Merge branch 'gajdusek_clean' into 'master'

Gajdusek clean

See merge request !166

docs.it4i/anselm/storage.md

@@ -251,7 +251,7 @@ other::---
 
 Default ACL mechanism can be used to replace setuid/setgid permissions on directories. Setting a default ACL on a directory (-d flag to setfacl) will cause the ACL permissions to be inherited by any newly created file or subdirectory within the directory. Refer to this page for more information on Linux ACL:
 
-[http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html](http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
+[redhat guide](https://access.redhat.com/documentation/en-US/Red_Hat_Storage/2.0/html/Administration_Guide/ch09s05.html)
 
 ## Local Filesystems
 

docs.it4i/modules-anselm.md

@@ -96,7 +96,7 @@
 | [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](http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html) | The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. |
+| makedepend | The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. |
 | 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. |
@@ -371,7 +371,7 @@
 | Lmod |   |
 | MATLAB |   |
 | memoryscape |   |
-| [Mercurial](http://mercurial.selenic.com/) | Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. |
+| [Mercurial](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 |   |
 | MIKE |   |
 | mono |   |
@@ -398,7 +398,7 @@
 | [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 |
 | tcl |   |
-| [tcsh](http://www.tcsh.org) | Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. |
+| 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. |
 | tk |   |
 | tmux |   |
 | totalview |   |

docs.it4i/modules-salomon-uv.md

@@ -19,7 +19,7 @@
 
 | Module | Description |
 | -------| ----------- |
-| [ABINIT](http://www.abinit.org/) | Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT. |
+| [ABINIT](https://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. |
 
@@ -146,12 +146,12 @@
 | [gzip](http://www.gnu.org/software/gzip/) | gzip (GNU zip) is a popular data compression program as a replacement for compress |
 | help2man |   |
 | MATLAB |   |
-| [Mercurial](http://mercurial.selenic.com/) | Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. |
+| [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. |
 | [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. |
 | [Szip](http://www.hdfgroup.org/doc_resource/SZIP/) | Szip compression software, providing lossless compression of scientific data |
-| [tcsh](http://www.tcsh.org) | Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. |
+| [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. |
 | [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 |   |

docs.it4i/modules-salomon.md

@@ -42,7 +42,7 @@
 
 | Module | Description |
 | ------ | ----------- |
-| [ABINIT](http://www.abinit.org/) | Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT. |
+| [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. |
@@ -53,7 +53,7 @@
 | [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](http://infochim.u-strasbg.fr/spip.php?rubrique152) | S4MPLE (Sampler For Multiple Protein-Ligand Entities) is a flexible molecular modeling tool, supporting empirical force field-driven conformational sampling and geometry optimization heuristics using a hybrid genetic algorithm (GA). |
+| 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 |
 
@@ -111,7 +111,7 @@
 | [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](http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html) | The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. |
+| 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. |
@@ -323,7 +323,7 @@
 | [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](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](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. |
@@ -338,7 +338,7 @@
 | 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](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. |
+| 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 |

docs.it4i/salomon/storage.md

@@ -222,7 +222,7 @@ other::---
 
 Default ACL mechanism can be used to replace setuid/setgid permissions on directories. Setting a default ACL on a directory (-d flag to setfacl) will cause the ACL permissions to be inherited by any newly created file or subdirectory within the directory. Refer to this page for more information on Linux ACL:
 
-[http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html](http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
+[redhat guide](https://access.redhat.com/documentation/en-US/Red_Hat_Storage/2.0/html/Administration_Guide/ch09s05.html)
 
 ## Shared Workspaces
 

docs.it4i/software/csc.md

+# CSharp
+
+C# is available on the cluster. Activate C# by loading the Mono module:
+
+```console
+$ ml Mono
+```
+
+## Examples
+
+### Hello World
+
+Copy this code to new file hello.cs:
+
+```csc
+using System;
+
+class HelloWorld {
+  static void Main() {
+    Console.WriteLine("Hello world!!!");
+  }
+}
+```
+
+Compile the program and make *Windows executable*.
+
+```console
+$ mcs -out:hello.exe hello.cs
+```
+
+Now run the program:
+
+```console
+$ mono hello.exe
+Hello world!!!
+```
+
+### Interactive Console
+
+Type:
+
+```console
+$ csharp
+Mono C# Shell, type "help;" for help
+
+Enter statements below.
+csharp>
+```
+
+Now you are in interactive mode. You can try following example.
+
+```csc
+csharp> using System;
+csharp> int a = 5;
+csharp> double b = 1.5;
+csharp> Console.WriteLine("{0}*{1} is equal to {2}", a,b,a*b);
+5*1.5 is equal to 7.5
+csharp> a == b
+false
+```
+
+Show all files modified in last 5 days:
+```csc
+csharp> using System.IO;
+csharp> from f in Directory.GetFiles ("mydirectory")
+      > let fi = new FileInfo (f)
+      > where fi.LastWriteTime > DateTime.Now-TimeSpan.FromDays(5) select f;
+{ "mydirectory/mynewfile.cs", "mydirectory/script.sh" }
+```
+
+## MPI.NET
+
+MPI is available for mono.
+
+```csc
+using System;
+using MPI;
+
+class MPIHello
+{
+    static void Main(string[] args)
+    {
+        using (new MPI.Environment(ref args))
+        {
+           Console.WriteLine("Greetings from node {0} of {1} running on {2}",
+           Communicator.world.Rank, Communicator.world.Size,
+           MPI.Environment.ProcessorName);
+        }
+    }
+}
+```
+
+Compile and run the program on Anselm:
+
+```console
+$ qsub -I -A DD-13-5 -q qexp -l select=2:ncpus=16,walltime=00:30:00
+
+$ ml mpi.net
+
+$ mcs -out:csc.exe -reference:/apps/tools/mpi.net/1.0.0-mono-3.12.1/lib/MPI.dll csc.cs
+
+$ mpirun -n 4 mono csc.exe
+Greetings from node 2 of 4 running on cn204
+Greetings from node 0 of 4 running on cn204
+Greetings from node 3 of 4 running on cn199
+Greetings from node 1 of 4 running on cn199
+```
+
+For more informations look at [Mono documentation page](http://www.mono-project.com/docs/).

docs.it4i/software/debuggers/intel-vtune-amplifier.md

@@ -89,6 +89,5 @@ You can obtain this command line by pressing the "Command line..." button on Ana
 
 ## References
 
-1. [Performance Tuning for Intel® Xeon Phi™ Coprocessors](https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf)
 1. [Intel® VTune™ Amplifier Support](https://software.intel.com/en-us/intel-vtune-amplifier-xe-support/documentation)
 1. [https://software.intel.com/en-us/amplifier_help_linux](https://software.intel.com/en-us/amplifier_help_linux)

mkdocs.yml

@@ -138,6 +138,7 @@ pages:
       - Trilinos: software/numerical-libraries/trilinos.md
     - 'Programming Languages':
       - Java: software/java.md
+      - C#: software/csc.md
     - 'Phys':
       - LMGC90: salomon/software/phys/LMGC90.md
     - 'Tools':