HPC - User contributions [en-gb]

Training/Getting Connected

2017-08-16T09:30:32Z

MSummerbell: /* Connecting to Viper from a Windows PC */

__TOC__
==Introduction==
You'll need to make a secure remote connection from your local computer to Viper.
To use Viper off campus a VPN is required. For more information of working remotely on Viper please visit [[Training/Working Remotely on Viper|Working Remotely on Viper]]

==Connecting to Viper from a Windows PC==
Connecting to Viper from a Windows PC can be achieved by a number of different applications. One listed here is 'MobaXterm'

Download and install [http://mobaxterm.mobatek.net/ MobaXterm from the website], ensuring you comply with the license agreement stated.

{|
|style="width:5%; border-width: 0" | [[File:icon_exclam1.png]]
|style="width:95%; border-width: 0" | Note: On University imaged PCs only the portable version of MobaXterm is compatable
|-
|}

1. Launch MobaXterm

2. Click 'Session'

[[File:Session.JPG|none]]

3. Select the 'SSH' type connection
[[File:moba_ssh.JPG|none]]
4. Enter the Remote host: viper.hull.ac.uk
[[File:Moba_remotehost.JPG|none]]
5. Enter your Username (University User ID)
[[File:moba_username.JPG|none]]
6. Click OK

7. A terminal window will appear, enter your password followed by ''enter'', this will not be echoed to the screen
[[File:moba_password.JPG|none]]

==Connecting to Viper from an Apple Mac==
1. Go to Applications -> Utilities and open Terminal

2. Type 'ssh -Y <''yourusername''>@viper.hull.ac.uk

3. The first time you connect to Viper, a message asks if you want to continue connecting. This message appears because Viper has an RSA key that is not stored in your system registry/keychain, the identity of which cannot be verified. Type 'yes' and press ''enter''.

4. Enter your password followed by ''enter'' this will not be echoed to the screen.

[[File:mac_getting_connected2.png]]

==Connecting to Viper from a Linux Computer==
1. Open a Terminal application

2. Type ssh -Y <''yourusername''>@viper.hull.ac.uk

3. The first time you connect to Viper, a message asks if you want to continue connecting. This message appears because Viper has an RSA key that is not stored in your system registry/keychain, the identity of which cannot be verified. Type 'yes' and press ''enter''.

4. Enter your password followed by ''enter'', this will not be echoed to the screen

[[File:linux_getting_connected.jpg]]

General/Visualisation Nodes

2017-07-26T08:02:01Z

MSummerbell: /* X2go */

== Introduction ==
There are two visualisation nodes on Viper, visu01.hpc.hull.ac.uk and visu02.hpc.hull.ac.uk each with dual NVidia GeForce GTX 980 Ti graphics cards.

There are two main ways of using the visualisation nodes, X2go or VNC. VNC will tend to provide better performance on a fast network (i.e. when connected directly to the university network) while X2go will provide better performance on lower bandwidth connections (i.e. connecting remotely via the VPN).
{|
|style="width:5%; border-width: 0" | [[File:icon_warning.png]]
|style="width:95%; border-width: 0" | Please note if you are using X2go off campus you must be connected to the university VPN.
|-
|}
=== Usage Example ===
A typical work flow to use the visualisation nodes is as follows:

==== VNC ====
* SSH into one of the visualisation nodes with X11 forwarding [ ]
* [[General/Visualisation_Nodes#vnc-start|Start a VNC session]]
* [[General/Visualisation_Nodes#vnc-viewer|Connect to the VNC session]]
* ''In VNC Session:'' [[General/Visualisation_Nodes#MATE_Desktop|Start a terminal in the VNC session and load the relevant application module]]
* ''In VNC Session:'' [[General/Visualisation_Nodes#VirtualGL|Start the application using VirtualGL]]
* ''In VNC Session:'' Close application
* Disconnect from VNC session
* [[General/Visualisation_Nodes#vnc-stop|Stop running VNC session]]

==== X2go ====
* Connect to visu01.hpc.hull.ac.uk
* [[General/Visualisation_Nodes#MATE_Desktop|Start a terminal in the VNC session and load the relevant application module]]
* [[General/Visualisation_Nodes#VirtualGL|Start the application using VirtualGL]]

== Connecting to the Visualisation Nodes ==
=== VNC ===
==== vnc-start ====
The first time you start a VNC session, you will be prompted to set a VNC password,. This is not linked to your university credentials, but should follow standard security advice so that it is a complex password. You will need this password to connect to future VNC sessions.

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">[username@rvisu01 ~]$ vnc-start

You will require a password to access your desktops.

Password:
Verify:
Would you like to enter a view-only password (y/n)? n

Desktop 'TurboVNC: rvisu01:3 (username)' started on display rvisu01:3

Starting applications specified in /home/username/.vnc/xstartup.turbovnc
Log file is /home/username/.vnc/rvisu01:3.log
</pre>

If you forget the password you set, you will need to stop your running VNC session (see vnc-stop) then delete the directory ~/.vnc and run vnc-start again to set a new password.

When you next start a session you will see a message to say which session you have open:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@rvisu01 ~]$ vnc-start

Desktop 'TurboVNC: rvisu01:3 (username)' started on display rvisu01:3

Starting applications specified in /home/username/.vnc/xstartup.turbovnc
Log file is /home/username/.vnc/rvisu01:3.log
</pre>

If you try and start a session while you have an existing session open, you will see the following message:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@rvisu01 ~]$ vnc-start
Please use the existing VNC session available on rvisu01:3
</pre>

==== vnc-check ====
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@rvisu01 ~]$ vnc-check
username rvisu01:3
</pre>

==== vnc-stop ====
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@rvisu01 ~]$ vnc-stop
Terminating VNC session on localhost:3
Killing Xvnc process ID 4718
</pre>

==== vnc-viewer ====
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@rvisu01 ~]$ vnc-viewer
Opening VNC session on localhost:3
libjawt.so path: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.77-0.b03.el7_2.x86_64/jre/lib/amd64
CConn: connected to host localhost port 5903
CConnection: Server supports RFB protocol version 3.8
CConnection: Using RFB protocol version 3.8
</pre>

You should then see a new window open titled "Standard VNC Authentication [VncAuth]@rvisu01" with a password prompt. Enter your VNC password (not your university credentials) and you should then see a MATE desktop.

=== X2go ===
(Currently only available on visu01.hpc.hull.ac.uk )

* In the "Session" tab:
** In "Session name:" to visu01.hpc.hull.ac.uk
** In "Host:" enter visu01.hpc.hull.ac.uk
** In "Login:" enter your username
** Select '''Session type''' to MATE (or custom desktop with command MATE)
* In the "Connection" tab
** When connecting from a university connection, set connection speed to LAN for best performance
** When connecting from outside the university ADSL should be adequate
* In the "Media" tab
** Uncheck the "Enable sound support" box
** Uncheck the "Client side printing support" box

There are two main ways to use X2go, which are configured in the "Session" tab by using "Session type"

====X2Go macOS====
For info on using X2Go on macOS visit: [[Training/X2Go macOS| X2Go macOS]]

==== xterm ====
To use a standard xterm terminal, in the "Session type" drop down menu select "Single application" and set command to /usr/bin/xterm

==== Full Desktop Environment ====
To use a full desktop environment, in "Session type" drop down menu select MATE. See further information about the MATE desktop environment below.

== MATE Desktop ==
The MATE desktop environment, based on the popular GNOME2 environment and is available in both VNC and X2go. MATE is a relatively lightweight desktop environment.

[[File:MATEdesktop.png]]

When connected to your MATE session, start a terminal by either going to '''Applications > System Tools > MATE Terminal''' or '''Applications > System Tools > XTerm''' at the top of the screen, or using the black icon on the task bar at the top of the screen.

Note: If you leave your desktop session inactive for a period of time, the screen will lock. To open this you need to use your normal university credentials

Note: While the MATE desktop contains applications such as Firefox and PDF viewer, these are only available to support research use of visualisation tools and the visualisation nodes should not be used as a desktop replacement.

== NVidia SMI ==
The command ''nvidia-smi'' can be used to see what is currently running on each of the GPU cards on the visualisation nodes. The nvidia-smi command can be used to access all sorts of information about the GPU cards, but just running the command with no options will provide basic information about the utilisation of each card:

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@rvisu01 ~]$ nvidia-smi
Mon Feb 13 12:46:42 2017
+------------------------------------------------------+
| NVIDIA-SMI 361.42 Driver Version: 361.42 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
|===============================+======================+======================|
| 0 GeForce GTX 980 Ti Off | 0000:02:00.0 Off | N/A |
| 22% 49C P0 79W / 250W | 5662MiB / 6143MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
| 1 GeForce GTX 980 Ti Off | 0000:82:00.0 Off | N/A |
| 22% 26C P8 15W / 250W | 28MiB / 6143MiB | 0% Default |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
| GPU PID Type Process name Usage |
|=============================================================================|
| 0 1206 G .../9.2.0/bin/arch-LinuxAMD64-Optimize/Avizo 5530MiB |
| 0 2785 G /usr/bin/X 46MiB |
| 0 12468 G ....1/bin/arch-LinuxAMD64-Optimize/AvizoLite 46MiB |
| 1 2785 G /usr/bin/X 6MiB |
+-----------------------------------------------------------------------------+
</pre>

== Virtual GL ==
With VirtualGL, OpenGL commands and 3D data are redirected to a 3D graphics accelerator (each visualisation node has 2x Nvidia GTX 980Ti) before the rendered 3D images are sent to the client machine.

=== vglrun ===
Using the nvidia-smi command you can see what processes are running on card 0 and card 1. If there are any processes listed on either card other than ''/usr/bin/X'' then you need to ensure you use the other card (see the example above). For example, to do this you use the vglrun command as shown below:

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@rvisu01 ~]$ vglrun -d0.0 command
</pre>

or

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@rvisu01 ~]$ vglrun -d0.1 command
</pre>

=== vglwrapper ===
The command vglwrapper will round robin tasks between the two cards on the visualisation nodes:

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@rvisu01 ~]$ vglwrapper command
</pre>

Training/Working Remotely on Viper

2017-06-28T14:12:11Z

MSummerbell:

__TOC__
==Introduction==
To work on Viper remotely off campus, you will need to setup a VPN connection.

A VPN (Virtual Private Network) is a method of extending a private network (such as the University) over a public network (such as the Internet). It enables you to send and receive data across a public network as though you were directly connected to the private network in a secure way.

The University VPN service operates using a 'split-tunnel' policy. This means:

*Network traffic to/from Unviersity-hosted resources will be handled by the VPN connection.
*Connectivity to your local network and the Internet will continue as normal.
*Geo-located services will not be affected. E.g. the Google Australia page will appear if you connect from Australia.
*The University does not track or log your activity outside of its jurisdiction.

For security and compliance reasons, not all on-campus services are available via a VPN connection. If you cannot access a service while using the VPN; please contact the Service Desk.

Instructions on setting up the VPN client can be found [https://share.hull.ac.uk/Services/ICT/SitePages/VPN%20-%20Working%20Remotely.aspx here]. Log in to SharePoint using your University credentials.

==Configuring Access==
1. Download the VPN software from [https://share.hull.ac.uk/Services/ICT/SitePages/VPN%20-%20Working%20Remotely.aspx ICT Support] for your specific operating system.

2. Once installed launch the BIG-IP Edge Client.

3. Click Connect
[[File:vpnclient.JPG]]
4. Enter your University User ID and Password
[[File:vpnlogon.JPG]]
5. You should now be connected to the University VPN, continue connecting to Viper as described in Getting Connected.
[[File:vpn_connected.JPG]]

Training/Working Remotely on Viper

2017-06-28T14:11:42Z

MSummerbell: /* Introduction */

__TOC__
==Introduction==
To work on Viper remotely off campus, you will need to setup a VPN connection.

A VPN (Virtual Private Network) is a method of extending a private network (such as the University) over a public network (such as the Internet). It enables you to send and receive data across a public network as though you were directly connected to the private network in a secure way.

Instructions on setting up the VPN client can be found [https://share.hull.ac.uk/Services/ICT/SitePages/VPN%20-%20Working%20Remotely.aspx here]. Log in to SharePoint using your University credentials.

The University VPN service operates using a 'split-tunnel' policy. This means:

*Network traffic to/from Unviersity-hosted resources will be handled by the VPN connection.
*Connectivity to your local network and the Internet will continue as normal.
*Geo-located services will not be affected. E.g. the Google Australia page will appear if you connect from Australia.
*The University does not track or log your activity outside of its jurisdiction.
For security and compliance reasons, not all on-campus services are available via a VPN connection. If you cannot access a service while using the VPN; please contact the Service Desk.

==Configuring Access==
1. Download the VPN software from [https://share.hull.ac.uk/Services/ICT/SitePages/VPN%20-%20Working%20Remotely.aspx ICT Support] for your specific operating system.

2. Once installed launch the BIG-IP Edge Client.

3. Click Connect
[[File:vpnclient.JPG]]
4. Enter your University User ID and Password
[[File:vpnlogon.JPG]]
5. You should now be connected to the University VPN, continue connecting to Viper as described in Getting Connected.
[[File:vpn_connected.JPG]]

Training/Working Remotely on Viper

2017-06-28T14:10:30Z

MSummerbell:

2017-06-05T13:20:31Z

MSummerbell: /* Pre-usage */

Applications

2017-04-24T08:21:11Z

MSummerbell: /* Application Support */

==Application Support==

Click on the links below for support on the individual and library packages:

* Jump to [[#Libraries|Libraries]] or [[#Test Modules|Test Modules]]

{| class="wikitable"
| style="width:25%" | Package
| style="width:75%" | Description
|-
| [[applications/ABySS|ABySS]]
| Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler.
|-
| [[applications/Anaconda|Anaconda]]
| Anaconda is the leading open data science platform powered by Python.
|-
| [[applications/Ansys|Ansys]]
| ANSYS Fluent software includes broad physical modelling capabilities to model flow, turbulence, heat transfer, and reactions for industrial applications.
|-
| [[applications/Avizo|Avizo]]
| Avizo data visualisation and analysis tool
|-
| [[applications/Beast|Beast]]
| BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
|-
| [[applications/Bison|Bison]]
| Bison, is a parser generator that is part of the GNU Project.
|-
| [[applications/Bowtie1|Bowtie1]]
| The aligner is typically used with short reads and a large reference genome, or for whole genome analysis. Bowtie is promoted as an ultrafast, memory-efficient short aligner for short DNA sequences.
|-
| [[applications/Bowtie2|Bowtie2]]
| Bowtie 2 is more suited to finding longer, gapped alignments in comparison with the original Bowtie1 method.
|-
| [[applications/Cmake|CMake]]
| CMake is cross-platform free and open-source software for managing the build process of software using a compiler-independent method.
|-
| [[applications/COMSOL|COMSOL]]
| COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems
|-
| [[applications/CP2K|CP2K]]
| CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.
|-
| [[applications/Crop|Crop]]
| CROP is an unsupervised nucleic acid sequence clustering algorithm.
|-
| [[applications/Cuda|CUDA]]
| CUDA is NVIDIA’s parallel computing architecture that enables dramatic increases in computing performance by harnessing the power of the GPU nodes.
|-
| [[applications/Cufflinks|Cufflinks]]
| Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
|-
| [[applications/Delft3D|Delft3D]]
| Delft3D is a world leading 3D modeling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments.
|-
| [[applications/Discovardenovo|Discovardenovo]]
| DISCOVAR de novo can generate de novo assemblies for both large and small genomes.
|-
| [[applications/FDS-SMV|FDS-SMV]]
| Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. Smokeview (SMV) is a visualization program used to display the output of FDS and CFAST simulations.
|-
| [[Applications/ffmpeg|Ffmpeg]]
| ffmpeg is a very fast video and audio converter that can also grab from a live audio/video source.
|-
| [[Applications/Flex|Flex]]
| Flex (Fast lexical analyser), Flex is a tool for generating scanners: programs which recognize lexical patterns in text.
|-
| [[Applications/FreeIPMI|FreeIPMI]]
| FreeIPMI provides in-band and out-of-band IPMI software based on the IPMI v1.5/2.0 specification.
|-
| [[Applications/Fiji|Fiji]]
| Fiji Is Just ImageJ—a "batteries-included" distribution of ImageJ which includes many useful plugins contributed by the community.
|-
| [[applications/Gcc|Gcc]]
| gcc (GNU Compiler Collection) is a collection of compilers consisting of C, C++, Fortran and more.
|-
| [[applications/Gnuplot|GNUplot]]
| Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.
|-
| [[applications/Hwloc|Hwloc]]
| hwloc provides command line tools and a C API to obtain the hierarchical map of key computing elements
|-
|[[applications/Java|Java]]
| Java is a general-purpose computer programming language that is concurrent, class-based, object-oriented.
|-
|[[applications/Hpl|HPL]]
| HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers as well as freely available implementation of the High Performance Computing Linpack Benchmark.
|-
|[[applications/IDL|IDL]]
| IDL, short for Interactive Data Language, is a programming language used for data analysis. It is popular in particular areas of science, such as astronomy, atmospheric physics and medical imaging.
|-
|[[applications/Insighttoolkit|Insighttoolkit]]
| ITK is an open-source software toolkit for performing registration and segmentation.
|-
|[[applications/Intel|Intel Parallel Studio]]
| Intel Parallel Studio is a software development product that facilitates native code development on Viper in C, C++ and Fortran for parallel computing.
|-
| [[applications/Likwid|Libwid]]
| Likwid is a simple to install and use toolsuite of command line applications for performance oriented programmers.
|-
|[[applications/LS-DYNA|LS-DYNA]]
| General-purpose finite element program capable of simulating complex real world problems.
|-
| [[Applications/Maker|Maker]]
| MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.
|-
| [[Applications/Matlab|Matlab]]
| Numerical Computing Environment.
|-
| [[Applications/Mercurial|Mercurial]]
| Mercurial is truly distributed, giving each developer a local copy of the entire development history. This way it works independent of network access or a central server. Committing, branching and merging are fast and cheap.
|-
| [[applications/Mpich|Mpich]]
| MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
|-
| [[Applications/Mono|Mono]]
| .NET Framework-compatible set of tools including, among others, a C# compiler and a Common Language Runtime.
|-
| [[Applications/MrBayes|MrBayes]]
| MrBayes: Bayesian Inference of Phylogeny
|-
| [[Applications/Munge|Munge]]
| It is an authentication service that creates and validates user credentials.
|-
| [[applications/Mvapich2|Mvapich2]]
| MVAPICH2 is a BSD-licensed implementation of the MPI standard with support for Intel Omni-Path is a high performance.
|-
| [[Applications/Ncbi-blast|Ncbi blast]]
| It finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
|-
| [[Applications/Ncurses|Ncurses]]
| ncurses (new curses) is a programming library providing an application programming interface (API) that allows the programmer to write text-based user interfaces in a terminal-independent manner.
|-
| [[Applications/Netloc|Netloc]]
| Netloc software package provides network topology discovery tools, and an abstract representation of those networks topologies for a range of network types and configurations.
|-
| [[Applications/Ngspice|NgSpice]]
| Ngspice is a mixed-level/mixed-signal circuit simulator. Its code is based on three open source software packages: Spice3f5, Cider1b1 and Xspice.
|-
| [[applications/Nwchem|Nwchem]]
| NWChem provides computational chemistry tools and particularly large scientific computational chemistry problems.
|-
| [[applications/Open64|Open64]]
| Open64 is a discontinued, free, open source, optimizing compiler for the Itanium and x86-64 microprocessor architectures.
|-
| [[applications/Openuh|Openuh]]
| Openuh is an open version of the openACC compiler suite.
|-
| [[applications/Obitools|Obitools]]
| The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, taking into account taxonomic information.
|-
| [[applications/Openfoam|Openfoam]]
| OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.
|-
| [[applications/OpenMPI|OpenMPI]]
| Open MPI is a Message Passing Interface (MPI) library used for communicating between HPC nodes.
|-
|[[applications/Orca|Orca]]
| 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.
|-
|[[applications/Paraview|Paraview]]
| ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques.
|-
|[[applications/Petsc|Petsc]]
| PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modelled by partial differential equations. It supports MPI, and GPUs through CUDA or OpenCL, as well as hybrid MPI-GPU parallelism.
|-
|[[applications/Perl|Perl]]
| Perl is a fantastic high-level, general-purpose, interpreted, dynamic programming languages with a large amount of libraries.
|-
|[[applications/Planatus|Planatus]]
| Platanus is a novel ''de novo'' sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data.
|-
|[[applications/Python|Python]]
| Python is a family of high-level, general-purpose, interpreted, dynamic programming languages and includes IPython.
|-
|[[applications/R|R]]
| R is an open source programming language and software environment for statistical computing and graphics.
|-
|[[applications/Readline|Readline]]
| GNU Readline is a software library that provides line-editing and history capabilities for interactive programs with a command-line interface, such as Bash.
|-
|[[applications/Readline|Readline]]
| GNU Readline is a software library that provides line-editing and history capabilities for interactive programs with a command-line interface, such as Bash.
|-
|[[applications/Rsem|Rsem]]
| RSEM is an RNA-Seq transcript quantification program.
|-
| [[applications/Samtools|Samtools]]
| Tools (written in C using htslib) for manipulating next-generation sequencing data
|-
| [[applications/SAS|SAS]]
| Statistical Analysis System.
|-
| [[applications/Scalapack|Scalapack]]
| The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers
|-
| [[applications/Siesta|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.
|-
| [[applications/ssw|SSW]]
| Integrated software libraries, data bases, and system utilities which provide a common programming and data analysis environment for Solar Physics
|-
| [[applications/STAR|STAR]]
| Ultrafast universal RNA-seq aligner.
|-
| [[applications/Star-ccm+|Star-ccm+]]
| Computational Fluid Package.
|-
| [[applications/Stata|Stata]]
| Stata is a commercial statistical package, which provides a complete solution for data analysis, data management, and graphics.
|-
| [[applications/Tophat|Tophat]]
| It is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyses the mapping results to identify splice junctions between exons.
|-
| [[applications/Transrate|Transrate]]
| Transrate is software for de-novo transcriptome assembly quality analysis
|-
| [[applications/Trinityrnaseq|Trinityrnaseq]]
| Trinity assembles transcript sequences from Illumina RNA-Seq data.
|-
| [[applications/Utilities|Utilities]]
| General utilities module including zip, wget and git utilities.
|-
| [[applications/Voxfe|Voxfe]]
| VOX-FE is voxel-based FE software with a sophisticated graphical user interface that allows the complex loading regimes that are inevitably present in biomechanical analyses to be readily applied to the model geometry, and the resultant 3D stress and strain patterns to be visualized easily.
|-
| [[applications/Yt|Yt]]
| yt supports structured, variable-resolution meshes, unstructured meshes, and discrete or sampled data such as particles. Focused on driving physically-meaningful inquiry, yt has been applied in domains such as astrophysics, seismology, nuclear engineering, molecular dynamics, and oceanography.
|-
|}

===Libraries===

{| class="wikitable"
| style="width:25%" | Library
| style="width:75%" | Description
|-
| [[applications/Boost|Boost]]
| C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications.
|-
| [[applications/Cfitsio|Cfitsio]]
| CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS.
|-
| [[applications/Expat|Expat]]
| Expat XML parser library in C
|-
| [[applications/Fftw3|Fftw3]]
| FFTW is a C subroutine library for computing the discrete Fourier transform (DFT).
|-
| [[applications/Jemalloc|Jemalloc]]
| jemalloc is a general purpose malloc implementation that emphasizes fragmentation avoidance and scalable concurrency support.
|-
| [[applications/Libgd|Libgd]]
| The module LibGD is an open source code library for the dynamic creation of images.
|-
| [[applications/Libjpeg-turbo|Libjpeg-turbo]]
| The module Libjpeg-turbo is a JPEG image codec that uses SIMD instructions (''MMX, SSE2, AVX2, NEON, AltiVec'') to accelerate baseline JPEG compression and decompression
|-
| [[applications/Parmetis|Parmetis]]
| 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.
|-
| [[applications/Libpng|Libpng]]
| The reference library for use in applications that read, create, and manipulate PNG (''Portable Network Graphics'') raster image files.
|-
| [[applications/Netcdf-c|Netcdf-c]]
| 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.
|-
| [[applications/Openblas|Openblas]]
| OpenBLAS is an optimized BLAS library (based on ''GotoBLAS2'' 1.13 BSD version).
|-
| [[applications/Osmesa|Osmesa]]
| Mesa's off-screen interface is used for rendering into user-allocated memory without any sort of window system or operating system dependencies.
|-
|[[applications/Qt|Qt]]
| Qt is a cross-platform framework, that is usually used as a graphical toolkit, although it is also very helpful in creating CLI applications on Viper.
|-
|[[applications/Sparsehash|Sparsehash]]
| Sparsehash Package (formerly ''Google Sparsehash'')
|-
| [[applications/Zlib|Zlib]]
| zlib is a software library used for data compression.
|-
|}

===Test Modules===

{| class="wikitable"
| style="width:25%" | Library
| style="width:75%" | Description
|-
| [[applications/test-modules|Test-Modules]]
| Access to modules currently in development
|-
|}
{|
|style="width:5%; border-width: 0" | [[File:icon_up.png]]
|style="width:95%; border-width: 0" | [[#Application Support|Top]]
|-
|}

* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]

Applications/Bison

2017-04-24T08:19:40Z

MSummerbell: MSummerbell moved page Bison to Applications/Bison without leaving a redirect

__TOC__

==Application Details==
*Description: Bison, is a parser generator that is part of the GNU Project. Bison reads a specification of a context-free language, warns about any parsing ambiguities, and generates a parser (either in C, C++, or Java) which reads sequences of tokens and decides whether the sequence conforms to the syntax specified by the grammar
*Version: 3.0.4
*Modules: bison/3.0.4
*License: GNU Licence

==Usage==
===Load Module===
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ module add bison/3.0.4
</pre>

==Further Information==
[https://www.gnu.org/software/bison/ GNU Bison]

2017-03-23T14:45:07Z

MSummerbell: /* rmdir */

== Introduction ==

This represents a series of teaching pages to allow you to learn more about Viper's Linux command line interface

== Command Line ==

Like other operating systems Linux does have a window’s type environment too called X and hopefully in the future its successor Wayland. (Linux refers to X and Wayland with the term Display Server). However, with VIPER the vast majority of work will be carried out on the command line.

The command line in Linux is referred to as a shell. The shell is a program that allows the user to interact with Linux at the command line. In true Linux style there are a few different ones to choose from, however the one used predominantly is BASH. The name BASH is an acronym for “Bourne Again SHell”, a reference to BASH is an enhanced replacement for sh, the original Unix shell program written by Steve Bourne.

Below is an example of Viper's command line interface using the terminal program [http://mobaxterm.mobatek.net/ MobaXterm].

[[File:commandline.jpg]]

== Man pages ==

This will explain the use of man pages (also called manual pages) on Linux. Most Linux files and commands have pretty good man pages to explain their use.
Type man followed by a command (for which you want help) and start reading. Press q to quit the man page. See below:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ man whois (shows manual page for the command whois)
username@viper:~$ man syslog.config (shows the manual page for a configuration file)
username@viper:~$ man syslogd (show the manual for a daemon (background program))
username@viper:~$ man –k syslog (an apropos which shows a list of available man pages with this string contained within it)

</pre>

== Working with directories ==

As with other operating systems such as Microsoft Windows the filesystem is based around files and directories. Linux is no exception to this and uses a number of commands for the user to navigate around its own filesystem.

This module is a brief overview of the most common commands to work with directories: '''pwd, cd, ls, mkdir''' and '''rmdir'''. These commands are available on any Linux system.

This section will also discuss absolute and relative paths and path completion in the bash shell.

=== pwd ===

On the command line pwd (or print working directory) basically displays the current directory you are in. This would appear as:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ pwd
/home/dbird

</pre>

=== cd ===

On the command line cd (or change directory) changes your current directory to the one specified:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cd /var
username@viper:~$ pwd
/var
username@viper:~$ cd /home/user
username@viper:~$ pwd
/home/user

</pre>

There is also a shortcut back to your home directory by typing the character ~ (tilda) which has the same effect as typing (for example) /home/user.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cd ~
username@viper:~$ pwd
/home/user

</pre>

To go to the directory above (or parent directory), we use the characters ..

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ pwd
/home/user

username@viper:~$ cd ..
username@viper:~$ pwd
/home

</pre>

There is also the character . which means the current directory. This is not useful for the cd command but is very useful for copying files to your current directory.

=== Absolute and relative paths ===
{|
|style="width:5%; border-width: 0" | [[File:icon_pencil.png]]
|style="width:95%; border-width: 0" | Although an important concept to understand the rule here is very simple. When you type a path starting with a slash (/), then the root of the file tree is assumed. If you don't start your path with a slash, then the current directory is the assumed starting point.

Here are two examples, firstly of absolute path:
|-
|}
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ pwd
/home/user

user@viper:~$ cd /var
user@viper:~$ pwd
/var

</pre>

And relative path

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ pwd
/home/user

username@viper:~$ cd myfiles
username@viper:~$ pwd
/home/user/myfiles

</pre>

The command line will help you in typing a path without errors. If you type a partial command such as:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cd /home/user/my

</pre>

Pressing the '''TAB''' key will fill in the rest of the directory name, if that directory exists and it is unique). So the following would appear

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cd /home/user/myfiles

</pre>

=== ls ===

This command lists the contents of a directory:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ ls
myfile1.txt myfile2.txt mydirectory1

</pre>

'''ls''' has a number of useful different options

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ ls –l (show a long listing with more information)
username@viper:~$ ls –a (show all files including those that are hidden)
username@viper:~$ ls –la (combines both of the options above)

</pre>

=== mkdir ===

This commands makes a directory from the specified directory:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ mkdir mydirectory1
username@viper:~$ cd mydirectory1
username@viper:~$ pwd
/home/user/mydirectory1

</pre>

=== rmdir ===

This command removes the specified directory, note the directory must be empty and must not be the directory you are currently in:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ rmdir mydirectory1

</pre>

== Working with files ==

In this section we learn how to recognise, create, remove, copy and move files using commands like '''file''', '''touch''', '''rm''', '''cp''', '''mv''' and '''rename'''.

Just before we start looking at these commands we need to cover two important areas:

* Files on Linux are case sensitive. This means that FILE1 is different from file1, and /etc/hosts is different from /etc/Hosts (the latter one does not exist on a typical Linux computer).
* Everything on Linux is a file. A directory is a special kind of file, but it is still a (case sensitive!) file. Each terminal window (for example /dev/pts/4), any hard disk or partition (for example /dev/sdb1) and any process are all represented somewhere in the file system as a file.

=== file ===

This command determines the file type. Unlike Windows, Linux does not determine the file type from the extension but from examining the file header/contents itself.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ file mypicture.png
pic33.png: PNG image data, 3840 x 1200, 8-bit/color RGBA, non-interlaced

username@viper:~$ file parallel.c
parallel.c: ASCII C program text

</pre>

=== touch ===

This creates an empty file, which can be useful for various uses.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ touch newfile.c
username@viper:~$ ls
newfile.c

</pre>

=== rm ===

Remove a file, as always be very careful with this command and without a backup this file will be lost forever.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ ls
newfile.c backup.c
username@viper:~$ rm newfile.c
username@viper:~$ ls
backup.c

</pre>

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ rm –i backup.c (this is interactive delete and will ask you to delete the file before it occurs)
username@viper:~$ rm –r mydirectory (works recursively down the specified directory but not removing any non-empty directories)
username@viper:~$ rm –rf mydirectory (works recursively down the specified directory however the –f option means force. This option is very powerful but also needs to be used with extreme care!)

</pre>

As with many Linux commands there are a few options with can be used with '''rm''' (these can be view by typing '''man rm''').

=== cp ===

Copy files or directories from a source to a destination:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cp parallel.c mybackup.c (copies parallel.c to mybackup.c)
username@viper:~$ cp parallel.c mydirectory1 (copies parallel.c to mydirectory1)
username@viper:~$ cp *c backupdirectory/ (copies all *.c files to backupdirectory)
username@viper:~$ cp –r mydirectory1 mydirectory2 (copies one directory to another, note the option –r for recursive copying)

</pre>

As with many Linux commands there are a few options with can be used with '''cp''' (these can be view by typing '''man cp''').

=== mv ===

Move files from a source to a destination. A versatile command that can rename a file too:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ mv file1.c testfile.c (rename file1.c to testfile.c)
username@viper:~$ mv directory1 directory2 (rename directory)
username@viper:~$ mv file1.c /home/user/myrepo (mv file1.c to /home/user/myrepo/file1.c)

</pre>

=== rename ===

Although preferably to use the '''mv''' command, this command does exist to rename files

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ touch file1.c file2.c file3.c
username@viper:~$ ls
file1.c file2.c file3.c

username@viper:~$ rename .c .backup *.c
username@viper:~$ ls
file1.backup file2.backup file3.backup

</pre>

== Working with file contents ==

This section will look at working with file contents themselves, such commands are '''head''', '''tail''', '''cat''', '''tac''', '''more''' and '''less'''.

=== head ===

By default head will show the first ten lines of a file.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ head /etc/passwd

root:x:0:0:root:/root:/bin/bash
daemon:x:1:1:daemon:/usr/sbin:/bin/sh
bin:x:2:2:bin:/bin:/bin/sh
sys:x:3:3:sys:/dev:/bin/sh
sync:x:4:65534:sync:/bin:/bin/sync
games:x:5:60:games:/usr/games:/bin/sh
man:x:6:12:man:/var/cache/man:/bin/sh
lp:x:7:7:lp:/var/spool/lpd:/bin/sh
mail:x:8:8:mail:/var/mail:/bin/sh
news:x:9:9:news:/var/spool/news:/bin/sh

</pre>

=== tail ===

Similar to '''head''' but this time it will show the last 10 lines of file by default.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ tail /etc/services
vboxd 20012/udp
binkp 24554/tcp # binkp fidonet protocol
asp 27374/tcp # Address Search Protocol
asp 27374/udp
csync2 30865/tcp # cluster synchronization tool
dircproxy 57000/tcp # Detachable IRC Proxy
tfido 60177/tcp # fidonet EMSI over telnet
fido 60179/tcp # fidonet EMSI over TCP

</pre>

=== cat ===

The '''cat''' command (short for concatenate) one of the most universal tools, yet all it does is copy standard input to standard output. In combination with the shell this can be very powerful and diverse. Some examples will give a glimpse into the possibilities.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cat /etc/resolv.conf

domain example.com
search example.com
nameserver 192.168.1.42

username@viper:~$ cat file1.c file2.c >file3.all (concatenate c files into file3.all)

</pre>

=== tac ===

Works the same as '''cat''' but will show you the file backwards:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cat numbers
one
two
three

username@viper:~$ tac numbers
three
two
one

</pre>

=== more ===

The more command is useful for displaying files that take up more than one screen. More will allow you to see the contents of the file page by page. Use the space bar to see the next page, or q to quit. Some people prefer the less command to more.

=== less ===

Very similar to more but with some additional features

== Basic Linux Tools ==

This chapter introduces commands to find or locate files and to compress files, together with other common tools that were not discussed before.

=== find ===

This command is very useful to find files, more options are provided on the command line by typing '''man find'''. Here are some useful examples below:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ find /etc (find all files in the /etc directory)
username@viper:~$ find . –name “*.conf” (find all files that end in .conf from the current directory)
username@viper:~$ find . –newer file1.c (find all files newer than file1.c)
username@viper:~$ find /etc >etcfiles.txt (find all files but this time put them in (pipe) to the file etcfiles.txt)

</pre>

=== locate ===

The '''locate''' command is very different from find in that it uses an index to locate files. This is a lot faster than traversing all the directories, but it also means that it may be outdated too.

=== date ===

The '''date''' command can display the date, time, time zone and more.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ date
Sat Feb 23 12:44:30 BST 2017

</pre>

=== cal ===

The '''cal''' command displays the current month, with the current day highlighted.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cal
April 2016
Su Mo Tu We Th Fr Sa
1 2
3 4 5 6 7 8 9
10 11 12 13 14 15 16
17 18 19 20 21 22 23
24 25 26 27 28 29 30

</pre>

=== sleep ===

The '''sleep''' command is sometimes used in scripts to wait a number of seconds. This example shows a five second sleep.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ sleep 5 (five seconds later)
username@viper:~$

</pre>

=== sort ===

The command '''sort''' will sort lines of text files. By default the output is to the screen but this can be piped to a file or another program.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ sort myfile.txt
apple
banana
cherry

</pre>

=== time ===

The time command can display how long it takes to execute a command. The date command takes only a little time.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ time date
Sat Feb 23 13:08:27 BST 2016
real 0m0.014s
user 0m0.008s
sys 0m0.006s

</pre>

=== gzip – gunzip ===

This is a useful compression program (like '''zip''' which also exists in Linux). The '''gzip''' command can make files take up less space.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ gzip myfile.c (will create myfile.c.gz)
username@viper:~$ gunzip myfile.c.gz (will create myfile.c again)

</pre>

=== bzip2 – bunzip2 ===

Files can also be compressed with '''bzip2''' which takes a little more time than '''gzip''', but compresses better.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ bzip2 myfile.c (will create myfile.c.bz2)
username@viper:~$ bunzip2 myfile.c.bz2 (will create myfile.c again)

</pre>

=== zip – unzip ===

A compression program which is compatible with other '''zip''' programs found in MS Windows and other OSes.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ zip myfile.c (will create myfile.c.zip)
username@viper:~$ unzip myfile.c.zip (will create myfile.c again)

</pre>

=== grep ===

The '''grep''' filter is famous among Linux (and UNIX) users. The most common use of '''grep''' is to filter lines of text containing (or not containing) a certain string.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ grep “Darren” /etc/passwd
user:x:1000:1000:Darren Bird,,,:/home/user:/bin/bash

</pre>

As with most Linux commands there are also a large amount of useful options that will go with each command and '''grep''' is certainly no exception here

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ grep –i “Darren” /etc/passwd (search in a case insensitive way)
username@viper:~$ grep –r “Darren” /etc/passwd (search recursively down any directories too)
username@viper:~$ grep –v “Darren” /etc/passwd (search for everything not containing “Darren”)

</pre>

=== wc ===

Counting words, lines and characters is easy with '''wc'''.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ wc myfile.c (show number of words, lines and characters)
5 10 100 tennis.txt

</pre>

== File Permissions ==

=== Introduction ===

Similar to many other operating systems Linux uses a method of access rights on files and directories. These can be view by using the ls command

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ ls –l (option l is for long listing)

-rw-r--r-- 1 dbird admin 12211 May 11 2016 template.countries
-rw-r--r-- 1 dbird admin 3097 May 11 2016 template.languages (1)
drwxr-x--- 2 dbird admin 4096 Dec 1 10:54 Templates (2)
-rw-r--r-- 1 dbird admin 8087 Feb 12 14:05 temp.txt
-rwx------ 1 dbird admin 1110 Mar 8 10:53 test4pisignage.pl (3)

</pre>

Each file and directory has access rights that are associated with each one. When we look at the 10 symbol string above on the left hand side (e.g. '''drwxr-xr-x''').

* The first letter present whether the file is a directory or not.
* The next three represents the file permission for the user that owns that file (i.e. dbird in this example).
* The next three represent the file permission of the group to whom that user belongs to (i.e. group admin).
* The last three represent the file permissions for everyone else (i.e. all users).

For each of the permission parts the letters mean the following in their groups:

* r indicates read permission to read and copy the file, its absence indicates this is not available.
* w indicates write permission to write the file, its absence indicates this is not available.
* x indicates execution permission to allow the file to be executed, its absence indicates this is not available.

Using the example above would mean:

* Example '''(1)''' has read/write access for user dbird and read access only for everyone else.
* Example '''(2)''' is a directory with full access for user dbird and read access for only users in the admin group.
* Example '''(3)''' is an application which is only accessible by the user dbird, note not only is it read and write but it also has its ‘execution’ permission set for that user also.

=== Changing access rights ===

This command allows the user to change file (and directory) permissions.

* u User
* g Group
* o Other
* a All
* r Read
* w Write (and erase)
* x Execution (and access directory
* + Add permission
* - Remove permission

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ chmod go-rwx myfile.c (remove read, write and execute permissions removed for group and other)
username@viper:~$ chmod u+x myapp.pl (make the program myapp.pl executable to user (i.e. the owner of the file))

</pre>

== Further Information ==

* [http://www.ee.surrey.ac.uk/Teaching/Unix/ http://www.ee.surrey.ac.uk/Teaching/Unix/]

Training/XQuartz

2017-03-21T20:27:58Z

MSummerbell: /* Installing XQuartz */

__TOC__

==Introduction==
XQuartz is an open-source version of X.Org X Window System that runs on macOS, it is required to run certain cross-platform applications on macOS.
XQuartx was included with Mac OSX 10.5 (Leopard) to Mac OSX 10.7 (Lion), for all subsequent releases XQuartz is not included and must be downloaded separately.

==Installing XQuartz==
1. Download the latest version of XQuartz from https://www.xquartz.org 
2.Navigate to the downloads folder and open the XQuartz Disk Image (XQuartz-2.7.11.dmg) 
[[File:Download_XQuartz.png]]
3.Open the the XQuartz package (XQuartz.pkg) 
[[File:XQuartz_Package.png]]
4.Follow the installation steps, accepting the licence agreement and choose an installation destination. 
[[File:XQuartz_Install.png]]
5.Once installation is complete logout and log in. 
[[File:XQuartz_Complete.png]]
6.Open the Terminal App 
7.Login to Viper ssh -Y <username>@viper.hull.ac.uk
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ ssh -Y <username>@viper.hull.ac.uk
</pre>
{|
|style="width:5%; border-width: 0" | [[File:icon_exclam1.png]]
|style="width:95%; border-width: 0" | Note: -Y is used to enable the X window system..
|-
|}

==Test XQuartz==
To test X11 support type xclock, an analogue clock should appear.
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ xclock
</pre>
[[File:XClock.png]]

==Further Information==
Licence: Apple Public Source Licence and MIT 
[https://www.xquartz.org/ XQuartz] 
[https://support.apple.com/en-gb/HT201341 Apple Support - X11]