19.600 39.200
+ 58.800 117.600 156.800
+ 254.800 411.600 686.000
+
+Work with some big matrixes ...
+Sum ...
+Multiplication ...
+r21u01n577-mic0:~$ cat test.mat
+# Created by Octave 3.8.2, Thu Dec 07 11:11:09 2017 CET <kru0052@r21u01n577-mic0>
+# name: m3
+# type: matrix
+# rows: 3
+# columns: 3
+ 39.2 19.6 39.2
+ 58.8 117.6 156.8
+ 254.8 411.6 686
+```
+
+## Native Build Software With Devel Environment
+
+Compiler
+
+* gcc (GCC) 5.1.1 **without** gfortran support
+
+Architecture (depends on compiled software):
+
+* k1om-unknown-linux-gnu
+* k1om-mpss-linux-gnu
+* x86_64-k1om-linux
+* k1om-mpss-linux
+
+Configure step (for `configure`,`make` and `make install` software)
+
+* specify architecture `--build=`
+
+```console
+./configure --prefix=/apps/phi/software/ncurses/6.0 --build=k1om-mpss-linux
+```
+
+Modulefile and Lmod
+
+* Read [Lmod](../modules/lmod/)
diff --git a/mkdocs.yml b/mkdocs.yml
index a26ec4bf0607c6f091cf7a8aeeb15e2e0a3ada9e..e0f3310ef4631d7adbd3375659d9201d978f80f8 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -61,9 +61,11 @@ pages:
- Software:
- Modules:
- Lmod Environment: software/modules/lmod.md
+ - Intel Xeon Phi Environment: software/mic/mic_environment.md
- Modules Matrix: modules-matrix.md
- Available Salomon Modules: modules-salomon.md
- Available Salomon Modules on UV: modules-salomon-uv.md
+ - Available Salomon Modules on PHI Cards: modules-salomon-phi.md
- Available Anselm Modules: modules-anselm.md
- ISV Licenses: software/isv_licenses.md
- Bioinformatics:
@@ -110,8 +112,8 @@ pages:
- Intel TBB: software/intel/intel-suite/intel-tbb.md
- Intel Trace Analyzer and Collector: software/intel/intel-suite/intel-trace-analyzer-and-collector.md
- Intel Xeon Phi:
- - Intel Xeon Phi Salomon: software/intel/intel-xeon-phi.md
- - Intel Xeon Phi Anselm: software/intel/intel-xeon-phi.anselm.md
+ - Intel Xeon Phi Salomon: software/intel/intel-xeon-phi-salomon.md
+ - Intel Xeon Phi Anselm: software/intel/intel-xeon-phi-anselm.md
- Machine Learning:
- Introduction: software/machine-learning/introduction.md
- TensorFlow: software/machine-learning/tensorflow.md
diff --git a/scripts/get_cvs.sh b/scripts/get_cvs.sh
index 92e50152df10eb9aed365e204237312fbf58b412..703af83ef4e0e0e28942f250927db5e0517ab735 100755
--- a/scripts/get_cvs.sh
+++ b/scripts/get_cvs.sh
@@ -2,3 +2,4 @@
curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/anselm.csv -o modules-anselm.csv
curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/salomon.csv -o modules-salomon.csv
curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/uv2000.csv -o modules-salomon-uv.csv
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/phi.csv -o modules-salomon-phi.csv
diff --git a/scripts/get_modules.sh b/scripts/get_modules.sh
index 8e9a985479b871249ac26d8a81be70ed0a13a9b9..bade433dacc2632b0fb12cad3e606f5340edd70f 100755
--- a/scripts/get_modules.sh
+++ b/scripts/get_modules.sh
@@ -2,6 +2,8 @@
curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/anselm.md -o docs.it4i/modules-anselm.md
curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/salomon.md -o docs.it4i/modules-salomon.md
curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/uv2000.md -o docs.it4i/modules-salomon-uv.md
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/phi.md -o docs.it4i/modules-salomon-phi.md
curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/anselm.csv -o scripts/modules-anselm.csv
curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/salomon.csv -o scripts/modules-salomon.csv
curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/uv2000.csv -o scripts/modules-salomon-uv.csv
+curl -s https://code.it4i.cz/sccs/it4i-modules/raw/master/phi.csv -o scripts/modules-salomon-phi.csv
diff --git a/scripts/modules-json.py b/scripts/modules-json.py
index f5abe70efbc797b62ec0f642bc11d29351e0ab6c..57474110d6e3271443fc895a48a1283569aeb427 100755
--- a/scripts/modules-json.py
+++ b/scripts/modules-json.py
@@ -9,7 +9,7 @@ def get_data(filename):
'''function to read the data form the input csv file to use in the analysis'''
reader = [] # Just in case the file open fails
with open(filename, 'rb') as f:
- reader = csv.reader(f,delimiter=',')
+ reader = csv.reader(f,delimiter=',')
#returns all the data from the csv file in list form
#f.close() # May need to close the file when done
return list(reader) # only return the reader when you have finished.
@@ -63,5 +63,5 @@ packages = {}
for m in sorted(software.items(), key=lambda i: i[0].lower()):
packages[m[0]]=sorted(m[1], key=LooseVersion)[len(m[1])-1]
-data = {'total': len(packages), 'projects': packages }
+data = {'total': len(packages), 'projects': packages }
print json.dumps(data)
diff --git a/scripts/modules-matrix.py b/scripts/modules-matrix.py
index eab86f22b7953ab637699f35c7b441bb7038c0d6..d84745504d38a8225cce36fe834bbfea56d2fa41 100755
--- a/scripts/modules-matrix.py
+++ b/scripts/modules-matrix.py
@@ -8,7 +8,7 @@ def get_data(filename):
'''function to read the data form the input csv file to use in the analysis'''
reader = [] # Just in case the file open fails
with open(filename, 'rb') as f:
- reader = csv.reader(f,delimiter=',')
+ reader = csv.reader(f,delimiter=',')
#returns all the data from the csv file in list form
#f.close() # May need to close the file when done
return list(reader) # only return the reader when you have finished.
diff --git a/todelete b/todelete
deleted file mode 100644
index b42e29bda03bfe0d52ee37f5493b08f4938c2208..0000000000000000000000000000000000000000
--- a/todelete
+++ /dev/null
@@ -1,83 +0,0 @@
-docs.it4i/anselm/software/numerical-languages/introduction.md
-docs.it4i/anselm/software/numerical-languages/matlab.md
-docs.it4i/anselm/software/numerical-languages/matlab_1314.md
-docs.it4i/anselm/software/numerical-languages/octave.md
-docs.it4i/anselm/software/numerical-languages/r.md
-docs.it4i/salomon/software/comsol/licensing-and-available-versions.md
-docs.it4i/salomon/software/java.md
-docs.it4i/salomon/software/numerical-languages/introduction.md
-docs.it4i/salomon/software/numerical-languages/matlab.md
-docs.it4i/salomon/software/numerical-languages/octave.md
-docs.it4i/salomon/software/numerical-languages/opencoarrays.md
-docs.it4i/salomon/software/numerical-languages/r.md
-./docs.it4i/anselm/software/ansys/ansys-cfx.md
-./docs.it4i/anselm/software/ansys/ansys-fluent.md
-./docs.it4i/anselm/software/ansys/ansys-ls-dyna.md
-./docs.it4i/anselm/software/ansys/ansys-mechanical-apdl.md
-./docs.it4i/anselm/software/ansys/ansys.md
-./docs.it4i/anselm/software/ansys/ls-dyna.md
-./docs.it4i/salomon/software/ansys/ansys-cfx.md
-./docs.it4i/salomon/software/ansys/ansys-fluent.md
-./docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
-./docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
-./docs.it4i/salomon/software/ansys/ansys.md
-./docs.it4i/salomon/software/ansys/licensing.md
-./docs.it4i/salomon/software/ansys/setting-license-preferences.md
-./docs.it4i/salomon/software/ansys/workbench.md
-./docs.it4i/anselm/software/machine-learning/introduction.md
-./docs.it4i/anselm/software/machine-learning/tensorflow.md
-./docs.it4i/salomon/software/machine-learning/introduction.md
-./docs.it4i/salomon/software/machine-learning/tensorflow.md
-./docs.it4i/anselm/software/debuggers
-./docs.it4i/anselm/software/debuggers/allinea-ddt.md
-./docs.it4i/anselm/software/debuggers/allinea-performance-reports.md
-./docs.it4i/anselm/software/debuggers/cube.md
-./docs.it4i/anselm/software/debuggers/debuggers.md
-./docs.it4i/anselm/software/debuggers/intel-performance-counter-monitor.md
-./docs.it4i/anselm/software/debuggers/intel-vtune-amplifier.md
-./docs.it4i/anselm/software/debuggers/papi.md
-./docs.it4i/anselm/software/debuggers/scalasca.md
-./docs.it4i/anselm/software/debuggers/score-p.md
-./docs.it4i/anselm/software/debuggers/total-view.md
-./docs.it4i/anselm/software/debuggers/valgrind.md
-./docs.it4i/anselm/software/debuggers/vampir.md
-./docs.it4i/salomon/software/debuggers
-./docs.it4i/salomon/software/debuggers/Introduction.md
-./docs.it4i/salomon/software/debuggers/aislinn.md
-./docs.it4i/salomon/software/debuggers/allinea-ddt.md
-./docs.it4i/salomon/software/debuggers/allinea-performance-reports.md
-./docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md
-./docs.it4i/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.html
-./docs.it4i/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.txt
-./docs.it4i/salomon/software/debuggers/total-view.md
-./docs.it4i/salomon/software/debuggers/valgrind.md
-./docs.it4i/salomon/software/debuggers/vampir.md
-./docs.it4i/anselm/software/numerical-libraries
-./docs.it4i/anselm/software/numerical-libraries/fftw.md
-./docs.it4i/anselm/software/numerical-libraries/gsl.md
-./docs.it4i/anselm/software/numerical-libraries/hdf5.md
-./docs.it4i/anselm/software/numerical-libraries/intel-numerical-libraries.md
-./docs.it4i/anselm/software/numerical-libraries/magma-for-intel-xeon-phi.md
-./docs.it4i/anselm/software/numerical-libraries/petsc.md
-./docs.it4i/anselm/software/numerical-libraries/trilinos.md
-./docs.it4i/anselm/software/intel-suite
-./docs.it4i/anselm/software/intel-suite/intel-compilers.md
-./docs.it4i/anselm/software/intel-suite/intel-debugger.md
-./docs.it4i/anselm/software/intel-suite/intel-integrated-performance-primitives.md
-./docs.it4i/anselm/software/intel-suite/intel-mkl.md
-./docs.it4i/anselm/software/intel-suite/intel-tbb.md
-./docs.it4i/anselm/software/intel-suite/introduction.md
-./docs.it4i/salomon/software/intel-suite
-./docs.it4i/salomon/software/intel-suite/intel-advisor.md
-./docs.it4i/salomon/software/intel-suite/intel-compilers.md
-./docs.it4i/salomon/software/intel-suite/intel-debugger.md
-./docs.it4i/salomon/software/intel-suite/intel-inspector.md
-./docs.it4i/salomon/software/intel-suite/intel-integrated-performance-primitives.md
-./docs.it4i/salomon/software/intel-suite/intel-mkl.md
-./docs.it4i/salomon/software/intel-suite/intel-parallel-studio-introduction.md
-./docs.it4i/salomon/software/intel-suite/intel-tbb.md
-./docs.it4i/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
-./docs.it4i/anselm/software/paraview.md
-./docs.it4i/anselm/software/compilers.md
-./docs.it4i/salomon/software/compilers.md
-./docs.it4i/salomon/software/paraview.md