HPC - User contributions [en-gb]

FurtherTopics/FurtherTopics

2025-11-27T10:10:26Z

Pysdlb:

If you are new to Viper, you may find our [[Main Page #Quickstart| Quickstart]] useful.
==Further Reading==
[https://hpc.wordpress.hull.ac.uk/ Viper Website]

Research produced with the aid of Viper:
[https://hpc.wordpress.hull.ac.uk/research-outputs/ Research]

Issues with Scaling:
[[Scaling|Scaling programs on HPC]]

[[FurtherTopics/Additional Information On Viper| Viper Specifications and Infrastructure]]

==Linux Command Line==
[[Quickstart/Linux Command Line| Basic Linux Command Line]]

[[FurtherTopics/Linux Command Line Advanced| Additional Linux Command Line]]

[[FurtherTopics/Command Line File Permissions| File Permissions]]

==Interactive Sessions==
[[Quickstart/Interactive| Interactive Sessions Quickstart]]

[[FurtherTopics/FurtherInteractive|Further Information on Interactive Sessions]]

==Slurm==
[[Quickstart/Slurm| Slurm Quickstart]]

[[FurtherTopics/Sinfo|Sinfo]]

[https://slurm.schedmd.com/ Slurm Website]

==Batch Jobs==
[[Quickstart/Batch Jobs|Batch Jobs Quickstart]]

[[FurtherTopics/Advanced Batch Jobs| Advanced Batch Jobs]]

==Visualisation Nodes==
[[General/Visualisation Nodes|Visualisation Nodes]]

==Data Management==
[[Quickstart/Data Management| Data Management]]

[[FurtherTopics/WinSCP|Windows WinSCP]]

==Modules==
{| class="wikitable mw-collapsible mw-collapsed "
| style="width:25%; background: #f5a091;" | Modules
| style="width:25%; background: #f5a091;" |
|-
|[[Quickstart/Using Modules|Using Modules]]
| Learn how to use modules.
|-
|[[FurtherTopics/Further Modules|Further Module Information]]
| More about modules and some extra commands.
|-
|[[Modules| Modules Available]]
| Modules are available without the use of a special license.
|-
|[[Applications/Special Licenses| Modules requiring special licenses]]
|Modules are available requiring the use of a special license.
|-
|[[Modules #Test Modules| Test Modules]]
|Test Modules.
|-
|}

==Programming==
{| class="wikitable mw-collapsible mw-collapsed "
| style="width:25%; background: #f5a091;" | Programming
| style="width:25%; background: #f5a091;" |
|-
|[[Programming/Languages|Languages]]
| Information on the languages available for use on Viper
|-
|[[Modules #Libraries| Libraries]]
| Information on what programming libraries are available on Viper.
|-
|[[Programming/Style|Viper programming guidelines and style]]
| Guidance on the readability of code.
|-
|[[Programming/OpenMPI| OpenMPI]]
|A more detailed look at OpenMPI.
|-
|[[Programming/GitHub| GitHub]]
| Information on using source control.
|-
|[http://hpc.wordpress.hull.ac.uk/support/research-software-engineering/ Research software engineering]
| How code can be improved.
|-
|[[Training/Linux_-_vi_editor|Vi]] [[Training/Linux - Nano editor| Nano]]
| Text Editors on Linux.
|-
| [[Quickstart/Virtual Environments| Virtual Environment Quickstart]]
| Get started using Miniconda.
|-
|[[Programming/Deep Learning| Deep Learning]]
| Deep Learning.
|-
|}

==Compatibility==
'''Visualisation Nodes'''

X2Go enables remote access to Viper's Visualisation Nodes.
[[Training/X2Go macOS| X2Go]]

On newer macOS, XQuartz is required to use X2Go:
[[Training/XQuartz| XQuartz]]

'''Connecting on Windows'''

To connect to Viper on Windows, an application that enables SSH connections is required; we recommend [[Quickstart/Connect #Connecting on a Windows PC| MobaXterm]]

==Support==
[[General/UserDropin|User Drop-in Sessions]] are held every Wednesday from 09:30-10:30 on Teams.

There is a selection of [[Tutorial Videos/Tutorial Videos|Tutorial Videos]] to help get you started using Viper.

In the [https://hull.service-now.com/ Support Portal], you can find forms to request VPN access, report an issue with a job, request software installation, and request a runtime extension.

[[Main Page|Back Home]]

Modules

2025-11-27T10:07:45Z

Pysdlb:

[[FurtherTopics/FurtherTopics #Modules| Back to Further Topics]]
==Applications==
The following is a list of core applications installed on Viper, with links to further information on using those applications on Viper. If you are looking for an application that requires a special license, visit: [[Applications/Special Licenses| Applications requiring special licenses]].

If you are looking for how to use a module, use the [[Quickstart/Using Modules| Quickstart]].

An up-to-date list of all modules available on Viper can be found at [https://hpc.hull.ac.uk/upload/module.html Module List]

Click on the links below for support on the individual applications:

{| class="wikitable mw-collapsible"
| style="width:25%; background: #f5a091;" | Package
| style="width:75%; background: #f5a091;" | Description
|-
| [[applications/ABySS|ABySS]]
| Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler.
|-
| [[applications/Miniconda|Anaconda]]
| Anaconda is the leading open data science platform powered by Python.
|-
| Arnold
| Monte Carlo ray tracing renderer.
|-
| Autotools
| Autotools, is a suite of programming tools designed to assist in making source code packages portable. Provides common tools such as m4-1.4.17, autoconf-2.69, automake-1.15, flex-2.6.2, libtool-2.4, gettext-0.19.8.1, bison-3.0.4 .
|-
| [[applications/BayesTraits|BayesTraits]]
| BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available.
|-
| Bison
| Bison, is a parser generator that is part of the GNU Project.
|-
| [[applications/Blender|Blender]]
| Blender is a free and open-source 3D creation suite. It supports the entirety of the 3D pipeline—modelling, rigging, animation, simulation, rendering, compositing and motion tracking, and even video editing and game creation.
|-
| [[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/Bridger|Bridger]]
| Bridger is an efficient ''de novo'' transcriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference.
|-
| [[applications/Centrifuge|Centrifuge]]
| Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimised specifically for the metagenomic classification problem.
|-
| [[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/Crop|Crop]]
| CROP is an unsupervised nucleic acid sequence clustering algorithm. The algorithm sees the OTUs as a Gaussian mixture and models the clustering process using Birth-death MCMC. This approach makes the OTU prediction more accurate.
|-
| [[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/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 modelling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments.
|-
| [[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 visualisation 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 be grabbed from a live audio/video source.
|-
| Flex
| Flex (Fast lexical analyser), Flex is a tool for generating scanners: programs that recognise lexical patterns in text.
|-
| [[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/Grace|Grace]]
| Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif. Grace is a descendant of ACE/gr, also known as Xmgr.
|-
| [[applications/guppy|Guppy]]
| Local accelerated basecalling for Nanopore data.
|-
|[[applications/HyPhy|HyPhy]]
| HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning.
|-
|[[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/iqtree|IQtree]]
| stochastic algorithm to reconstruct phylogenetic trees using maximum likelihood.
|-
|[[applications/Java|Java]]
| Java is a general-purpose computer programming language that is concurrent, class-based, and object-oriented.
|-
| [[Applications/Mafft|Mafft]]
| MAFFT is a multiple sequence alignment program for Unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), and FFT-NS-2 (fast; for alignment of <∼30,000 sequences).
|-
| [[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 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 independently of network access or a central server. Committing, branching and merging are fast and cheap.
|-
| [[Applications/modflow|Modflow]]
| Program and framework were developed to provide a platform for supporting multiple models and multiple types of models within the same simulation.
|-
| [[applications/Mpich|Mpich]]
| MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard.
|-
| [[applications/Miniconda|Miniconda]]
| Miniconda is a lite version of Anaconda used for creating virtual environments.
|-
| [[applications/Minimap2|Minimap2]]
| Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
|-
| [[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/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/Netcdf-c|Netcdf-c]]
| NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support creating, accessing, and sharing array-oriented scientific data.
|-
| [[applications/Nwchem|Nwchem]]
| NWChem provides computational chemistry tools and particularly large scientific computational chemistry problems.
|-
| [[applications/Obitools|Obitools]]
| The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, considering 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/Orca|Orca]]
| ORCA is a flexible, efficient and easy-to-use general-purpose tool for quantum chemistry with a specific emphasis on the spectroscopic properties of open-shell molecules.
|-
|[[applications/Packmol|Packmol]]
| PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short-range repulsive interactions do not disrupt the simulations.
|-
|[[applications/Paraview|Paraview]]
| ParaView is an open-source, multi-platform data analysis and visualisation application. ParaView users can quickly build visualisations to analyse their data using qualitative and quantitative techniques.
|-
|[[applications/Perl|Perl]]
| Perl is a general-purpose, interpreted, dynamic programming language with a large number of libraries.
|-
|[[applications/Prinseq-lite|Prinseq-lite]]
| PRINSEQ can be used to filter, reformat, or trim genomic and metagenomic sequence data.
|-
|[[applications/Python|Python]]
| Python is an interpreted, dynamic programming language with a massive set of libraries covering just about every area.
|-
|[[applications/Qiime2|Qiime2]]
| QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open-source, and community-developed.
|-
|[[applications/R|R]]
| R is an open-source programming language and software environment for statistical computing and graphics.
|-
|[[applications/RaXML|RaXML]]
| RaXML is an open-source tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
|-
|[[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/RStudio|RStudio]]
| RStudio provides popular open-source and enterprise-ready professional software for the R statistical computing environment.
|-
| [[applications/Samtools|Samtools]]
| Tools (written in C using htslib) for manipulating next-generation sequencing data
|-
| [[applications/Savu|Savu]]
| Python package to assist with the processing and reconstruction of parallel-beam tomography data.
|-
| [[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/STAR|STAR]]
| Ultrafast universal RNA-seq aligner.
|-
| [[applications/Star-ccm+|Star-ccm+]]
| Star-ccm+ package.
|-
| [[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/transabyss|Transabyss]]
| Software pipeline for analysing ABySS-assembled transcriptome contigs
|-
| [[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 utility 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 bio-mechanical analyses to be readily applied to the model geometry, and the resultant 3D stress and strain patterns to be visualised 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==
Library software listed here refers to those listed in the libs section of the typing module avail.
{| class="wikitable mw-collapsible"
| style="width:25%; background: #f5a091;" | Library
| style="width:75%; background: #f5a091;" | Description
|-
| Boost
| C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications.
|-
| [[programming/Cuda|Cuda]]
| CUDA is a parallel computing platform and application programming interface (API) model created by Nvidia.
|-
| [[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/Gsl|Gsl]]
| The GNU Scientific Library ('''GSL''') is a numerical library for C and C++ programmers.
|-
| [[applications/Hdf5|Hdf5]]
| HDF5 is a data model, library, and file format for storing and managing data.
|-
| [[applications/Hypre|Hypre]]
| A library of high-performance preconditioners and solvers featuring multi-grid methods for the solution of large, sparse linear systems of equations on massively parallel computers.
|-
| [[applications/Libbeagle|Libbeagle]]
| BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.
|-
| [[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/Libpng|Libpng]]
| The reference library for use in applications that read, create, and manipulate PNG (''Portable Network Graphics'') raster image files.
|-
| [[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.
|-
| [[programming/OpenACC|OpenACC]]
| OpenACC is an implementation of multithreading, a method of parallelising whereby a master thread (a series of instructions executed consecutively) forks a specified number of slave threads and the system divides a task among them. This is similar to OpenMP but has had CPU/GPU support from the beginning. There is language support from C/C++ and Fortran.
|-
| [[applications/Openblas|Openblas]]
| OpenBLAS is an optimised BLAS library (based on ''GotoBLAS2'' 1.13 BSD version).
|-
| [[programming/OpenCL|OpenCL]]
| A framework for writing programs that execute across heterogeneous platforms consisting of central processing units (CPUs), graphics processing units (GPUs), digital signal processors (DSPs), and field-programmable gate arrays (FPGAs) and other processors or hardware accelerators.
|-
| [[programming/OpenMP|OpenMP]]
| OpenMP is an implementation of multithreading, a method of parallelising whereby a master thread (a series of instructions executed consecutively) forks a specified number of slave threads and the system divides a task among them. There is language support from C/C++ and Fortran.
|-
| [[applications/OpenMPI|OpenMPI]]
| Open MPI is a Message Passing Interface (MPI) library used for communicating between HPC nodes.
|-
| [[applications/Parmetis|Parmetis]]
| ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs and meshes, and for computing fill-reducing orderings of sparse matrices.
|-
|[[applications/Qt|Qt]]
| Qt is a cross-platform framework, usually used as a graphical toolkit, although it is also very helpful in creating CLI applications on Viper.
|-
| [[applications/Zlib|Zlib]]
| zlib is a software library used for data compression.
|-
|}

==Test Modules==
The test-modules module does not provide access to a specific application; instead, it provides access to a set of additional modules in development.

These modules should not be relied on to be stable modules and are subject to change as software installations are tuned.

If you request an application to be installed, we may ask you to test the module in the test modules area before we make it widely available as a standard module.

<pre style="background-color:#000000; color: white; font-family: monospace, sans-serif;">
[username@login01 ~]$ module add test-modules
[username@login01 ~]$ module avail
--------------------------------------------------- /usr/share/Modules/modulefiles ----------------------------------------------------
dot module-git module-info modules null use.own

--------------------------------------------- /trinity/clustervision/CentOS/7/modulefiles ---------------------------------------------
abyss/1.5.2/gcc-4.9.3 gsl/gcc/2.1 java/jdk1.8.0_102 ospray/0.10.1
<standard output>
-------------------------------------------- /trinity/clustervision/CentOS/7/test-modules ---------------------------------------------
SAS/9.4 gettext/gcc/0.19.8.1 netcdf-c/intel/intelmpi/4.4.1
ansys/v170_test glib/gcc/2.50.2 netcdf-f/intel/intelmpi/4.4.4
ansys/v172sj grackle/gcc/serial/2.2 ood/anaconda/2021.11
cairo/1.14.6 harfbuzz/gcc/1.3.3 openfoam-org/10.0/openmpi-4.0.5/gcc-7.3.0
comsol/52a libffi/gcc/3.2.1 pango/1.40.3
comsol/53 libxml2/gcc/2.9.4 pcre/gccc/8.38
comsol/53a matlab/2021a pixman/0.34.0
comsol/54 matlab/test ruby/2.3.1
enzo/gcc/2016-09-28 mercurial/3.9.1-2016-09-28 singularity/3.5.3/gccc-8.2.0
fontconfig/gcc/2.12.1 mpich/3.2/gcc-5.2.0 scotch/7.0.1/openmpi-4.05/gcc-7.3.0
fontconfig/gcc/2.8.0 music/gcc/1.53 transabyss/1.5.5
freetype/2.7 nas./gcc/2.12.02

</pre>

[[FurtherTopics/FurtherTopics #Modules| Back to Further Topics]] / [[Main Page| Main Page]]

Modules

2025-11-27T09:55:09Z

Pysdlb:

[[FurtherTopics/FurtherTopics #Modules| Back to Further Topics]]
==Applications==
The following is a list of core applications installed on Viper, with links to further information on using those applications on Viper. If you are looking for an application that requires a special license, visit: [[Applications/Special Licenses| Applications requiring special licenses]].

If you are looking for how to use a module, use the [[Quickstart/Using Modules| Quickstart]].

An up-to-date list of all modules available on Viper can be found at [https://hpc.hull.ac.uk/upload/module.html Module List]

Click on the links below for support on the individual applications:

{| class="wikitable mw-collapsible"
| style="width:25%; background: #f5a091;" | Package
| style="width:75%; background: #f5a091;" | Description
|-
| [[applications/ABySS|ABySS]]
| Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler.
|-
| [[applications/Miniconda|Anaconda]]
| Anaconda is the leading open data science platform powered by Python.
|-
| Arnold
| Monte Carlo ray tracing renderer.
|-
| Autotools
| Autotools, is a suite of programming tools designed to assist in making source code packages portable. Provides common tools such as m4-1.4.17, autoconf-2.69, automake-1.15, flex-2.6.2, libtool-2.4, gettext-0.19.8.1, bison-3.0.4 .
|-
| [[applications/BayesTraits|BayesTraits]]
| BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available.
|-
| Bison
| Bison, is a parser generator that is part of the GNU Project.
|-
| [[applications/Blender|Blender]]
| Blender is a free and open-source 3D creation suite. It supports the entirety of the 3D pipeline—modelling, rigging, animation, simulation, rendering, compositing and motion tracking, and even video editing and game creation.
|-
| [[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/Bridger|Bridger]]
| Bridger is an efficient ''de novo'' transcriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference.
|-
| [[applications/Centrifuge|Centrifuge]]
| Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimised specifically for the metagenomic classification problem.
|-
| [[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/Crop|Crop]]
| CROP is an unsupervised nucleic acid sequence clustering algorithm. The algorithm sees the OTUs as a Gaussian mixture and models the clustering process using Birth-death MCMC. This approach makes the OTU prediction more accurate.
|-
| [[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/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 modelling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments.
|-
| [[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 visualisation 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 be grabbed from a live audio/video source.
|-
| Flex
| Flex (Fast lexical analyser), Flex is a tool for generating scanners: programs that recognise lexical patterns in text.
|-
| [[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/Grace|Grace]]
| Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif. Grace is a descendant of ACE/gr, also known as Xmgr.
|-
| [[applications/guppy|Guppy]]
| Local accelerated basecalling for Nanopore data.
|-
|[[applications/HyPhy|HyPhy]]
| HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning.
|-
|[[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/iqtree|IQtree]]
| stochastic algorithm to reconstruct phylogenetic trees using maximum likelihood.
|-
|[[applications/Java|Java]]
| Java is a general-purpose computer programming language that is concurrent, class-based, and object-oriented.
|-
| [[Applications/Mafft|Mafft]]
| MAFFT is a multiple sequence alignment program for Unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), and FFT-NS-2 (fast; for alignment of <∼30,000 sequences).
|-
| [[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 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 independently of network access or a central server. Committing, branching and merging are fast and cheap.
|-
| [[Applications/modflow|Modflow]]
| Program and framework were developed to provide a platform for supporting multiple models and multiple types of models within the same simulation.
|-
| [[applications/Mpich|Mpich]]
| MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard.
|-
| [[applications/Miniconda|Miniconda]]
| Miniconda is a lite version of Anaconda used for creating virtual environments.
|-
| [[applications/Minimap2|Minimap2]]
| Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
|-
| [[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/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/Netcdf-c|Netcdf-c]]
| NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support creating, accessing, and sharing array-oriented scientific data.
|-
| [[applications/Nwchem|Nwchem]]
| NWChem provides computational chemistry tools and particularly large scientific computational chemistry problems.
|-
| [[applications/Obitools|Obitools]]
| The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, considering 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/Orca|Orca]]
| ORCA is a flexible, efficient and easy-to-use general-purpose tool for quantum chemistry with a specific emphasis on the spectroscopic properties of open-shell molecules.
|-
|[[applications/Packmol|Packmol]]
| PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short-range repulsive interactions do not disrupt the simulations.
|-
|[[applications/Paraview|Paraview]]
| ParaView is an open-source, multi-platform data analysis and visualisation application. ParaView users can quickly build visualisations to analyse their data using qualitative and quantitative techniques.
|-
|[[applications/Perl|Perl]]
| Perl is a flexible high-level, general-purpose, interpreted, dynamic programming language with a large number of libraries.
|-
|[[applications/Prinseq-lite|Prinseq-lite]]
| PRINSEQ can be used to filter, reformat, or trim genomic and metagenomic sequence data.
|-
|[[applications/Python|Python]]
| Python is a family of high-level, general-purpose, interpreted, dynamic programming languages and includes IPython.
|-
|[[applications/Qiime2|Qiime2]]
| QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open-source, and community-developed.
|-
|[[applications/R|R]]
| R is an open-source programming language and software environment for statistical computing and graphics.
|-
|[[applications/RaXML|RaXML]]
| RaXML is an open-source tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
|-
|[[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/RStudio|RStudio]]
| RStudio provides popular open-source and enterprise-ready professional software for the R statistical computing environment.
|-
| [[applications/Samtools|Samtools]]
| Tools (written in C using htslib) for manipulating next-generation sequencing data
|-
| [[applications/Savu|Savu]]
| Python package to assist with the processing and reconstruction of parallel-beam tomography data.
|-
| [[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/STAR|STAR]]
| Ultrafast universal RNA-seq aligner.
|-
| [[applications/Star-ccm+|Star-ccm+]]
| Star-ccm+ package.
|-
| [[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/transabyss|Transabyss]]
| Software pipeline for analysing ABySS-assembled transcriptome contigs
|-
| [[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 utility 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 bio-mechanical analyses to be readily applied to the model geometry, and the resultant 3D stress and strain patterns to be visualised 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==
Library software listed here refers to those listed in the libs section of the typing module avail.
{| class="wikitable mw-collapsible"
| style="width:25%; background: #f5a091;" | Library
| style="width:75%; background: #f5a091;" | Description
|-
| Boost
| C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications.
|-
| [[programming/Cuda|Cuda]]
| CUDA is a parallel computing platform and application programming interface (API) model created by Nvidia.
|-
| [[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/Gsl|Gsl]]
| The GNU Scientific Library ('''GSL''') is a numerical library for C and C++ programmers.
|-
| [[applications/Hdf5|Hdf5]]
| HDF5 is a data model, library, and file format for storing and managing data.
|-
| [[applications/Hypre|Hypre]]
| A library of high-performance preconditioners and solvers featuring multi-grid methods for the solution of large, sparse linear systems of equations on massively parallel computers.
|-
| [[applications/Libbeagle|Libbeagle]]
| BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.
|-
| [[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/Libpng|Libpng]]
| The reference library for use in applications that read, create, and manipulate PNG (''Portable Network Graphics'') raster image files.
|-
| [[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.
|-
| [[programming/OpenACC|OpenACC]]
| OpenACC is an implementation of multithreading, a method of parallelizing whereby a master thread (a series of instructions executed consecutively) forks a specified number of slave threads and the system divides a task among them. This is similar to OpenMP but has had CPU/GPU support from the beginning. There is language support from C/C++ and Fortran.
|-
| [[applications/Openblas|Openblas]]
| OpenBLAS is an optimized BLAS library (based on ''GotoBLAS2'' 1.13 BSD version).
|-
| [[programming/OpenCL|OpenCL]]
| A framework for writing programs that execute across heterogeneous platforms consisting of central processing units (CPUs), graphics processing units (GPUs), digital signal processors (DSPs), and field-programmable gate arrays (FPGAs) and other processors or hardware accelerators.
|-
| [[programming/OpenMP|OpenMP]]
| OpenMP is an implementation of multithreading, a method of parallelising whereby a master thread (a series of instructions executed consecutively) forks a specified number of slave threads and the system divides a task among them. There is language support from C/C++ and Fortran.
|-
| [[applications/OpenMPI|OpenMPI]]
| Open MPI is a Message Passing Interface (MPI) library used for communicating between HPC nodes.
|-
| [[applications/Parmetis|Parmetis]]
| ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs and meshes, and for computing fill-reducing orderings of sparse matrices.
|-
|[[applications/Qt|Qt]]
| Qt is a cross-platform framework, usually used as a graphical toolkit, although it is also very helpful in creating CLI applications on Viper.
|-
| [[applications/Zlib|Zlib]]
| zlib is a software library used for data compression.
|-
|}

==Test Modules==
The test-modules module does not provide access to a specific application; instead, it provides access to a set of additional modules in development.

These modules should not be relied on to be stable modules and are subject to change as software installations are tuned.

If you request an application to be installed, we may ask you to test the module in the test modules area before we make it widely available as a standard module.

<pre style="background-color:#000000; color: white; font-family: monospace, sans-serif;">
[username@login01 ~]$ module add test-modules
[username@login01 ~]$ module avail
--------------------------------------------------- /usr/share/Modules/modulefiles ----------------------------------------------------
dot module-git module-info modules null use.own

--------------------------------------------- /trinity/clustervision/CentOS/7/modulefiles ---------------------------------------------
abyss/1.5.2/gcc-4.9.3 gsl/gcc/2.1 java/jdk1.8.0_102 ospray/0.10.1
<standard output>
-------------------------------------------- /trinity/clustervision/CentOS/7/test-modules ---------------------------------------------
SAS/9.4 gettext/gcc/0.19.8.1 netcdf-c/intel/intelmpi/4.4.1
ansys/v170_test glib/gcc/2.50.2 netcdf-f/intel/intelmpi/4.4.4
ansys/v172sj grackle/gcc/serial/2.2 ood/anaconda/2021.11
cairo/1.14.6 harfbuzz/gcc/1.3.3 openfoam-org/10.0/openmpi-4.0.5/gcc-7.3.0
comsol/52a libffi/gcc/3.2.1 pango/1.40.3
comsol/53 libxml2/gcc/2.9.4 pcre/gccc/8.38
comsol/53a matlab/2021a pixman/0.34.0
comsol/54 matlab/test ruby/2.3.1
enzo/gcc/2016-09-28 mercurial/3.9.1-2016-09-28 singularity/3.5.3/gccc-8.2.0
fontconfig/gcc/2.12.1 mpich/3.2/gcc-5.2.0 scotch/7.0.1/openmpi-4.05/gcc-7.3.0
fontconfig/gcc/2.8.0 music/gcc/1.53 transabyss/1.5.5
freetype/2.7 nas./gcc/2.12.02

</pre>

[[FurtherTopics/FurtherTopics #Modules| Back to Further Topics]] / [[Main Page| Main Page]]

Modules

2025-11-27T09:50:24Z

Pysdlb:

[[FurtherTopics/FurtherTopics #Modules| Back to Further Topics]]
==Applications==
The following is a list of core applications installed on Viper, with links to further information on using those applications on Viper. If you are looking for an application that requires a special license, visit: [[Applications/Special Licenses| Applications requiring special licenses]].

If you are looking for how to use a module, use the [[Quickstart/Using Modules| Quickstart]].

An up-to-date list of all modules available on Viper can be found at [https://hpc.hull.ac.uk/upload/module.html Module List]

Click on the links below for support on the individual applications:

{| class="wikitable mw-collapsible"
| style="width:25%; background: #f5a091;" | Package
| style="width:75%; background: #f5a091;" | Description
|-
| [[applications/ABySS|ABySS]]
| Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler.
|-
| [[applications/Miniconda|Anaconda]]
| Anaconda is the leading open data science platform powered by Python.
|-
| Arnold
| Monte Carlo ray tracing renderer.
|-
| Autotools
| Autotools, is a suite of programming tools designed to assist in making source code packages portable. Provides common tools such as m4-1.4.17, autoconf-2.69, automake-1.15, flex-2.6.2, libtool-2.4, gettext-0.19.8.1, bison-3.0.4 .
|-
| [[applications/BayesTraits|BayesTraits]]
| BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available.
|-
| Bison
| Bison, is a parser generator that is part of the GNU Project.
|-
| [[applications/Blender|Blender]]
| Blender is a free and open-source 3D creation suite. It supports the entirety of the 3D pipeline—modelling, rigging, animation, simulation, rendering, compositing and motion tracking, and even video editing and game creation.
|-
| [[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/Bridger|Bridger]]
| Bridger is an efficient ''de novo'' transcriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference.
|-
| [[applications/Centrifuge|Centrifuge]]
| Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimised specifically for the metagenomic classification problem.
|-
| [[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/Crop|Crop]]
| CROP is an unsupervised nucleic acid sequence clustering algorithm. The algorithm sees the OTUs as a Gaussian mixture and models the clustering process using Birth-death MCMC. This approach makes the OTU prediction more accurate.
|-
| [[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/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 modelling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments.
|-
| [[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 visualisation 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 be grabbed from a live audio/video source.
|-
| Flex
| Flex (Fast lexical analyser), Flex is a tool for generating scanners: programs that recognise lexical patterns in text.
|-
| [[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/Grace|Grace]]
| Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif. Grace is a descendant of ACE/gr, also known as Xmgr.
|-
| [[applications/guppy|Guppy]]
| Local accelerated basecalling for Nanopore data.
|-
|[[applications/HyPhy|HyPhy]]
| HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning.
|-
|[[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/iqtree|IQtree]]
| stochastic algorithm to reconstruct phylogenetic trees using maximum likelihood.
|-
|[[applications/Java|Java]]
| Java is a general-purpose computer programming language that is concurrent, class-based, and object-oriented.
|-
| [[Applications/Mafft|Mafft]]
| MAFFT is a multiple sequence alignment program for Unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), and FFT-NS-2 (fast; for alignment of <∼30,000 sequences).
|-
| [[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 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 independently of network access or a central server. Committing, branching and merging are fast and cheap.
|-
| [[Applications/modflow|Modflow]]
| Program and framework were developed to provide a platform for supporting multiple models and multiple types of models within the same simulation.
|-
| [[applications/Mpich|Mpich]]
| MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard.
|-
| [[applications/Miniconda|Miniconda]]
| Miniconda is a lite version of Anaconda used for creating virtual environments.
|-
| [[applications/Minimap2|Minimap2]]
| Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
|-
| [[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/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/Netcdf-c|Netcdf-c]]
| NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support creating, accessing, and sharing array-oriented scientific data.
|-
| [[applications/Nwchem|Nwchem]]
| NWChem provides computational chemistry tools and particularly large scientific computational chemistry problems.
|-
| [[applications/Obitools|Obitools]]
| The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, considering 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/Orca|Orca]]
| ORCA is a flexible, efficient and easy-to-use general-purpose tool for quantum chemistry with a specific emphasis on the spectroscopic properties of open-shell molecules.
|-
|[[applications/Packmol|Packmol]]
| PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short-range repulsive interactions do not disrupt the simulations.
|-
|[[applications/Paraview|Paraview]]
| ParaView is an open-source, multi-platform data analysis and visualisation application. ParaView users can quickly build visualisations to analyse their data using qualitative and quantitative techniques.
|-
|[[applications/Perl|Perl]]
| Perl is a flexible high-level, general-purpose, interpreted, dynamic programming language with a large number of libraries.
|-
|[[applications/Prinseq-lite|Prinseq-lite]]
| PRINSEQ can be used to filter, reformat, or trim genomic and metagenomic sequence data.
|-
|[[applications/Python|Python]]
| Python is a family of high-level, general-purpose, interpreted, dynamic programming languages and includes IPython.
|-
|[[applications/Qiime2|Qiime2]]
| QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open-source, and community-developed.
|-
|[[applications/R|R]]
| R is an open-source programming language and software environment for statistical computing and graphics.
|-
|[[applications/RaXML|RaXML]]
| RaXML is an open-source tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
|-
|[[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/RStudio|RStudio]]
| RStudio provides popular open-source and enterprise-ready professional software for the R statistical computing environment.
|-
| [[applications/Samtools|Samtools]]
| Tools (written in C using htslib) for manipulating next-generation sequencing data
|-
| [[applications/Savu|Savu]]
| Python package to assist with the processing and reconstruction of parallel-beam tomography data.
|-
| [[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/STAR|STAR]]
| Ultrafast universal RNA-seq aligner.
|-
| [[applications/Star-ccm+|Star-ccm+]]
| Star-ccm+ package.
|-
| [[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/transabyss|Transabyss]]
| Software pipeline for analysing ABySS-assembled transcriptome contigs
|-
| [[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 utility 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 bio-mechanical analyses to be readily applied to the model geometry, and the resultant 3D stress and strain patterns to be visualised 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==
Library software listed here refers to those listed in the libs section of the typing module avail.
{| class="wikitable mw-collapsible"
| style="width:25%; background: #f5a091;" | Library
| style="width:75%; background: #f5a091;" | Description
|-
| Boost
| C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications.
|-
| [[programming/Cuda|Cuda]]
| CUDA is a parallel computing platform and application programming interface (API) model created by Nvidia.
|-
| [[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/Gsl|Gsl]]
| The GNU Scientific Library ('''GSL''') is a numerical library for C and C++ programmers.
|-
| [[applications/Hdf5|Hdf5]]
| HDF5 is a data model, library, and file format for storing and managing data.
|-
| [[applications/Hypre|Hypre]]
| A library of high-performance preconditioners and solvers featuring multi-grid methods for the solution of large, sparse linear systems of equations on massively parallel computers.
|-
| [[applications/Libbeagle|Libbeagle]]
| BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.
|-
| [[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/Libpng|Libpng]]
| The reference library for use in applications that read, create, and manipulate PNG (''Portable Network Graphics'') raster image files.
|-
| [[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.
|-
| [[programming/OpenACC|OpenACC]]
| OpenACC is an implementation of multithreading, a method of parallelizing whereby a master thread (a series of instructions executed consecutively) forks a specified number of slave threads and the system divides a task among them. This is similar to OpenMP but has had CPU/GPU support from the beginning. There is language support from C/C++ and Fortran.
|-
| [[applications/Openblas|Openblas]]
| OpenBLAS is an optimized BLAS library (based on ''GotoBLAS2'' 1.13 BSD version).
|-
| [[programming/OpenCL|OpenCL]]
| A framework for writing programs that execute across heterogeneous platforms consisting of central processing units (CPUs), graphics processing units (GPUs), digital signal processors (DSPs), and field-programmable gate arrays (FPGAs) and other processors or hardware accelerators.
|-
| [[programming/OpenMP|OpenMP]]
| OpenMP is an implementation of multithreading, a method of parallelising whereby a master thread (a series of instructions executed consecutively) forks a specified number of slave threads and the system divides a task among them. There is language support from C/C++ and Fortran.
|-
| [[applications/OpenMPI|OpenMPI]]
| Open MPI is a Message Passing Interface (MPI) library used for communicating between HPC nodes.
|-
| [[applications/Parmetis|Parmetis]]
| ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs and meshes, and for computing fill-reducing orderings of sparse matrices.
|-
|[[applications/Qt|Qt]]
| Qt is a cross-platform framework, usually used as a graphical toolkit, although it is also very helpful in creating CLI applications on Viper.
|-
| [[applications/Zlib|Zlib]]
| zlib is a software library used for data compression.
|-
|}

==Test Modules==
The test-modules module does not provide access to a specific application; instead, it provides access to a further set of modules that are in a development state.

These modules should not be relied on to be stable modules and are subject to change as software installations are tuned.

If you request an application to be installed, we may ask you to test the module while it is in the test modules area before we make it widely available as a standard module.

<pre style="background-color:#000000; color: white; font-family: monospace, sans-serif;">
[username@login01 ~]$ module add test-modules
[username@login01 ~]$ module avail
--------------------------------------------------- /usr/share/Modules/modulefiles ----------------------------------------------------
dot module-git module-info modules null use.own

--------------------------------------------- /trinity/clustervision/CentOS/7/modulefiles ---------------------------------------------
abyss/1.5.2/gcc-4.9.3 gsl/gcc/2.1 java/jdk1.8.0_102 ospray/0.10.1
<standard output>
-------------------------------------------- /trinity/clustervision/CentOS/7/test-modules ---------------------------------------------
SAS/9.4 gettext/gcc/0.19.8.1 netcdf-c/intel/intelmpi/4.4.1
ansys/v170_test glib/gcc/2.50.2 netcdf-f/intel/intelmpi/4.4.4
ansys/v172sj grackle/gcc/serial/2.2 ood/anaconda/2021.11
cairo/1.14.6 harfbuzz/gcc/1.3.3 openfoam-org/10.0/openmpi-4.0.5/gcc-7.3.0
comsol/52a libffi/gcc/3.2.1 pango/1.40.3
comsol/53 libxml2/gcc/2.9.4 pcre/gccc/8.38
comsol/53a matlab/2021a pixman/0.34.0
comsol/54 matlab/test ruby/2.3.1
enzo/gcc/2016-09-28 mercurial/3.9.1-2016-09-28 singularity/3.5.3/gccc-8.2.0
fontconfig/gcc/2.12.1 mpich/3.2/gcc-5.2.0 scotch/7.0.1/openmpi-4.05/gcc-7.3.0
fontconfig/gcc/2.8.0 music/gcc/1.53 transabyss/1.5.5
freetype/2.7 nas./gcc/2.12.02

</pre>

[[FurtherTopics/FurtherTopics #Modules| Back to Further Topics]] / [[Main Page| Main Page]]

Main Page

2025-06-16T14:38:30Z

Pysdlb:

__NOTOC__
==Welcome To Viper!==
'''Viper''' is the University's supercomputer in {{CURRENTYEAR}} , often termed an '''HPC''' (or '''H'''igh-'''P'''erformance '''C'''omputer).

It is located on-site with a dedicated team to operate Viper and support users.

* '''New user'''
**[[#introduction|'''With no knowledge of Viper''']]
**[[#Quickstart| '''Who already knows what Viper is''']]
**[[DAIM_Guide| '''Are you a DAIM MSc student needing to use Viper for your project?''']]
*''' Existing Users'''
** [[FurtherTopics/FurtherTopics| '''Looking for further information?''']]
** [[#Support|'''Need support?''']]
[[ File:Hpc-tidied2.jpg |center| Viper]]

<div id="introduction"></div>
[[#introduction|'''What is a supercomputer?''']]

A supercomputer has a much higher processing power than a general-purpose computer. Viper is composed of:
*180 compute nodes, each with 28 processing cores and 128GB of memory
*4 high-memory nodes with 1TB of memory
*9 GPU nodes with Nvidia A100s, 4 A40s and a twin P100.
*2 Visualisation nodes

'''Why is Viper useful?'''

*Many jobs can be run at once.
*These jobs can be split into tasks and run in parallel.
*Or these jobs can be run with many different scenarios in parallel.
*Using Viper frees up your personal computer.
*Viper has significant resources that your desktop computer does not.

'''Who might use Viper?'''

Viper is currently being used for:

* Astrophysics
* BioEngineering
* Business Analysis
* Computer Science
* Geographical research
* Artificial Intelligence
* And many more

==Quickstart==
Here is a step-by-step guide to help you run your first job. Feel free to skip any topics you may already be comfortable with.

# [[Quickstart/What Is Viper|What is Viper]]
# [https://hull.service-now.com/student/ Apply for an account (Student portal)]
# [[Quickstart/Connect|Getting Connected]]
# [[Quickstart/Linux Command Line|Linux command line]]
# [[Quickstart/Using Modules| Using Modules]]
# [[Quickstart/Interactive|Interactive Sessions]]
# [[Quickstart/Slurm|Slurm]]
# [[Quickstart/Batch Jobs|Batch Jobs]]
# [[Quickstart/Data Management|Data Management]]
# [[Quickstart/Virtual Environments| Virtual Environments]]
# [[Quickstart/Tutorial Videos|Tutorial Videos]]

==Support==

* '''[[General/UserDropin|User Drop-in Sessions]] are held every Wednesday from 09:30 to 10:30 am on Teams'''.
* There is a selection of [[Tutorial Videos/Tutorial Videos|Tutorial Videos]] to help get you started using Viper.
* In the [https://hull.service-now.com/ Support Portal] you can find forms to request VPN access, report an issue with a job, request a software install, and request a runtime extension.

==Further Topics==

[[FurtherTopics/FurtherTopics| Further Topics]]

Quickstart/What Is Viper

2025-06-16T14:35:13Z

Pysdlb:

==What is Viper?==
Viper is the University of Hull's supercomputer and is located on-site with its dedicated team to administrate it and develop applications upon it.

==What is a supercomputer?==
[[ File:Vipero1cropped.jpg|frame|These 4 racks contain 180x compute nodes, 4x high memory nodes, and 5x accelerator nodes which form part of Viper.]][[ File:Storage01cropped.jpg|frame|These racks contain the storage which is 0.5 Petabyte and the controller nodes, two login nodes, and two visualisation nodes.]]
Supercomputers are computers with a high level of computing performance compared to general-purpose computers. A supercomputer like Viper has a lot of elements of a desktop computer — processors, memory, disk, operating system — just more of them.

==Why do we need a supercomputer?==
The point of having a high-performance computer is so that the individual nodes can work together to solve a problem larger than any one computer can easily solve.

Supercomputers generally aim for maximum in capability computing rather than capacity computing. Capability computing is typically thought of as using the maximum computing power to solve a single large problem in the shortest amount of time. Often, a capability system can solve a problem of a size or complexity that no other computer can, e.g., ''a very complex weather simulation application''.

==How does Viper work?==
High-performance computers achieve a high level of performance by allowing the user to split a large job into smaller computation tasks, which then run in parallel, or by running a single task with many different scenarios on the data across parallel processing units.

Similar to all other supercomputers, Viper runs on [http://linux.co.uk Linux], which is similar to UNIX in many ways and has a wide body of software to support it.

==Who can use Viper?==
Viper is available to all research staff and postgraduates at the University of Hull for free and provides an environment that will stimulate innovation and support world-class [https://hpc.wordpress.hull.ac.uk/research-outputs/ research].

Viper is currently used for:

* Astrophysics
* BioEngineering
* Business School
* Chemistry
* Computer Science
* Computational Linguistics
* Geography
* And many more

== Viper's hardware ==

{| class="wikitable mw-collapsible "
| style="width:25%; background: #ecc;" | Hardware
| style="width:75%;background: #ecc; " |
|-
|[[File: Computenodes.jpg]]
| '''Compute Nodes''' These make up most of the computing nodes and perform most of the standard computing processes within the HPC. Each node has 128 GB of RAM.
|-
|[[File: Highmemorynodes.jpg]]
| '''High Memory Nodes''' These are very similar to the compute nodes, but they have much more memory; ours have 1 Terabyte of RAM each, which makes them ideal for research involving large memory models like engineering and DNA analysis in biology.
|-
|[[File:Acceleratornodes.jpg]]
|'''Accelerator Nodes''' Also known as GPU nodes. We have 9 GPU nodes, each identical to compute nodes with the addition of an Nvidia Ampere A100, A40 GPU and a twin P100 per node. These are almost similar to high-end graphics cards found in gaming rigs. The usefulness of these cards lies in their thousands of very small processing cores, which enable them to execute small amounts of code in a massively parallel manner. This is why these cards are used in the areas of machine learning and deep learning.
|-
|[[File: Visualisationnodes.jpg]]
|'''Visualisation Nodes''' These are used for connecting from remote computers, such as desktops, and allow the rendered outputs from data to be viewed on a local computer. There are two visualisation nodes with 2x Nvidia GTX 980TI.
|-
|[[File: Highspeednetwork.jpg]]
|'''High Speed Network''' All these compute nodes are connected by a very fast Intel Omni-Path network to allow the compute nodes to act together. This runs at 100Gbit/s.
|-
|[[File: Storagenodes.jpg]]
|'''Storage Nodes''' These are servers in their own right, which allow access to the actual storage arrays (hard disks), Viper accesses its disk storage via these nodes.
|-
|[[File: Storagearray.jpg]]
|'''Storage Array''' These are the actual disks held in a chassis and make up the whole file storage for Viper. Viper has a total file space of 0.5 Petabytes or 500 Terabytes.
|-
|[[File:Controllernodes.jpg]]
|'''Controller Node''' The controller nodes are responsible for the management of all the compute nodes. Managing the loading of jobs, their termination and completion via the job scheduler, for Viper, this is SLURM.
|-
|[[ File:Loginnodes.jpg ]]
|'''Login Nodes''' These are the nodes which allow the user to log in to the cluster, and this area is then used by the user to prepare jobs for the cluster. Although this is a server in its own right, it is not used for computing work.
|-
|}

[[Main Page #Quickstart| Back]] / [https://viper.hull.ac.uk/ Next (Apply for an account)]

Quickstart/What Is Viper

2025-06-16T14:33:26Z

Pysdlb:

==What is Viper?==
Viper is the University of Hull's supercomputer and is located on-site with its own dedicated team to administrate it and develop applications upon it.

==What is a supercomputer?==
[[ File:Vipero1cropped.jpg|frame|These 4 racks contain 180x compute nodes, 4x high memory nodes, and 5x accelerator nodes which form part of Viper.]][[ File:Storage01cropped.jpg|frame|These racks contain the storage which is 0.5 Petabyte and the controller nodes, two login nodes, and two visualisation nodes.]]
Supercomputers are computers with a high level of computing performance compared to general-purpose computers. A supercomputer like Viper has a lot of elements of a desktop computer — processors, memory, disk, operating system — just more of them.

==Why do we need a supercomputer?==
The point of having a high-performance computer is so that the individual nodes can work together to solve a problem larger than any one computer can easily solve.

Supercomputers generally aim for the maximum in capability computing rather than capacity computing. Capability computing is typically thought of as using the maximum computing power to solve a single large problem in the shortest amount of time. Often a capability system is able to solve a problem of a size or complexity that no other computer can, e.g., ''a very complex weather simulation application''.

==How does Viper work?==
High-performance computers achieve a high level of performance by allowing the user to split a large job into smaller computation tasks which then run in parallel, or by running a single task with many different scenarios on the data across parallel processing units.

Similar to all other supercomputers Viper runs on [http://linux.co.uk Linux], which is similar to UNIX in many ways and has a wide body of software to support it.

==Who can use Viper?==
Viper is available to all research staff and postgraduates at the University of Hull for free and provides an environment that will stimulate innovation and support world-class [https://hpc.wordpress.hull.ac.uk/research-outputs/ research].

Viper is currently used for:

* Astrophysics
* BioEngineering
* Business School
* Chemistry
* Computer Science
* Computation Linguistics
* Geography
* And many more

== Viper's hardware ==

{| class="wikitable mw-collapsible "
| style="width:25%; background: #ecc;" | Hardware
| style="width:75%;background: #ecc; " |
|-
|[[File: Computenodes.jpg]]
| '''Compute Nodes''' These make up most of the computing nodes and perform most of the standard computing processes within the HPC. Each node has 128 GB of RAM.
|-
|[[File: Highmemorynodes.jpg]]
| '''High Memory Nodes''' These are very similar to the compute nodes, but they have much more memory; ours have 1 Terabyte of RAM each, which makes them ideal for research involving large memory models like engineering and DNA analysis in biology.
|-
|[[File:Acceleratornodes.jpg]]
|'''Accelerator Nodes''' Also known as GPU nodes. We have 9 GPU nodes, each identical to compute nodes with the addition of an Nvidia Ampere A100, A40 GPU and a twin P100 per node. These are almost similar to high-end graphics cards found in gaming rigs. The usefulness of these cards lies in their thousands of very small processing cores, which enable them to execute small amounts of code in a massively parallel manner. This is why these cards are used in the areas of machine learning and deep learning.
|-
|[[File: Visualisationnodes.jpg]]
|'''Visualisation Nodes''' These are used for connecting from remote computers, such as desktops, and allow the rendered outputs from data to be viewed on a local computer. There are two visualisation nodes with 2x Nvidia GTX 980TI.
|-
|[[File: Highspeednetwork.jpg]]
|'''High Speed Network''' All these compute nodes are connected by a very fast Intel Omni-Path network to allow the compute nodes to act together. This runs at 100Gbit/s.
|-
|[[File: Storagenodes.jpg]]
|'''Storage Nodes''' These are servers in their own right, which allow access to the actual storage arrays (hard disks), Viper accesses its disk storage via these nodes.
|-
|[[File: Storagearray.jpg]]
|'''Storage Array''' These are the actual disks held in a chassis and make up the whole file storage for Viper. Viper has a total file space of 0.5 Petabytes or 500 Terabytes.
|-
|[[File:Controllernodes.jpg]]
|'''Controller Node''' The controller nodes are responsible for the management of all the compute nodes. Managing the loading of jobs, their termination and completion via the job scheduler, for Viper, this is SLURM.
|-
|[[ File:Loginnodes.jpg ]]
|'''Login Nodes''' These are the nodes which allow the user to log in to the cluster, and this area is then used by the user to prepare jobs for the cluster. Although this is a server in its own right, it is not used for computing work.
|-
|}

[[Main Page #Quickstart| Back]] / [https://viper.hull.ac.uk/ Next (Apply for an account)]

Quickstart/Connect

2025-02-17T09:56:54Z

Pysdlb:

__TOC__

A VPN is required to connect to Viper off campus or from the university guest's wifi. Connections from Eduroam don't require VPN.

* If you have a managed PC then VPN access is already provided.
* If you have your own computer and want VPN access you can request access through the [https://hull.service-now.com/ Support Portal].

==Connection Method 1 - Web browser==

Viper can be accessed through a browser using the Viper Ondemand service which allows you to run jobs without using an SSH terminal

* [https://viperood.hpc.hull.ac.uk/pun/sys/dashboard Viper Ondemand]

==Connection Method 2 - SSH==

If you wish to use an SSH terminal follow the instructions below.

''If this is your first time connecting please note that you may see an error message in .XAuthority, this is normal and you can ignore it.''

===Connection Method 2 - Connecting with a Windows PC===

An application that allows SSH connections must be installed to connect to Viper from a Windows PC. We recommend MobaXterm.

'''Installing MobaXterm'''

1. Visit [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Website]

2. Complying with the license agreement download the ''portable version''

[[File:Mobaxtermportable.png| none|link=https://mobaxterm.mobatek.net/download-home-edition.html]]

3. Unzip the file

4. Double-click MobaXterm_Personal_24.2 (or later)

'''Using MobaXterm To Connect'''

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

<pre>
password:
</pre>

8. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

===Connection Method 2 - Connecting on Mac===

1. Go to Applications -> Utilities and open Terminal

2. Type ssh -Y <''yourusername''>@viperlogin.hpc..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 on the screen.

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

===Connection Method 2 - Connecting on Linux===

1. Open a Terminal application

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

<pre>
password:
</pre>

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

[[Main Page#Quickstart| Back]] / [[Quickstart/Linux Command Line| Next (Linux Command Line)]]

Quickstart/Connect

2025-01-22T16:39:11Z

Pysdlb:

__TOC__

To connect to Viper off campus a VPN is required.

* If you have a managed PC then VPN access is already provided.
* If you have your own computer and want VPN access you can request access through the [https://hull.service-now.com/ Support Portal].

==Connection Method 1 - Web browser==

Viper can be accessed through a browser using the Viper Ondemand service which allow you to run jobs without using an SSH terminal

* [https://viperood.hpc.hull.ac.uk/pun/sys/dashboard Viper Ondemand]

==Connection Method 2 - SSH==

If you wish to use an SSH terminal following the instructions below.

''If this is your first time connecting please note that you may see an error message in .XAuthority, this is normal and you can ignore it.''

===Connection Method 2 - Connecting with a Windows PC===

An application that allows SSH connections must be installed to connect to Viper from a Windows PC. We recommend MobaXterm.

'''Installing MobaXterm'''

1. Visit [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Website]

2. Complying with the license agreement download the ''portable version''

[[File:Mobaxtermportable.png| none|link=https://mobaxterm.mobatek.net/download-home-edition.html]]

3. Unzip the file

4. Double-click MobaXterm_Personal_24.2 (or later)

'''Using MobaXterm To Connect'''

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

<pre>
password:
</pre>

8. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

===Connection Method 2 - Connecting on Mac===

1. Go to Applications -> Utilities and open Terminal

2. Type ssh -Y <''yourusername''>@viperlogin.hpc..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 on the screen.

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

===Connection Method 2 - Connecting on Linux===

1. Open a Terminal application

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

<pre>
password:
</pre>

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

[[Main Page#Quickstart| Back]] / [[Quickstart/Linux Command Line| Next (Linux Command Line)]]

Quickstart/Connect

2025-01-22T15:36:42Z

Pysdlb: /* Connection Method 2 */

__TOC__

To connect to Viper off campus a VPN is required.

* If you have a managed PC then VPN access is already provided.
* If you have your own computer and want VPN access you can request access through the [https://hull.service-now.com/ Support Portal].

==Connection Method 1==

Viper can be accessed through a browser using the Viper Ondemand service which allow you to run jobs without using an SSH terminal

* [https://viperood.hpc.hull.ac.uk/pun/sys/dashboard Viper Ondemand]

==Connection Method 2==

If you wish to use an SSH terminal following the instructions below.

''If this is your first time connecting please note that you may see an error message in .XAuthority, this is normal and you can ignore it.''

===Connection Method 2 - Connecting with a Windows PC===

An application that allows SSH connections must be installed to connect to Viper from a Windows PC. We recommend MobaXterm.

'''Installing MobaXterm'''

1. Visit [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Website]

2. Complying with the license agreement download the ''portable version''

[[File:Mobaxtermportable.png| none|link=https://mobaxterm.mobatek.net/download-home-edition.html]]

3. Unzip the file

4. Double-click MobaXterm_Personal_24.2 (or later)

'''Using MobaXterm To Connect'''

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

<pre>
password:
</pre>

8. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

===Connection Method 2 - Connecting on Mac===

1. Go to Applications -> Utilities and open Terminal

2. Type ssh -Y <''yourusername''>@viperlogin.hpc..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 on the screen.

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

===Connection Method 2 - Connecting on Linux===

1. Open a Terminal application

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

<pre>
password:
</pre>

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

[[Main Page#Quickstart| Back]] / [[Quickstart/Linux Command Line| Next (Linux Command Line)]]

Quickstart/Connect

2025-01-22T15:36:04Z

Pysdlb:

__TOC__

To connect to Viper off campus a VPN is required.

* If you have a managed PC then VPN access is already provided.
* If you have your own computer and want VPN access you can request access through the [https://hull.service-now.com/ Support Portal].

==Connection Method 1==

Viper can be accessed through a browser using the Viper Ondemand service which allow you to run jobs without using an SSH terminal

* [https://viperood.hpc.hull.ac.uk/pun/sys/dashboard Viper Ondemand]

==Connection Method 2==

If you wish to use an SSH terminal following the instructions below.

* Jump ahead to your operating system: [[#Connecting on a Windows PC| Windows]] / [[#Connecting on Mac| Mac]] / [[#Connecting on Linux| Linux]]

''If this is your first time connecting please note that you may see an error message in .XAuthority, this is normal and you can ignore it.''

===Connection Method 2 - Connecting with a Windows PC===

An application that allows SSH connections must be installed to connect to Viper from a Windows PC. We recommend MobaXterm.

'''Installing MobaXterm'''

1. Visit [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Website]

2. Complying with the license agreement download the ''portable version''

[[File:Mobaxtermportable.png| none|link=https://mobaxterm.mobatek.net/download-home-edition.html]]

3. Unzip the file

4. Double-click MobaXterm_Personal_24.2 (or later)

'''Using MobaXterm To Connect'''

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

<pre>
password:
</pre>

8. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

===Connection Method 2 - Connecting on Mac===

1. Go to Applications -> Utilities and open Terminal

2. Type ssh -Y <''yourusername''>@viperlogin.hpc..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 on the screen.

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

===Connection Method 2 - Connecting on Linux===

1. Open a Terminal application

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

<pre>
password:
</pre>

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

[[Main Page#Quickstart| Back]] / [[Quickstart/Linux Command Line| Next (Linux Command Line)]]

Quickstart/Connect

2025-01-22T15:35:42Z

Pysdlb:

To connect to Viper off campus a VPN is required.

* If you have a managed PC then VPN access is already provided.
* If you have your own computer and want VPN access you can request access through the [https://hull.service-now.com/ Support Portal].

==Connection Method 1==

Viper can be accessed through a browser using the Viper Ondemand service which allow you to run jobs without using an SSH terminal

* [https://viperood.hpc.hull.ac.uk/pun/sys/dashboard Viper Ondemand]

==Connection Method 2==

If you wish to use an SSH terminal following the instructions below.

* Jump ahead to your operating system: [[#Connecting on a Windows PC| Windows]] / [[#Connecting on Mac| Mac]] / [[#Connecting on Linux| Linux]]

''If this is your first time connecting please note that you may see an error message in .XAuthority, this is normal and you can ignore it.''

===Connection Method 2 - Connecting with a Windows PC===

An application that allows SSH connections must be installed to connect to Viper from a Windows PC. We recommend MobaXterm.

'''Installing MobaXterm'''

1. Visit [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Website]

2. Complying with the license agreement download the ''portable version''

[[File:Mobaxtermportable.png| none|link=https://mobaxterm.mobatek.net/download-home-edition.html]]

3. Unzip the file

4. Double-click MobaXterm_Personal_24.2 (or later)

'''Using MobaXterm To Connect'''

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

<pre>
password:
</pre>

8. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

===Connection Method 2 - Connecting on Mac===

1. Go to Applications -> Utilities and open Terminal

2. Type ssh -Y <''yourusername''>@viperlogin.hpc..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 on the screen.

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

===Connection Method 2 - Connecting on Linux===

1. Open a Terminal application

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

<pre>
password:
</pre>

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

[[Main Page#Quickstart| Back]] / [[Quickstart/Linux Command Line| Next (Linux Command Line)]]

Quickstart/Connect

2025-01-22T15:34:07Z

Pysdlb:

To connect to Viper off campus a VPN is required. If you do not have access to the VPN you can request access through the [https://hull.service-now.com/ Support Portal].

==Connection Method 1==

Viper can be accessed through a browser using the Viper Ondemand service which allow you to run jobs without using an SSH terminal

* [https://viperood.hpc.hull.ac.uk/pun/sys/dashboard Viper Ondemand]

==Connection Method 2==

If you wish to use an SSH terminal following the instructions below.

* Jump ahead to your operating system: [[#Connecting on a Windows PC| Windows]] / [[#Connecting on Mac| Mac]] / [[#Connecting on Linux| Linux]]

''If this is your first time connecting please note that you may see an error message in .XAuthority, this is normal and you can ignore it.''

===Connection Method 2 - Connecting with a Windows PC===

An application that allows SSH connections must be installed to connect to Viper from a Windows PC. We recommend MobaXterm.

'''Installing MobaXterm'''

1. Visit [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Website]

2. Complying with the license agreement download the ''portable version''

[[File:Mobaxtermportable.png| none|link=https://mobaxterm.mobatek.net/download-home-edition.html]]

3. Unzip the file

4. Double-click MobaXterm_Personal_24.2 (or later)

'''Using MobaXterm To Connect'''

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

<pre>
password:
</pre>

8. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

===Connection Method 2 - Connecting on Mac===

1. Go to Applications -> Utilities and open Terminal

2. Type ssh -Y <''yourusername''>@viperlogin.hpc..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 on the screen.

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

===Connection Method 2 - Connecting on Linux===

1. Open a Terminal application

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

<pre>
password:
</pre>

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

[[Main Page#Quickstart| Back]] / [[Quickstart/Linux Command Line| Next (Linux Command Line)]]

Quickstart/Connect

2025-01-22T15:32:34Z

Pysdlb:

To connect to Viper off campus a VPN is required. If you do not have access to the VPN you can request access through the [https://hull.service-now.com/ Support Portal].

'''Connection Method 1''' : Viper can be accessed through a browser using the Viper Ondemand service which allow you to run jobs without using an SSH terminal

* [https://viperood.hpc.hull.ac.uk/pun/sys/dashboard Viper Ondemand]

'''Connection Method 2''' : If you wish to use an SSH terminal following the instructions below.

* Jump ahead to your operating system: [[#Connecting on a Windows PC| Windows]] / [[#Connecting on Mac| Mac]] / [[#Connecting on Linux| Linux]]

''If this is your first time connecting please note that you may see an error message in .XAuthority, this is normal and you can ignore it.''

==Connection Method 2 - Connecting with a Windows PC==

An application that allows SSH connections must be installed to connect to Viper from a Windows PC. We recommend MobaXterm.

'''Installing MobaXterm'''

1. Visit [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Website]

2. Complying with the license agreement download the ''portable version''

[[File:Mobaxtermportable.png| none|link=https://mobaxterm.mobatek.net/download-home-edition.html]]

3. Unzip the file

4. Double-click MobaXterm_Personal_24.2 (or later)

'''Using MobaXterm To Connect'''

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

<pre>
password:
</pre>

8. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

==Connection Method 2 - Connecting on Mac==

1. Go to Applications -> Utilities and open Terminal

2. Type ssh -Y <''yourusername''>@viperlogin.hpc..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 on the screen.

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

==Connecting on Linux==
1. Open a Terminal application

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

<pre>
password:
</pre>

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

[[Main Page#Quickstart| Back]] / [[Quickstart/Linux Command Line| Next (Linux Command Line)]]

Quickstart/Connect

2025-01-22T15:30:42Z

Pysdlb:

To connect to Viper off campus a VPN is required. If you do not have access to the VPN you can request access through the [https://hull.service-now.com/ Support Portal].

'''Connection Method 1''' : Viper can be accessed through a browser using the Viper Ondemand service which allow you to run jobs without using an SSH terminal

* [https://viperood.hpc.hull.ac.uk/pun/sys/dashboard Viper Ondemand]

'''Connection Method 2''' : If you wish to use an SSH terminal following the instructions below.

* Jump ahead to your operating system: [[#Connecting on a Windows PC| Windows]] / [[#Connecting on Mac| Mac]] / [[#Connecting on Linux| Linux]]

If this is your first time connecting please note that you may see an error message in .XAuthority, this is normal and you can ignore it.
==Connecting on a Windows PC==
An application that allows SSH connections must be installed to connect to Viper from a Windows PC. We recommend MobaXterm.

'''Installing MobaXterm'''

1. Visit [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Website]

2. Complying with the license agreement download the ''portable version''

[[File:Mobaxtermportable.png| none|link=https://mobaxterm.mobatek.net/download-home-edition.html]]

3. Unzip the file

4. Double-click MobaXterm_Personal_24.2 (or later)

'''Using MobaXterm To Connect'''

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

<pre>
password:
</pre>

8. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

==Connecting on Mac==
1. Go to Applications -> Utilities and open Terminal

2. Type ssh -Y <''yourusername''>@viperlogin.hpc..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 on the screen.

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

==Connecting on Linux==
1. Open a Terminal application

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

<pre>
password:
</pre>

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

[[Main Page#Quickstart| Back]] / [[Quickstart/Linux Command Line| Next (Linux Command Line)]]

Quickstart/Connect

2025-01-22T15:24:05Z

Pysdlb:

To connect to Viper off campus a VPN is required. If you do not have access to the VPN you can request access through the [https://hull.service-now.com/ Support Portal].

'''Connection Method 1''' : Viper can be accessed through a browser using the Viper Ondemand service which allow you to run jobs without using an SSH terminal

[https://viperood.hpc.hull.ac.uk/pun/sys/dashboard Viper Ondemand]

'''Connection Method 2''' : If you wish to use an SSH terminal following the instructions below.

Jump ahead to your operating system: [[#Connecting on a Windows PC| Windows]] / [[#Connecting on Mac| Mac]] / [[#Connecting on Linux| Linux]]

If this is your first time connecting please note that you may see an error message in .XAuthority, this is normal and you can ignore it.
==Connecting on a Windows PC==
An application that allows SSH connections must be installed to connect to Viper from a Windows PC. We recommend MobaXterm.

'''Installing MobaXterm'''

1. Visit [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Website]

2. Complying with the license agreement download the ''portable version''

[[File:Mobaxtermportable.png| none|link=https://mobaxterm.mobatek.net/download-home-edition.html]]

3. Unzip the file

4. Double-click MobaXterm_Personal_24.2 (or later)

'''Using MobaXterm To Connect'''

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

<pre>
password:
</pre>

8. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

==Connecting on Mac==
1. Go to Applications -> Utilities and open Terminal

2. Type ssh -Y <''yourusername''>@viperlogin.hpc..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 on the screen.

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

==Connecting on Linux==
1. Open a Terminal application

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

<pre>
password:
</pre>

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

[[Main Page#Quickstart| Back]] / [[Quickstart/Linux Command Line| Next (Linux Command Line)]]

Quickstart/Connect

2025-01-22T15:22:21Z

Pysdlb:

To connect to Viper off campus a VPN is required. If you do not have access to the VPN you can request access through the [https://hull.service-now.com/ Support Portal].

Viper can be accessed through the Viper Ondemand pages which allow you to run jobs without using an SSH terminal

[https://viperood.hpc.hull.ac.uk/pun/sys/dashboard Viper Ondemand]

However, if you wish to use an SSH terminal following the instructions below.

Jump ahead to your operating system: [[#Connecting on a Windows PC| Windows]] / [[#Connecting on Mac| Mac]] / [[#Connecting on Linux| Linux]]

If this is your first time connecting please note that you may see an error message in .XAuthority, this is normal and you can ignore it.
==Connecting on a Windows PC==
An application that allows SSH connections must be installed to connect to Viper from a Windows PC. We recommend MobaXterm.

'''Installing MobaXterm'''

1. Visit [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Website]

2. Complying with the license agreement download the ''portable version''

[[File:Mobaxtermportable.png| none|link=https://mobaxterm.mobatek.net/download-home-edition.html]]

3. Unzip the file

4. Double-click MobaXterm_Personal_24.2 (or later)

'''Using MobaXterm To Connect'''

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

<pre>
password:
</pre>

8. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

==Connecting on Mac==
1. Go to Applications -> Utilities and open Terminal

2. Type ssh -Y <''yourusername''>@viperlogin.hpc..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 on the screen.

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

==Connecting on Linux==
1. Open a Terminal application

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

<pre>
password:
</pre>

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

[[Main Page#Quickstart| Back]] / [[Quickstart/Linux Command Line| Next (Linux Command Line)]]

Quickstart/Connect

2025-01-22T15:21:54Z

Pysdlb:

To connect to Viper off campus a VPN is required. If you do not have access to the VPN you can request access through the [https://hull.service-now.com/ Support Portal].

Viper can be accessed through the Viper Ondemand pages which allow you to run jobs without using an SSH terminal

[https://viperood.hpc.hull.ac.uk/pun/sys/dashboard]

However, if you wish to use an SSH terminal following the instructions below.

Jump ahead to your operating system: [[#Connecting on a Windows PC| Windows]] / [[#Connecting on Mac| Mac]] / [[#Connecting on Linux| Linux]]

If this is your first time connecting please note that you may see an error message in .XAuthority, this is normal and you can ignore it.
==Connecting on a Windows PC==
An application that allows SSH connections must be installed to connect to Viper from a Windows PC. We recommend MobaXterm.

'''Installing MobaXterm'''

1. Visit [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Website]

2. Complying with the license agreement download the ''portable version''

[[File:Mobaxtermportable.png| none|link=https://mobaxterm.mobatek.net/download-home-edition.html]]

3. Unzip the file

4. Double-click MobaXterm_Personal_24.2 (or later)

'''Using MobaXterm To Connect'''

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

<pre>
password:
</pre>

8. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

==Connecting on Mac==
1. Go to Applications -> Utilities and open Terminal

2. Type ssh -Y <''yourusername''>@viperlogin.hpc..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 on the screen.

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

==Connecting on Linux==
1. Open a Terminal application

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

<pre>
password:
</pre>

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

[[Main Page#Quickstart| Back]] / [[Quickstart/Linux Command Line| Next (Linux Command Line)]]

Quickstart/Connect

2024-12-16T14:10:54Z

Pysdlb:

To connect to Viper off campus a VPN is required. If you do not have access to the VPN you can request access through the [https://hull.service-now.com/ Support Portal].

Jump ahead to your operating system: [[#Connecting on a Windows PC| Windows]] / [[#Connecting on Mac| Mac]] / [[#Connecting on Linux| Linux]]

If this is your first time connecting please note that you may see an error message in .XAuthority, this is normal and you can ignore it.
==Connecting on a Windows PC==
An application that allows SSH connections must be installed to connect to Viper from a Windows PC. We recommend MobaXterm.

'''Installing MobaXterm'''

1. Visit [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Website]

2. Complying with the license agreement download the ''portable version''

[[File:Mobaxtermportable.png| none|link=https://mobaxterm.mobatek.net/download-home-edition.html]]

3. Unzip the file

4. Double-click MobaXterm_Personal_24.2 (or later)

'''Using MobaXterm To Connect'''

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

<pre>
password:
</pre>

8. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

==Connecting on Mac==
1. Go to Applications -> Utilities and open Terminal

2. Type ssh -Y <''yourusername''>@viperlogin.hpc..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 on the screen.

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

==Connecting on Linux==
1. Open a Terminal application

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

<pre>
password:
</pre>

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

[[Main Page#Quickstart| Back]] / [[Quickstart/Linux Command Line| Next (Linux Command Line)]]

DAIM Guide

2024-10-07T08:40:26Z

Pysdlb:

__TOC__

== Introduction ==
Viper, the University of Hull’s High-Performance Computing facility, is used by research staff and students in many disciplines across the University and is a potentially significant tool for those with any computational element to their research.
Viper is a ‘cluster’ of approximately 200 computes built into a cluster and features more than 6000 compute cores, high memory systems and GPU technology together with dedicated high-performance storage and fast interconnect between systems to meet the needs of the most computationally demanding tasks.
Some notes about
* Viper runs Linux, though to make use of Viper you do not need to be a Linux expert – being familiar with just a few commands is enough to get started.
* Viper runs a scheduler, a piece of software which manages access to the computers across the cluster, monitoring what is running and how resources such as memory, CPU processors and GPU cards are being used.
* Users run ‘jobs’ some of which are interactive (like Jupyter Notebook sessions) but many of which are submitted to run automatically without user interaction. Jobs usually have a batch script, a text file containing the recipe for the job, for example, what resource is needed and what the job should do.

== Prerequisites ==
* Viper account - to apply for a Viper account, please see [https://hull.service-now.com/ DAIM MSc Project Account Request]
* VPN - You will need a VPN account to access Viper from off-campus. Please see [https://hull.service-now.com/ GlobalProtect Client VPN Service page on the Support Portal]

== Available Resource ==
'''Important''' While Viper has a range of GPU resources available for DAIM student use, including Nvidia A100 and Nvidia A40-based systems, such resource is in very high demand and as such at times there may be many people competing for GPU resources meaning long pend (queuing) times are likely.

Viper is a shared resource, so to help alleviate this for all users, could we suggest:

* Where possible, try and only run '''final''' GPU runs on Viper, and '''keep development of code to either other systems (e.g. own computer, DAIM lab computer or Viper CPU nodes)'''
* Don't request longer runtimes than are required or if you have resources allocated to you but are not going to work for a period of time ''' please cancel your allocation'''
* Please consider other users require GPU access, '''don't queue up multiple Jupyter sessions'''

{| class="wikitable" style="text-align:center;"
|- style="text-align:left;"
! Resource Type
! GPU RAM *
! System RAM
! Count
! Accessible as
! Notes
|-
| style="text-align:left;" | Nvidia A100 MIG 40GB
| 40GB
| 64GB
| 4
| style="text-align:left;" | [[DAIM_Guide#Web_Portal_Nvidia_A100_GPU_MIG_.28Multi-Instance_GPU.29_access | Web portal MIG version]]
| style="text-align:left;" | High demand
|-
| style="text-align:left;" | Nvidia A100 MIG 20GB
| 20GB
| 64GB
| 2
| style="text-align:left;" | [[DAIM_Guide#Web_Portal_Nvidia_A100_GPU_MIG_.28Multi-Instance_GPU.29_access | Web portal MIG version]]
| style="text-align:left;" | High demand
|-
| style="text-align:left;" | Nvidia A100 MIG 10GB
| 10GB
| 32GB
| 1
| style="text-align:left;" | [[DAIM_Guide#Web_Portal_Nvidia_A100_GPU_MIG_.28Multi-Instance_GPU.29_access | Web portal MIG version]]
| style="text-align:left;" | Medium demand

|-
| style="text-align:left;" | CPU only
| -
| 128GB / 1TB
| 10+
| style="text-align:left;" | [[DAIM_Guide#Pilot_Web_Portal_Access Ondemand | Web portal]]
| style="text-align:left;" | Lower demand but low performance for ML. Use for development and testing

|-
| style="text-align:left;" | NVidia A40
| 48GB
| 128GB
| 2
| style="text-align:left;" | [[DAIM_Guide#Web_Portal_Nvidia_A40_GPU_access | Web portal]]
| style="text-align:left;" | Very high demand, expect long wait times - these should only be used if the task exceeds GPU memory available on MIG instances
|}

<nowiki>*</nowiki> There are two specifications of DAIM lab PCs, the majority are equipped with Nvidia GeForce RTX 3070 GPU cards, with 8GB of GPU memory - all GPU instances on Viper have at least an equivalent amount of GPU memory available. There are also several lab PCs (dual monitor lab machines) with Nvidia RTX 3090 GPU cards with 24GB of GPU memory.

== OnDemand Web Portal Access (pilot) ==
We are currently testing a web route to provide Jupyter access via our pilot Viper OnDemand web portal - see http://hpc.mediawiki.hull.ac.uk/General/OOD

This service is in testing, please raise any issues via the University support portal, searching for '''Viper''' to find forms to help you request support.

'''Please note:'''
* VPN access is still required to connect to the Viper OnDemand web portal.
* The DAIM Jupyter apps are in testing and there may be issues which have yet to be resolved.

If you connect to the web portal, you will see several DAIM prefixed apps, which can be used to connect:
==== Create Python Virtual Environment ====
* '''DAIM Create Environment''' - this will create a base Python virtual environment. You can change the name of the base environment by changing the text in the Environment Name box. You can then select this environment kernel to use when in DAIM session notebooks.

==== Web Portal Nvidia A40 GPU access ====
* '''DAIM Jupyter''' - this will launch a Jupyter lab session in your browser tab
* '''DAIM Jupyter Desktop''' - similarly, this will launch a Jupyter session but with the web browser running on Viper OnDemand. This means you should be able to disconnect and reconnect with cells remaining active.

==== Web Portal Nvidia A100 GPU MIG (Multi-Instance GPU) access ====
* '''DAIM Jupyter Desktop MIG''' - this will launch a Jupyter session but with the web browser running on Viper OnDemand. This means you should be able to disconnect and reconnect with cells remaining active. Options are between a 10GB and 20GB VRAM instance. Please only select what is required.
* '''DAIM Jupyter MIG''' - this will launch a Jupyter lab session in your browser tab. Options are between a 10GB and 20GB VRAM instance. Please only select what is required.

==== Web Portal Nvidia A100 GPU MIG (Multi-Instance GPU) automated run ====
* '''TEST DAIM nbconvert Job''' - This will submit a task to run Jupyter-nbconvert to automatically execute the specific notebook when the resource is available without you needing to interact with the notebook. Specify a notebook using the "select path" button and click launch. Once complete nbconvert will produce an output notebook with nbconvert in the name (e.g. the input mynotebook.ipynb will produce mynotebook.nbconvert.ipynb). After you launch the task, it will just run automatically when the resource is available without you needing to interact with it and will be listed as "Running" in your session list. Note that there is very little in terms of output until the notebook execution is complete. Options are between a 10GB and 20GB VRAM instance. Please only select what is required.

==== Web Portal GPU and Job Status Page ====
To help work out what GPU resources are available for use, and how long a queued job may take, there is a monitor tool on the web portal accessible via '''Jobs > GPU Status and current jobs'''.

'''Warning:''' The first time this is run you will be presented with a warning about needing to restart your web server - doing this may terminate running Jupyter sessions, so do not proceed if you have active sessions.

Training/Transferring Data

2024-08-22T15:57:28Z

Pysdlb: /* Linux */

__TOC__

==Methods==

===Small to medium amounts of data===

This can be carried out using a number of SFTP-styled packages such as sftp, scp, rsync, and Filezilla to name a few. Filezilla can be downloaded as a Windows application and may be more suitable for people who prefer a Windows environment, rather than the command line.

'''Note''' FTP (insecure) is disabled on viper.hull.ac.uk and SFTP (secure FTP) is the recommended method.

===Large to a huge amount of data (100GB +)===
To avoid excessive network congestion and the long period to transfer such data please raise a [https://hull.service-now.com/ support ticket] for further details. This may typically involve connecting a USB data drive directly to VIPER to copy the data quickly into your user area.

===OneDrive to Viper===

With the University using MS OneDrive, it is possible to copy files to Viper. For multiple files, zip your files up on OneDrive first (considerably easier), as shown here:

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | From OneDrive to Viper
|-
|
* Starting with the zipped file MyData.zip on OneDrive, copied previously and compressed from local storage.
* Click on the '''share icon''' or options for the file here (three horizontal dots) and select '''share'''.

[[File:onedrive-01.png]]

* Then

[[File:onedrive-02.png]]

* Click on '''Copy'''

[[File:onedrive-03.png]]

* On your Viper console application, type '''wget''' and paste in the copied link and follow with '''-O yourfilename''' (otherwise Linux will name the file to the OneDrive link - ''argh!'')

[[File:onedrive-04.png]]

* And here is the received file

[[File:onedrive-05.png]]

'''Remember''' to un-share the file on OneDrive and use unzip (if required) on Linux to restore the file structure.

|}

==Universal==
The following can only be performed on Windows after installing MobaXterm or PuTTY.

The example user is user1; you will need to enter your username here:

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * To Viper from local computer
|-
|scp myfile user1@viperlogin.hpc.hull.ac.uk:myfile
|-
|rsync -av my-directory viper.hull.ac.uk:/data/users/YourID
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * From Viper to your local computer
|-
| scp user1@viperlogin.hpc.hull.ac.uk:bio/YourUCInetID/hpc-file
|-
|rsync -av viper.hull.ac.uk:/data/users/YourID/mydatadirectory
|}

==Windows==
The following example uses MobaXterm, for transferring large files it is recommended to use FileZilla. For instructions on how to use FileZilla view the Linux section. follow the instruction in the Getting Connected section for installing MobaXterm.

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * Uploading Files
|-
|* To upload files to Viper, navigate to the directory you wish to upload files to use the MobaXterm file browser.
* Choose the file/files to upload and click open or alternatively drag and drop the file/files you wish to upload over the Viper file browser.
* The upload may take some time depending on upload speed and file size.
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * Downloading Files
|-
|* To download files from Viper, navigate to the directory using the MobaXterm file browser.
[[File:mobaxterm_file_browser.jpg]]
* Select the file/files you wish to download and click the 'download selected files button'.
[[File:mobaxterm_download_icon.jpg]]
* Choose the directory where you want the files to download and click ok.
* The download will start, depending on download speed and file size this may take some time.
|}

==MacOS==
The following example uses Cyberduck, you can download Cyberduck from https://cyberduck.io macOS also supports FileZilla for an example of how to use FileZilla please view the Linux section.

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Connecting
|-
|
* Click Open Connection.
* From the drop-down menu select '''SFTP''' (SSH File Transfer Protocol)
* Enter server viperlogin.hpc.hull.ac.uk, Port: 22, Username: University UID, Password: university password
* Click Connect.

|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Uploading Files
|-
|
* Click Upload
* Choose the file/folder you want to upload and click Choose.
* The transfer window will appear.
* Please note due to file size the upload may take some time.
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Downloading Files
|-
|
* From the file browser right-click on the file/folder to download and select download from the menu.
* The transfer window will appear.
* Please note due to file size the download may take some time.
|}

==Linux==

The following example uses FileZilla, you can download FileZilla from https://filezilla-project.org/ (''Windows/Linux and MacOS'').
* '''Note''': the FileZilla installer sometimes comes with additional trial software packages. We would advise against installing these

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Using FileZilla
|-
|
*Enter the Host: viperlogin.hpc.hull.ac.uk, username, password, and port: 22, using an SFTP connection.

* A pop-up will appear informing that the server host key is unknown. Click Always trust this host and click ok. In the remote site box, your Viper directory will appear.
* To transfer files click and drag the file/folder from either your pc to Viper (left to right) or from Viper to your pc (right to left). The transfer will start depending on transfer speed and file size this may take some time.

|}

==Navigation==

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

Training/Transferring Data

2024-08-22T15:57:12Z

Pysdlb: /* Linux */

__TOC__

==Methods==

===Small to medium amounts of data===

This can be carried out using a number of SFTP-styled packages such as sftp, scp, rsync, and Filezilla to name a few. Filezilla can be downloaded as a Windows application and may be more suitable for people who prefer a Windows environment, rather than the command line.

'''Note''' FTP (insecure) is disabled on viper.hull.ac.uk and SFTP (secure FTP) is the recommended method.

===Large to a huge amount of data (100GB +)===
To avoid excessive network congestion and the long period to transfer such data please raise a [https://hull.service-now.com/ support ticket] for further details. This may typically involve connecting a USB data drive directly to VIPER to copy the data quickly into your user area.

===OneDrive to Viper===

With the University using MS OneDrive, it is possible to copy files to Viper. For multiple files, zip your files up on OneDrive first (considerably easier), as shown here:

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | From OneDrive to Viper
|-
|
* Starting with the zipped file MyData.zip on OneDrive, copied previously and compressed from local storage.
* Click on the '''share icon''' or options for the file here (three horizontal dots) and select '''share'''.

[[File:onedrive-01.png]]

* Then

[[File:onedrive-02.png]]

* Click on '''Copy'''

[[File:onedrive-03.png]]

* On your Viper console application, type '''wget''' and paste in the copied link and follow with '''-O yourfilename''' (otherwise Linux will name the file to the OneDrive link - ''argh!'')

[[File:onedrive-04.png]]

* And here is the received file

[[File:onedrive-05.png]]

'''Remember''' to un-share the file on OneDrive and use unzip (if required) on Linux to restore the file structure.

|}

==Universal==
The following can only be performed on Windows after installing MobaXterm or PuTTY.

The example user is user1; you will need to enter your username here:

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * To Viper from local computer
|-
|scp myfile user1@viperlogin.hpc.hull.ac.uk:myfile
|-
|rsync -av my-directory viper.hull.ac.uk:/data/users/YourID
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * From Viper to your local computer
|-
| scp user1@viperlogin.hpc.hull.ac.uk:bio/YourUCInetID/hpc-file
|-
|rsync -av viper.hull.ac.uk:/data/users/YourID/mydatadirectory
|}

==Windows==
The following example uses MobaXterm, for transferring large files it is recommended to use FileZilla. For instructions on how to use FileZilla view the Linux section. follow the instruction in the Getting Connected section for installing MobaXterm.

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * Uploading Files
|-
|* To upload files to Viper, navigate to the directory you wish to upload files to use the MobaXterm file browser.
* Choose the file/files to upload and click open or alternatively drag and drop the file/files you wish to upload over the Viper file browser.
* The upload may take some time depending on upload speed and file size.
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * Downloading Files
|-
|* To download files from Viper, navigate to the directory using the MobaXterm file browser.
[[File:mobaxterm_file_browser.jpg]]
* Select the file/files you wish to download and click the 'download selected files button'.
[[File:mobaxterm_download_icon.jpg]]
* Choose the directory where you want the files to download and click ok.
* The download will start, depending on download speed and file size this may take some time.
|}

==MacOS==
The following example uses Cyberduck, you can download Cyberduck from https://cyberduck.io macOS also supports FileZilla for an example of how to use FileZilla please view the Linux section.

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Connecting
|-
|
* Click Open Connection.
* From the drop-down menu select '''SFTP''' (SSH File Transfer Protocol)
* Enter server viperlogin.hpc.hull.ac.uk, Port: 22, Username: University UID, Password: university password
* Click Connect.

|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Uploading Files
|-
|
* Click Upload
* Choose the file/folder you want to upload and click Choose.
* The transfer window will appear.
* Please note due to file size the upload may take some time.
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Downloading Files
|-
|
* From the file browser right-click on the file/folder to download and select download from the menu.
* The transfer window will appear.
* Please note due to file size the download may take some time.
|}

==Linux==

The following example uses FileZilla, you can download FileZilla from https://filezilla-project.org/ (''Windows/Linux and MacOS'').
* '''Note''': the FileZilla installer sometimes comes with additional trial software packages. We would advise against installing these

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Using FileZilla
|-
|
*Enter the Host: viperlogin.hpc.hull.ac.uk, username, password, and port: 22, using an SFTP connection.
[[File:filezilla_linux_login.jpg]]
* A pop-up will appear informing that the server host key is unknown. Click Always trust this host and click ok. In the remote site box, your Viper directory will appear.
* To transfer files click and drag the file/folder from either your pc to Viper (left to right) or from Viper to your pc (right to left). The transfer will start depending on transfer speed and file size this may take some time.

|}

==Navigation==

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

Training/Transferring Data

2024-08-22T15:56:21Z

Pysdlb: /* Linux */

__TOC__

==Methods==

===Small to medium amounts of data===

This can be carried out using a number of SFTP-styled packages such as sftp, scp, rsync, and Filezilla to name a few. Filezilla can be downloaded as a Windows application and may be more suitable for people who prefer a Windows environment, rather than the command line.

'''Note''' FTP (insecure) is disabled on viper.hull.ac.uk and SFTP (secure FTP) is the recommended method.

===Large to a huge amount of data (100GB +)===
To avoid excessive network congestion and the long period to transfer such data please raise a [https://hull.service-now.com/ support ticket] for further details. This may typically involve connecting a USB data drive directly to VIPER to copy the data quickly into your user area.

===OneDrive to Viper===

With the University using MS OneDrive, it is possible to copy files to Viper. For multiple files, zip your files up on OneDrive first (considerably easier), as shown here:

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | From OneDrive to Viper
|-
|
* Starting with the zipped file MyData.zip on OneDrive, copied previously and compressed from local storage.
* Click on the '''share icon''' or options for the file here (three horizontal dots) and select '''share'''.

[[File:onedrive-01.png]]

* Then

[[File:onedrive-02.png]]

* Click on '''Copy'''

[[File:onedrive-03.png]]

* On your Viper console application, type '''wget''' and paste in the copied link and follow with '''-O yourfilename''' (otherwise Linux will name the file to the OneDrive link - ''argh!'')

[[File:onedrive-04.png]]

* And here is the received file

[[File:onedrive-05.png]]

'''Remember''' to un-share the file on OneDrive and use unzip (if required) on Linux to restore the file structure.

|}

==Universal==
The following can only be performed on Windows after installing MobaXterm or PuTTY.

The example user is user1; you will need to enter your username here:

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * To Viper from local computer
|-
|scp myfile user1@viperlogin.hpc.hull.ac.uk:myfile
|-
|rsync -av my-directory viper.hull.ac.uk:/data/users/YourID
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * From Viper to your local computer
|-
| scp user1@viperlogin.hpc.hull.ac.uk:bio/YourUCInetID/hpc-file
|-
|rsync -av viper.hull.ac.uk:/data/users/YourID/mydatadirectory
|}

==Windows==
The following example uses MobaXterm, for transferring large files it is recommended to use FileZilla. For instructions on how to use FileZilla view the Linux section. follow the instruction in the Getting Connected section for installing MobaXterm.

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * Uploading Files
|-
|* To upload files to Viper, navigate to the directory you wish to upload files to use the MobaXterm file browser.
* Choose the file/files to upload and click open or alternatively drag and drop the file/files you wish to upload over the Viper file browser.
* The upload may take some time depending on upload speed and file size.
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * Downloading Files
|-
|* To download files from Viper, navigate to the directory using the MobaXterm file browser.
[[File:mobaxterm_file_browser.jpg]]
* Select the file/files you wish to download and click the 'download selected files button'.
[[File:mobaxterm_download_icon.jpg]]
* Choose the directory where you want the files to download and click ok.
* The download will start, depending on download speed and file size this may take some time.
|}

==MacOS==
The following example uses Cyberduck, you can download Cyberduck from https://cyberduck.io macOS also supports FileZilla for an example of how to use FileZilla please view the Linux section.

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Connecting
|-
|
* Click Open Connection.
* From the drop-down menu select '''SFTP''' (SSH File Transfer Protocol)
* Enter server viperlogin.hpc.hull.ac.uk, Port: 22, Username: University UID, Password: university password
* Click Connect.

|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Uploading Files
|-
|
* Click Upload
* Choose the file/folder you want to upload and click Choose.
* The transfer window will appear.
* Please note due to file size the upload may take some time.
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Downloading Files
|-
|
* From the file browser right-click on the file/folder to download and select download from the menu.
* The transfer window will appear.
* Please note due to file size the download may take some time.
|}

==Linux==

The following example uses FileZilla, you can download FileZilla from https://filezilla-project.org/ (''Windows/Linux and MacOS'').
* '''Note''': the FileZilla installer sometimes comes with additional trial software packages. We would advise against installing these

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Using FileZilla
|-
|
*Enter the Host: viperlogin.hpc.hull.ac.uk, username, password, and port: 22, using an SFTP connection.
[[File:filezilla_linux_login.jpg]]
* A pop-up will appear informing that the server host key is unknown. Click Always trust this host and click ok. In the remote site box, your Viper directory will appear.
* To transfer files click and drag the file/folder from either your pc to Viper (left to right) or from Viper to your pc (right to left). The transfer will start depending on transfer speed and file size this may take some time.
[[File:filezilla_transferring_files.jpg]]
|}

==Navigation==

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

Training/Transferring Data

2024-08-22T15:56:04Z

Pysdlb: /* MacOS */

__TOC__

==Methods==

===Small to medium amounts of data===

This can be carried out using a number of SFTP-styled packages such as sftp, scp, rsync, and Filezilla to name a few. Filezilla can be downloaded as a Windows application and may be more suitable for people who prefer a Windows environment, rather than the command line.

'''Note''' FTP (insecure) is disabled on viper.hull.ac.uk and SFTP (secure FTP) is the recommended method.

===Large to a huge amount of data (100GB +)===
To avoid excessive network congestion and the long period to transfer such data please raise a [https://hull.service-now.com/ support ticket] for further details. This may typically involve connecting a USB data drive directly to VIPER to copy the data quickly into your user area.

===OneDrive to Viper===

With the University using MS OneDrive, it is possible to copy files to Viper. For multiple files, zip your files up on OneDrive first (considerably easier), as shown here:

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | From OneDrive to Viper
|-
|
* Starting with the zipped file MyData.zip on OneDrive, copied previously and compressed from local storage.
* Click on the '''share icon''' or options for the file here (three horizontal dots) and select '''share'''.

[[File:onedrive-01.png]]

* Then

[[File:onedrive-02.png]]

* Click on '''Copy'''

[[File:onedrive-03.png]]

* On your Viper console application, type '''wget''' and paste in the copied link and follow with '''-O yourfilename''' (otherwise Linux will name the file to the OneDrive link - ''argh!'')

[[File:onedrive-04.png]]

* And here is the received file

[[File:onedrive-05.png]]

'''Remember''' to un-share the file on OneDrive and use unzip (if required) on Linux to restore the file structure.

|}

==Universal==
The following can only be performed on Windows after installing MobaXterm or PuTTY.

The example user is user1; you will need to enter your username here:

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * To Viper from local computer
|-
|scp myfile user1@viperlogin.hpc.hull.ac.uk:myfile
|-
|rsync -av my-directory viper.hull.ac.uk:/data/users/YourID
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * From Viper to your local computer
|-
| scp user1@viperlogin.hpc.hull.ac.uk:bio/YourUCInetID/hpc-file
|-
|rsync -av viper.hull.ac.uk:/data/users/YourID/mydatadirectory
|}

==Windows==
The following example uses MobaXterm, for transferring large files it is recommended to use FileZilla. For instructions on how to use FileZilla view the Linux section. follow the instruction in the Getting Connected section for installing MobaXterm.

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * Uploading Files
|-
|* To upload files to Viper, navigate to the directory you wish to upload files to use the MobaXterm file browser.
* Choose the file/files to upload and click open or alternatively drag and drop the file/files you wish to upload over the Viper file browser.
* The upload may take some time depending on upload speed and file size.
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * Downloading Files
|-
|* To download files from Viper, navigate to the directory using the MobaXterm file browser.
[[File:mobaxterm_file_browser.jpg]]
* Select the file/files you wish to download and click the 'download selected files button'.
[[File:mobaxterm_download_icon.jpg]]
* Choose the directory where you want the files to download and click ok.
* The download will start, depending on download speed and file size this may take some time.
|}

==MacOS==
The following example uses Cyberduck, you can download Cyberduck from https://cyberduck.io macOS also supports FileZilla for an example of how to use FileZilla please view the Linux section.

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Connecting
|-
|
* Click Open Connection.
* From the drop-down menu select '''SFTP''' (SSH File Transfer Protocol)
* Enter server viperlogin.hpc.hull.ac.uk, Port: 22, Username: University UID, Password: university password
* Click Connect.

|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Uploading Files
|-
|
* Click Upload
* Choose the file/folder you want to upload and click Choose.
* The transfer window will appear.
* Please note due to file size the upload may take some time.
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Downloading Files
|-
|
* From the file browser right-click on the file/folder to download and select download from the menu.
* The transfer window will appear.
* Please note due to file size the download may take some time.
|}

==Linux==

The following example uses FileZilla, you can download FileZilla from https://filezilla-project.org/ (''Windows/Linux and MacOS'').
* '''Note''': the FileZilla installer sometimes comes with additional trial software packages. We would advise against installing these

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Using FileZilla
|-
|
*Enter the Host: viper.hull.ac.uk, username, password, and port: 22, using an SFTP connection.
[[File:filezilla_linux_login.jpg]]
* A pop-up will appear informing that the server host key is unknown. Click Always trust this host and click ok. In the remote site box, your Viper directory will appear.
* To transfer files click and drag the file/folder from either your pc to Viper (left to right) or from Viper to your pc (right to left). The transfer will start depending on transfer speed and file size this may take some time.
[[File:filezilla_transferring_files.jpg]]
|}

==Navigation==

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

Training/Transferring Data

2024-08-22T15:55:24Z

Pysdlb: /* Universal */

__TOC__

==Methods==

===Small to medium amounts of data===

This can be carried out using a number of SFTP-styled packages such as sftp, scp, rsync, and Filezilla to name a few. Filezilla can be downloaded as a Windows application and may be more suitable for people who prefer a Windows environment, rather than the command line.

'''Note''' FTP (insecure) is disabled on viper.hull.ac.uk and SFTP (secure FTP) is the recommended method.

===Large to a huge amount of data (100GB +)===
To avoid excessive network congestion and the long period to transfer such data please raise a [https://hull.service-now.com/ support ticket] for further details. This may typically involve connecting a USB data drive directly to VIPER to copy the data quickly into your user area.

===OneDrive to Viper===

With the University using MS OneDrive, it is possible to copy files to Viper. For multiple files, zip your files up on OneDrive first (considerably easier), as shown here:

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | From OneDrive to Viper
|-
|
* Starting with the zipped file MyData.zip on OneDrive, copied previously and compressed from local storage.
* Click on the '''share icon''' or options for the file here (three horizontal dots) and select '''share'''.

[[File:onedrive-01.png]]

* Then

[[File:onedrive-02.png]]

* Click on '''Copy'''

[[File:onedrive-03.png]]

* On your Viper console application, type '''wget''' and paste in the copied link and follow with '''-O yourfilename''' (otherwise Linux will name the file to the OneDrive link - ''argh!'')

[[File:onedrive-04.png]]

* And here is the received file

[[File:onedrive-05.png]]

'''Remember''' to un-share the file on OneDrive and use unzip (if required) on Linux to restore the file structure.

|}

==Universal==
The following can only be performed on Windows after installing MobaXterm or PuTTY.

The example user is user1; you will need to enter your username here:

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * To Viper from local computer
|-
|scp myfile user1@viperlogin.hpc.hull.ac.uk:myfile
|-
|rsync -av my-directory viper.hull.ac.uk:/data/users/YourID
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * From Viper to your local computer
|-
| scp user1@viperlogin.hpc.hull.ac.uk:bio/YourUCInetID/hpc-file
|-
|rsync -av viper.hull.ac.uk:/data/users/YourID/mydatadirectory
|}

==Windows==
The following example uses MobaXterm, for transferring large files it is recommended to use FileZilla. For instructions on how to use FileZilla view the Linux section. follow the instruction in the Getting Connected section for installing MobaXterm.

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * Uploading Files
|-
|* To upload files to Viper, navigate to the directory you wish to upload files to use the MobaXterm file browser.
* Choose the file/files to upload and click open or alternatively drag and drop the file/files you wish to upload over the Viper file browser.
* The upload may take some time depending on upload speed and file size.
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | * Downloading Files
|-
|* To download files from Viper, navigate to the directory using the MobaXterm file browser.
[[File:mobaxterm_file_browser.jpg]]
* Select the file/files you wish to download and click the 'download selected files button'.
[[File:mobaxterm_download_icon.jpg]]
* Choose the directory where you want the files to download and click ok.
* The download will start, depending on download speed and file size this may take some time.
|}

==MacOS==
The following example uses Cyberduck, you can download Cyberduck from https://cyberduck.io macOS also supports FileZilla for an example of how to use FileZilla please view the Linux section.

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Connecting
|-
|
* Click Open Connection.
* From the drop-down menu select '''SFTP''' (SSH File Transfer Protocol)
* Enter server viper.hull.ac.uk, Port: 22, Username: University UID, Password: university password
* Click Connect.

[[File:cyberduck_connection.jpg]]
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Uploading Files
|-
|
* Click Upload
* Choose the file/folder you want to upload and click Choose.
* The transfer window will appear.
* Please note due to file size the upload may take some time.
|}

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Downloading Files
|-
|
* From the file browser right-click on the file/folder to download and select download from the menu.
* The transfer window will appear.
* Please note due to file size the download may take some time.
|}

==Linux==

The following example uses FileZilla, you can download FileZilla from https://filezilla-project.org/ (''Windows/Linux and MacOS'').
* '''Note''': the FileZilla installer sometimes comes with additional trial software packages. We would advise against installing these

{| class="wikitable mw-collapsible"
| style="width:100%; background: #aaaaaa;" | Using FileZilla
|-
|
*Enter the Host: viper.hull.ac.uk, username, password, and port: 22, using an SFTP connection.
[[File:filezilla_linux_login.jpg]]
* A pop-up will appear informing that the server host key is unknown. Click Always trust this host and click ok. In the remote site box, your Viper directory will appear.
* To transfer files click and drag the file/folder from either your pc to Viper (left to right) or from Viper to your pc (right to left). The transfer will start depending on transfer speed and file size this may take some time.
[[File:filezilla_transferring_files.jpg]]
|}

==Navigation==

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

Training/XQuartz

2024-08-22T15:54:28Z

Pysdlb: /* 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.
* XQuartz was included with Mac OSX 10.5 (Leopard) onwards, for all subsequent releases XQuartz is not included and must be downloaded separately.

==Installing XQuartz==
# Download the latest version of XQuartz from https://www.xquartz.org/
# Navigate to the Downloads folder and open the XQuartz Disk Image (XQuartz-2.8.2.dmg)
# Open the XQuartz package (XQuartz.pkg)
[[File:XQuartz_Package.png]]
* Follow the installation steps, accept the licence agreement and choose an installation destination.
[[File:XQuartz_Install.png]]
* Once installation is complete log out and log in.
[[File:XQuartz_Complete.png]]
* Open the Terminal Application
* Login to Viper ssh -Y <username>@viperlogin.hpc.hull.ac.uk

'''IMPORTANT''' : Use the -Y option to enable windowing on the host computer.

==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]]

==Alternative options==

[https://www.macports.org/ MacPorts] 

==Next Steps==

* [https://www.xquartz.org/ XQuartz]
* [https://support.apple.com/en-gb/HT201341 Apple Support - X11]

[[Main Page]] / [[FurtherTopics/FurtherTopics #Compatibility| Back to Further Topics]]

Quickstart/Data Management

2024-08-22T15:53:08Z

Pysdlb: /* Linux */

__NOTOC__
{|
|style="width:5%; border-width: 0" | [[File:icon_warning.png]]
|style="width:95%; border-width: 0" | ''Viper storage is considered 'scratch', please remember to back up your data! '' ''Users are not permitted to store personal or sensitive information on Viper.''
|-
|}
__TOC__

==Transferring Data on Viper==

For less than 100GB: you can skip to using [[#Universal| universal method]] or skip to your OS: [[#Windows| Windows]] / [[#MacOS| Mac]] / [[#Linux| Linux]].
===Small to medium amounts of data===
This can be carried out using several SFTP-styled packages such as sftp, scp, rsync, and Filezilla to name a few. Filezilla can be downloaded as a Windows application and may be more suitable for people who prefer a Windows environment, rather than the command line.

'''Note''' that plain FTP is disabled on viper.hull.ac.uk and SFTP (secure FTP) is the recommended method.

====Universal====
The following can only be performed on Windows after installing MobaXterm or PuTTY.

The example user is user1; you will need to enter your username here:

{| class="wikitable"
| style="width:100%" | From your local computer to Viper
|-
|''scp myfile user1@viper.hull.ac.uk:myfile
|-''
|''rsync -av my-directory viperlogin.hpc.hull.ac.uk:/data/users/YourID''
|}
{| class="wikitable"
| style="width:100%" | From Viper to your local Computer
|-
|''scp user1@viperlogin.hpc.hull.ac.uk:bio/YourUCInetID/hpc-file''
|-
|''rsync -av viper.hull.ac.uk:/data/users/YourID/mydatadirectory''
|}

====Windows====
The following example uses MobaXterm, for transferring large files it is recommended to use FileZilla. For instructions on how to use FileZilla view the Linux section. follow the instructions in the Getting Connected section for installing MobaXterm.
=====Uploading Files=====
1. To upload files to Viper, navigate to the directory you wish to upload files to use the MobaXterm file browser and click the 'Upload to current folder' button.
[[File:upload_button.jpg]]
2. Choose the file/files to upload and click open or drag and drop the file/files you wish to upload over the Viper file browser.

3. The upload may take some time depending on upload speed and file size.

=====Downloading Files=====
1. To download files from Viper, navigate to the directory using the MobaXterm file browser.
[[File:mobaxterm_file_browser.jpg]]
2. Select the file/files you wish to download and click the 'download selected files button'.
[[File:mobaxterm_download_icon.jpg]]
3. Choose the directory where you want the files to download and click ok.

4. The download will start, depending on download speed and file size this may take some time.

====MacOS====
The following example uses Cyberduck, you can download Cyberduck from https://cyberduck.io macOS also supports FileZilla for an example of how to use FileZilla please view the Linux section
=====Connecting=====
1. Click Open Connection.

2. From the drop-down menu select '''SFTP''' (SSH File Transfer Protocol)

3. Enter server viperlogin.hpc.hull.ac.uk, Port: 22, Username: University UID, Password: university password

4. Click Connect

=====Uploading Files=====
1. Click Upload

2. Choose the file/folder you want to upload and click Choose

3. The transfer window will appear

4. Please note due to file size the upload may take some time

=====Downloading Files=====
1. From the file browser right-click on the file/folder to download and select download from the menu

2. The transfer window will appear

3. Please note due to file size the download may take some time
====Linux====

The following example uses FileZilla, you can download FileZilla from https://filezilla-project.org/

1. Enter the Host: viperlogin.hpc.hull.ac.uk, username, password, and port: 22, using an SFTP connection.

2. A pop-up will appear informing that the server host key is unknown. Click Always trust this host and click ok. In the remote site box, your Viper directory will appear.

3. To transfer files click and drag the file/folder from either your pc to Viper (left to right) or from Viper to your pc (right to left). The transfer will start depending on transfer speed and file size this may take some time.
[[File:filezilla_transferring_files.jpg]]

===Larger amounts of data (100GB +)===
To avoid excessive network congestion and the long period to transfer such data please contact us via the [https://hull.service-now.com/ Support Portal] for further details. This may typically involve connecting a USB data drive directly to Viper to copy the data quickly into your user area.

[[Main Page #Quickstart| Back]] / [[Quickstart/Virtual Environments| Next (Virtual Environments)]]

Quickstart/Data Management

2024-08-22T15:52:50Z

Pysdlb: /* Linux */

__NOTOC__
{|
|style="width:5%; border-width: 0" | [[File:icon_warning.png]]
|style="width:95%; border-width: 0" | ''Viper storage is considered 'scratch', please remember to back up your data! '' ''Users are not permitted to store personal or sensitive information on Viper.''
|-
|}
__TOC__

==Transferring Data on Viper==

For less than 100GB: you can skip to using [[#Universal| universal method]] or skip to your OS: [[#Windows| Windows]] / [[#MacOS| Mac]] / [[#Linux| Linux]].
===Small to medium amounts of data===
This can be carried out using several SFTP-styled packages such as sftp, scp, rsync, and Filezilla to name a few. Filezilla can be downloaded as a Windows application and may be more suitable for people who prefer a Windows environment, rather than the command line.

'''Note''' that plain FTP is disabled on viper.hull.ac.uk and SFTP (secure FTP) is the recommended method.

====Universal====
The following can only be performed on Windows after installing MobaXterm or PuTTY.

The example user is user1; you will need to enter your username here:

{| class="wikitable"
| style="width:100%" | From your local computer to Viper
|-
|''scp myfile user1@viper.hull.ac.uk:myfile
|-''
|''rsync -av my-directory viperlogin.hpc.hull.ac.uk:/data/users/YourID''
|}
{| class="wikitable"
| style="width:100%" | From Viper to your local Computer
|-
|''scp user1@viperlogin.hpc.hull.ac.uk:bio/YourUCInetID/hpc-file''
|-
|''rsync -av viper.hull.ac.uk:/data/users/YourID/mydatadirectory''
|}

====Windows====
The following example uses MobaXterm, for transferring large files it is recommended to use FileZilla. For instructions on how to use FileZilla view the Linux section. follow the instructions in the Getting Connected section for installing MobaXterm.
=====Uploading Files=====
1. To upload files to Viper, navigate to the directory you wish to upload files to use the MobaXterm file browser and click the 'Upload to current folder' button.
[[File:upload_button.jpg]]
2. Choose the file/files to upload and click open or drag and drop the file/files you wish to upload over the Viper file browser.

3. The upload may take some time depending on upload speed and file size.

=====Downloading Files=====
1. To download files from Viper, navigate to the directory using the MobaXterm file browser.
[[File:mobaxterm_file_browser.jpg]]
2. Select the file/files you wish to download and click the 'download selected files button'.
[[File:mobaxterm_download_icon.jpg]]
3. Choose the directory where you want the files to download and click ok.

4. The download will start, depending on download speed and file size this may take some time.

====MacOS====
The following example uses Cyberduck, you can download Cyberduck from https://cyberduck.io macOS also supports FileZilla for an example of how to use FileZilla please view the Linux section
=====Connecting=====
1. Click Open Connection.

2. From the drop-down menu select '''SFTP''' (SSH File Transfer Protocol)

3. Enter server viperlogin.hpc.hull.ac.uk, Port: 22, Username: University UID, Password: university password

4. Click Connect

=====Uploading Files=====
1. Click Upload

2. Choose the file/folder you want to upload and click Choose

3. The transfer window will appear

4. Please note due to file size the upload may take some time

=====Downloading Files=====
1. From the file browser right-click on the file/folder to download and select download from the menu

2. The transfer window will appear

3. Please note due to file size the download may take some time
====Linux====

The following example uses FileZilla, you can download FileZilla from https://filezilla-project.org/

1. Enter the Host: viperlogin.hpc.hull.ac.uk, username, password, and port: 22, using an SFTP connection.
[[File:filezilla_linux_login.jpg]]
2. A pop-up will appear informing that the server host key is unknown. Click Always trust this host and click ok. In the remote site box, your Viper directory will appear.

3. To transfer files click and drag the file/folder from either your pc to Viper (left to right) or from Viper to your pc (right to left). The transfer will start depending on transfer speed and file size this may take some time.
[[File:filezilla_transferring_files.jpg]]

===Larger amounts of data (100GB +)===
To avoid excessive network congestion and the long period to transfer such data please contact us via the [https://hull.service-now.com/ Support Portal] for further details. This may typically involve connecting a USB data drive directly to Viper to copy the data quickly into your user area.

[[Main Page #Quickstart| Back]] / [[Quickstart/Virtual Environments| Next (Virtual Environments)]]

Quickstart/Data Management

2024-08-22T15:52:29Z

Pysdlb: /* Connecting */

__NOTOC__
{|
|style="width:5%; border-width: 0" | [[File:icon_warning.png]]
|style="width:95%; border-width: 0" | ''Viper storage is considered 'scratch', please remember to back up your data! '' ''Users are not permitted to store personal or sensitive information on Viper.''
|-
|}
__TOC__

==Transferring Data on Viper==

For less than 100GB: you can skip to using [[#Universal| universal method]] or skip to your OS: [[#Windows| Windows]] / [[#MacOS| Mac]] / [[#Linux| Linux]].
===Small to medium amounts of data===
This can be carried out using several SFTP-styled packages such as sftp, scp, rsync, and Filezilla to name a few. Filezilla can be downloaded as a Windows application and may be more suitable for people who prefer a Windows environment, rather than the command line.

'''Note''' that plain FTP is disabled on viper.hull.ac.uk and SFTP (secure FTP) is the recommended method.

====Universal====
The following can only be performed on Windows after installing MobaXterm or PuTTY.

The example user is user1; you will need to enter your username here:

{| class="wikitable"
| style="width:100%" | From your local computer to Viper
|-
|''scp myfile user1@viper.hull.ac.uk:myfile
|-''
|''rsync -av my-directory viperlogin.hpc.hull.ac.uk:/data/users/YourID''
|}
{| class="wikitable"
| style="width:100%" | From Viper to your local Computer
|-
|''scp user1@viperlogin.hpc.hull.ac.uk:bio/YourUCInetID/hpc-file''
|-
|''rsync -av viper.hull.ac.uk:/data/users/YourID/mydatadirectory''
|}

====Windows====
The following example uses MobaXterm, for transferring large files it is recommended to use FileZilla. For instructions on how to use FileZilla view the Linux section. follow the instructions in the Getting Connected section for installing MobaXterm.
=====Uploading Files=====
1. To upload files to Viper, navigate to the directory you wish to upload files to use the MobaXterm file browser and click the 'Upload to current folder' button.
[[File:upload_button.jpg]]
2. Choose the file/files to upload and click open or drag and drop the file/files you wish to upload over the Viper file browser.

3. The upload may take some time depending on upload speed and file size.

=====Downloading Files=====
1. To download files from Viper, navigate to the directory using the MobaXterm file browser.
[[File:mobaxterm_file_browser.jpg]]
2. Select the file/files you wish to download and click the 'download selected files button'.
[[File:mobaxterm_download_icon.jpg]]
3. Choose the directory where you want the files to download and click ok.

4. The download will start, depending on download speed and file size this may take some time.

====MacOS====
The following example uses Cyberduck, you can download Cyberduck from https://cyberduck.io macOS also supports FileZilla for an example of how to use FileZilla please view the Linux section
=====Connecting=====
1. Click Open Connection.

2. From the drop-down menu select '''SFTP''' (SSH File Transfer Protocol)

3. Enter server viperlogin.hpc.hull.ac.uk, Port: 22, Username: University UID, Password: university password

4. Click Connect

=====Uploading Files=====
1. Click Upload

2. Choose the file/folder you want to upload and click Choose

3. The transfer window will appear

4. Please note due to file size the upload may take some time

=====Downloading Files=====
1. From the file browser right-click on the file/folder to download and select download from the menu

2. The transfer window will appear

3. Please note due to file size the download may take some time
====Linux====

The following example uses FileZilla, you can download FileZilla from https://filezilla-project.org/

1. Enter the Host: viper.hull.ac.uk, username, password, and port: 22, using an SFTP connection.
[[File:filezilla_linux_login.jpg]]
2. A pop-up will appear informing that the server host key is unknown. Click always trust this host and click ok. In the remote site box, your Viper directory will appear.

3. To transfer files click and drag the file/folder from either your pc to Viper (left to right) or from Viper to your pc (right to left). The transfer will start depending on transfer speed and file size this may take some time.
[[File:filezilla_transferring_files.jpg]]

===Larger amounts of data (100GB +)===
To avoid excessive network congestion and the long period to transfer such data please contact us via the [https://hull.service-now.com/ Support Portal] for further details. This may typically involve connecting a USB data drive directly to Viper to copy the data quickly into your user area.

[[Main Page #Quickstart| Back]] / [[Quickstart/Virtual Environments| Next (Virtual Environments)]]

Quickstart/Data Management

2024-08-22T15:52:07Z

Pysdlb: /* Universal */

__NOTOC__
{|
|style="width:5%; border-width: 0" | [[File:icon_warning.png]]
|style="width:95%; border-width: 0" | ''Viper storage is considered 'scratch', please remember to back up your data! '' ''Users are not permitted to store personal or sensitive information on Viper.''
|-
|}
__TOC__

==Transferring Data on Viper==

For less than 100GB: you can skip to using [[#Universal| universal method]] or skip to your OS: [[#Windows| Windows]] / [[#MacOS| Mac]] / [[#Linux| Linux]].
===Small to medium amounts of data===
This can be carried out using several SFTP-styled packages such as sftp, scp, rsync, and Filezilla to name a few. Filezilla can be downloaded as a Windows application and may be more suitable for people who prefer a Windows environment, rather than the command line.

'''Note''' that plain FTP is disabled on viper.hull.ac.uk and SFTP (secure FTP) is the recommended method.

====Universal====
The following can only be performed on Windows after installing MobaXterm or PuTTY.

The example user is user1; you will need to enter your username here:

{| class="wikitable"
| style="width:100%" | From your local computer to Viper
|-
|''scp myfile user1@viper.hull.ac.uk:myfile
|-''
|''rsync -av my-directory viperlogin.hpc.hull.ac.uk:/data/users/YourID''
|}
{| class="wikitable"
| style="width:100%" | From Viper to your local Computer
|-
|''scp user1@viperlogin.hpc.hull.ac.uk:bio/YourUCInetID/hpc-file''
|-
|''rsync -av viper.hull.ac.uk:/data/users/YourID/mydatadirectory''
|}

====Windows====
The following example uses MobaXterm, for transferring large files it is recommended to use FileZilla. For instructions on how to use FileZilla view the Linux section. follow the instructions in the Getting Connected section for installing MobaXterm.
=====Uploading Files=====
1. To upload files to Viper, navigate to the directory you wish to upload files to use the MobaXterm file browser and click the 'Upload to current folder' button.
[[File:upload_button.jpg]]
2. Choose the file/files to upload and click open or drag and drop the file/files you wish to upload over the Viper file browser.

3. The upload may take some time depending on upload speed and file size.

=====Downloading Files=====
1. To download files from Viper, navigate to the directory using the MobaXterm file browser.
[[File:mobaxterm_file_browser.jpg]]
2. Select the file/files you wish to download and click the 'download selected files button'.
[[File:mobaxterm_download_icon.jpg]]
3. Choose the directory where you want the files to download and click ok.

4. The download will start, depending on download speed and file size this may take some time.

====MacOS====
The following example uses Cyberduck, you can download Cyberduck from https://cyberduck.io macOS also supports FileZilla for an example of how to use FileZilla please view the Linux section
=====Connecting=====
1. Click Open Connection.

2. From the drop-down menu select '''SFTP''' (SSH File Transfer Protocol)

3. Enter server viper.hull.ac.uk, Port: 22, Username: University UID, Password: university password

4. Click Connect

[[File:cyberduck_connection.jpg]]

=====Uploading Files=====
1. Click Upload

2. Choose the file/folder you want to upload and click Choose

3. The transfer window will appear

4. Please note due to file size the upload may take some time

=====Downloading Files=====
1. From the file browser right-click on the file/folder to download and select download from the menu

2. The transfer window will appear

3. Please note due to file size the download may take some time
====Linux====

The following example uses FileZilla, you can download FileZilla from https://filezilla-project.org/

1. Enter the Host: viper.hull.ac.uk, username, password, and port: 22, using an SFTP connection.
[[File:filezilla_linux_login.jpg]]
2. A pop-up will appear informing that the server host key is unknown. Click always trust this host and click ok. In the remote site box, your Viper directory will appear.

3. To transfer files click and drag the file/folder from either your pc to Viper (left to right) or from Viper to your pc (right to left). The transfer will start depending on transfer speed and file size this may take some time.
[[File:filezilla_transferring_files.jpg]]

===Larger amounts of data (100GB +)===
To avoid excessive network congestion and the long period to transfer such data please contact us via the [https://hull.service-now.com/ Support Portal] for further details. This may typically involve connecting a USB data drive directly to Viper to copy the data quickly into your user area.

[[Main Page #Quickstart| Back]] / [[Quickstart/Virtual Environments| Next (Virtual Environments)]]

FurtherTopics/WinSCP

2024-08-22T15:51:08Z

Pysdlb: /* Setting up */

__TOC__

==Introduction==

WinSCP is an open source free SFTP client, FTP client, WebDAV client, S3 client and SCP client for Windows. Its main function is file transfer between a local and a remote computer. Beyond this, WinSCP offers scripting and basic file manager functionality.

It provides a more windows explorer-like interface which users might prefer over the command line or the application filezilla.

==Download and Install==

It can be downloaded from [https://www.winscp.net www.winscp.net] - if you're on a university-imaged PC you may need administrator rights to install this program.

==Setting up==

Add a new site by using the following details:

* File protocol: '''SFTP'''
* Hostname: '''viperlogin.hpc.hull.ac.uk'''
* User name: Your '''university ID''' (eg ''887766'')
* Password: Your '''university password'''

Click on '''Save''' and then click on '''Login''' (to start the session)

* You may get a "Continue connecting to an unknown server and add its host key to a cache?" - Select '''Yes'''

[[File:winscp02.jpg]]

* Files can now be dragged and placed onto the above window in the same way as using Window Explorer.

[[Main Page]] / [[FurtherTopics/FurtherTopics #Data Management| Back to Further Topics]]

FurtherTopics/WinSCP

2024-08-22T15:50:30Z

Pysdlb: /* Setting up */

__TOC__

==Introduction==

WinSCP is an open source free SFTP client, FTP client, WebDAV client, S3 client and SCP client for Windows. Its main function is file transfer between a local and a remote computer. Beyond this, WinSCP offers scripting and basic file manager functionality.

It provides a more windows explorer-like interface which users might prefer over the command line or the application filezilla.

==Download and Install==

It can be downloaded from [https://www.winscp.net www.winscp.net] - if you're on a university-imaged PC you may need administrator rights to install this program.

==Setting up==

Add a new site by using the following details:

* File protocol: '''SFTP'''
* Hostname: '''viperlogin.hpc.hull.ac.uk'''
* User name: Your '''university ID''' (eg ''887766'')
* Password: Your '''university password'''

Click on '''Save''' and then click on '''Login''' (to start the session)

[[File:winscp01.jpg]]

* You may get a "Continue connecting to an unknown server and add its host key to a cache?" - Select '''Yes'''

[[File:winscp02.jpg]]

* Files can now be dragged and placed onto the above window in the same way as using Window Explorer.

[[Main Page]] / [[FurtherTopics/FurtherTopics #Data Management| Back to Further Topics]]

General

2024-08-22T15:49:35Z

Pysdlb: /* General Support */

== General Support ==

Click on the links below for general support:

{| class="wikitable"
| style="width:25%; background: #cccccc;" | Topic
| style="width:75%; background: #cccccc;" | Description
|-
| [[General/What_is_Viper|What is Viper]]
| What is Viper?
|-
| [[General/Gallery|What does Viper look like?]]
| What does Viper look like?
|-
| [[General/Batch|Batch Jobs]]
| Viper batch jobs guide
|-
| [[General/Interactive|Interactive Sessions]]
| Viper Interactive session guide
|-
| [[General/Modules|Modules]]
| Application module guide.
|-
| [[General/Slurm|Slurm]]
| Slurm how-to
|-
| [[General/Visualisation Nodes|Visualisation Nodes]]
| Guide to using Viper's visualisation nodes
|-
| [[Training/Data_Backup|Data Backup]]
| Data backup for user accounts
|-
| [[General/Jupyternotebook|Running a jupyter notebook]]
| Instructions on running a jupyter notebook on a computing node
|-
| [[General/UserDropin|User Drop-in Sessions]]
| User Drop-in session for anyone with questions about Viper.
|-
|}

== Training ==

{| class="wikitable"
| style="width:25%; background: #cccccc;" | Training Area
| style="width:75%; background: #cccccc;" | Description
|-
| [[Training/Tutorial Videos|Tutorial Videos]]
| HPC Tutorial Videos from Linux to HPC
|-
| [[Training/Getting Connected|Getting Connected]]
| Learn how to connect to Viper
|-
| [[Training/XQuartz|XQuartz - macOS X11 ]]
| Learn how to enable X11 window support on macOS
|-
| [[Training/X2Go macOS|X2Go - macOS]]
| Learn how to install X2Go on macOS for use with Viper's Visualisation Nodes
|-
| [[Training/Transferring Data|Transferring Data]]
| Learn how to download and upload data.
|-
| [[Training/Linux - command line|Linux command line]]
| Learn the Linux command line with this extensive guide.
|-
| [[Training/Linux_-_vi_editor|Linux vi editor]]
| Learn the Linux editor vi for editing files
|-
| [[Training/Linux - Nano editor|Linux nano editor]]
| Learn the Linux editor nano for editing files
|-
| [[Training/Matlab-Viper-plugin|Parallel computing in Matlab]]
| Learn about Matlab parallel toolbox that speeds up your calculations on Viper.
|-
| [[Scaling|Scaling programs on HPC]]
| Learn about the issues of scaling programs up on HPC.
|-
|}

* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[Libraries|Library support]]
* [[Programming|Development support]]
* [[General|General]] *

General/Slurm

2024-08-22T15:47:53Z

Pysdlb: /* Introduction */

__TOC__
==Application Details==
*Description: SLURM is an open-source job scheduler, used by HPCs.
* Version: 15.08.8

==Introduction==
The SLURM (Simple Linux Utility for Resource Management) workload manager is a free and open-source job scheduler for the Linux kernel. It is used by Viper and many of the world's supercomputers (and clusters).
*First, it allocates exclusive and/or non-exclusive access to resources (computer nodes) to users for some duration of time so they can perform work.
*Second, it provides a framework for starting, executing, and monitoring work (typically a parallel job such as MPI) on a set of allocated nodes.
*Thirdly, it arbitrates contention for resources by managing a queue of pending jobs.

Slurm executes your batch job submission across Viper's computing nodes. How it is processed will depend on several factors including the queue it is submitted to, jobs already submitted to the queue etc.

==Common Slurm Commands==
{| class="wikitable"
| style="width:25%" | Command
| style="width:75%" | Description
|-
| sbatch
| Submits a batch script to SLURM. The batch script may be given to sbatch through a file name on the command line, or if no filename is specified, sbatch will read in a script from standard input.
|-
| squeue
| Used to view job and job step information for jobs managed by SLURM.
|-
| scancel
| Used to signal or cancel jobs, job arrays or job steps.
|-
| sinfo
| Used to view partition and node information for a system running SLURM.
|-
|}
===sbatch===
Used to submit a job to Slurm.
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ sbatch jobfile.job
Submitted batch job 289535
</pre>
{|
|style="width:5%; border-width: 0;cellpadding=0" | [[File:icon_exclam3.png]]
|style="width:95%; border-width: 0;cellpadding=0" | The number displayed (289535) is the Job ID
|-
|}
===squeue===
squeue shows information about jobs in the scheduling queue
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
306414 compute clasDFT user R 16:36 1 c006
306413 compute mpi_benc user R 31:02 2 c[005,007]
306411 compute orca_1n user R 1:00:32 1 c004
306410 compute orca_1n user R 1:04:17 1 c003
306409 highmem cnv_obit user R 11:37:17 1 c232
306407 compute 20M4_20 user R 11:45:54 1 c012
306406 compute 20_ML_20 user R 11:55:40 1 c012
</pre>
{| class="wikitable"
| style="width:25%" | Heading
| style="width:75%" | Description
|-
| JOBID
| The unique identifier assigned to a job
|-
| PARTITION
| The type of node the job is running on e.g. compute, highmem, GPU
|-
| NAME
| Name of job
|-
| USER
| User ID of job owner
|-
| ST
| Job state code e.g. R stands for 'Running'
|-
| TIME
| Length of time a job has been running
|-
| NODES
| Amount of nodes a job is running on
|-
| NODELIST(REASON)
| List of nodes a job is running on also provides a reason a job is not running e.g. a dependency on a node.
|}

===scancel===
scancel is used to cancel currently running jobs. Only jobs running under your userid may be cancelled.
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ scancel 289535</pre>
{|
|style="width:5%; border-width: 0;cellpadding=0" | [[File:icon_exclam3.png]]
|style="width:95%; border-width: 0;cellpadding=0" | No output is given by the command.
|-
|}

===sinfo===
sinfo shows the information on the partitions and nodes in the cluster.
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ sinfo
PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
compute* up 2-00:00:00 9 mix c[006,012,014,016,018-020,022,170]
compute* up 2-00:00:00 11 alloc c[003-004,008,015,046,086,093,098,138,167-168]
compute* up 2-00:00:00 156 idle c[001-002,005,007,009-011,013,017,021,023-045,047-085,087-092,094-097,099-137,139-166,169,171-176]
highmem up 4-00:00:00 1 mix c230
highmem up 4-00:00:00 2 alloc c[231-232]
highmem up 4-00:00:00 1 idle c233
gpu up 5-00:00:00 4 idle gpu[01-04]
</pre>

{| class="wikitable"
| style="width:25%" | Heading
| style="width:75%" | Description
|-
| PARTITION
| A group of nodes, on Viper partitions are organised by node type e.g compute, high memory and GPU
|-
| AVAIL
| Availability of a specific partition
|-
| TIMELIMIT
| Time limit for jobs running on a specific partition e.g. for the compute nodes the maximum time a job can run for is 2 days.
|-
| NODES
| Number of nodes in a specific state/partition
|-
| STATE
| The current status of a partition/group of nodes e.g. alloc (allocated)
|-
| NODELIST
| List of nodes in specific state/partition
|}

==Common Submission Flags==
For ease and repetition, it is much easier to build Slurm commands into batch files, the following are an example of the most commonly used commands.

'''Note''': The use of the --exclusive flag to indicate whether you require the whole node for your job if don't need a significant amount of processing cores then omitting this command will allow other users to use the unused resources of that node.

{| class="wikitable"
| style="width:25%" | Flag
| style="width:75%" | Description
|-
| -J / --job-name
| Specify a name for the job
|-
| -N / --nodes
| Specifies the number of nodes to be allocated to a job
|-
| -n / --ntasks
| Specifies the allocation of resources e.g. for 1 Compute Node the maximum would be 28
|-
| -o / --output
| Specifies the name of the output file
|-
| -e / --error
| Specifies the name of the error file
|-
| -p / --partition
|Specifies the specific partition for the job e.g. compute, highmem or GPU.
|-
| --exclusive
|Requests exclusive access to nodes preventing other jobs from running
|-
|}
===Example Job Submission Script===
<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
#!/bin/bash

#SBATCH -J Example_Slurm_Job
#SBATCH -N 1
#SBATCH -n 28
#SBATCH -o %N.%j.%a.out
#SBATCH -e %N.%j.%a.err
#SBATCH -p compute
#SBATCH --exclusive
#SBATCH --mail-user= your email address here

echo $SLURM_JOB_NODELIST

module purge
module add gcc/8.2.0

export I_MPI_DEBUG=5
export I_MPI_FABRICS=shm:tmi
export I_MPI_FALLBACK=no

/home/user/slurmexample
</pre>

===See Also===

For more information on creating batch jobs visit the [[General/Batch|Batch Jobs]] guide

==Next Steps==
* Slurm Website: [https://slurm.schedmd.com/ https://slurm.schedmd.com/]
* [https://slurm.schedmd.com/rosetta.pdf Slurm Rosetta] (Useful for converting submission scripts from other formats)
* You might find applications' specific submission scripts here [http://hpc.mediawiki.hull.ac.uk/Main_Page#Application_Support Application support]

==Navigation==

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

Training/Getting Connected

2024-08-20T11:13:39Z

Pysdlb: /* Connecting to Viper from a Linux Computer */

__TOC__
==Introduction==
You'll need to make a secure remote connection from your local computer to Viper.

'''Important:''' To use Viper off campus a VPN is required. For more information on 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 compatible
|-
|}

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

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

2. Type '''ssh -Y <yourusername>@viperlogin.hpc.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 on the screen.

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

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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.

==Navigation==

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

Training/Getting Connected

2024-08-20T11:12:57Z

Pysdlb: /* Connecting to Viper from an Apple Mac */

__TOC__
==Introduction==
You'll need to make a secure remote connection from your local computer to Viper.

'''Important:''' To use Viper off campus a VPN is required. For more information on 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 compatible
|-
|}

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

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

2. Type '''ssh -Y <yourusername>@viperlogin.hpc.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 on the screen.

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

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

==Navigation==

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

Training/Getting Connected

2024-08-20T11:12:43Z

Pysdlb: /* Connecting to Viper from an Apple Mac */

__TOC__
==Introduction==
You'll need to make a secure remote connection from your local computer to Viper.

'''Important:''' To use Viper off campus a VPN is required. For more information on 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 compatible
|-
|}

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

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

2. Type '''ssh -Y <yourusername>@viperlogin.hpc.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 on the screen.

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

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

==Navigation==

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

Training/Getting Connected

2024-08-20T11:11:53Z

Pysdlb: /* Connecting to Viper from an Apple Mac */

__TOC__
==Introduction==
You'll need to make a secure remote connection from your local computer to Viper.

'''Important:''' To use Viper off campus a VPN is required. For more information on 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 compatible
|-
|}

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

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

2. Type '''ssh -Y <yourusername>@viperlogin.hpc.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 on the screen.

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

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

==Navigation==

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

Training/Getting Connected

2024-08-20T11:11:34Z

Pysdlb: /* Connecting to Viper from an Apple Mac */

__TOC__
==Introduction==
You'll need to make a secure remote connection from your local computer to Viper.

'''Important:''' To use Viper off campus a VPN is required. For more information on 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 compatible
|-
|}

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

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

2. Type ssh -Y <'''yourusername>@viperlogin.hpc.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 on the screen.

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

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

==Navigation==

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

Training/Getting Connected

2024-08-20T11:11:05Z

Pysdlb: /* Connecting to Viper from an Apple Mac */

__TOC__
==Introduction==
You'll need to make a secure remote connection from your local computer to Viper.

'''Important:''' To use Viper off campus a VPN is required. For more information on 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 compatible
|-
|}

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

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

2. Type ssh -Y <''yourusername''>'''@viperlogin.hpc.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 on the screen.

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

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

==Navigation==

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

Training/Getting Connected

2024-08-20T11:10:38Z

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

__TOC__
==Introduction==
You'll need to make a secure remote connection from your local computer to Viper.

'''Important:''' To use Viper off campus a VPN is required. For more information on 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 compatible
|-
|}

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

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

2. Type ssh -Y <''yourusername''>@viperlogin.hpc.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 on the screen.

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

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

==Navigation==

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

Training/Getting Connected

2024-08-20T11:10:21Z

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

__TOC__
==Introduction==
You'll need to make a secure remote connection from your local computer to Viper.

'''Important:''' To use Viper off campus a VPN is required. For more information on 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 compatible
|-
|}

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: viperlogin.hpc.hull.ac.uk (''port 22 if required'')

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

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

2. Type ssh -Y <''yourusername''>@viperlogin.hpc.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 on the screen.

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

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

==Navigation==

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

Training/Getting Connected

2024-08-20T11:05:17Z

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

__TOC__
==Introduction==
You'll need to make a secure remote connection from your local computer to Viper.

'''Important:''' To use Viper off campus a VPN is required. For more information on 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 compatible
|-
|}

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 (''port 22 if required'')
[[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

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

2. Type ssh -Y <''yourusername''>@viperlogin.hpc.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 on the screen.

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

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

==Navigation==

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

Training/Getting Connected

2024-08-20T11:04:53Z

Pysdlb: /* Connecting to Viper from an Apple Mac */

__TOC__
==Introduction==
You'll need to make a secure remote connection from your local computer to Viper.

'''Important:''' To use Viper off campus a VPN is required. For more information on 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 (''port 22 if required'')
[[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''>@viperlogin.hpc.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 on the screen.

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

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

==Navigation==

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

Training/Getting Connected

2024-08-20T11:04:39Z

Pysdlb: /* Connecting to Viper from a Linux Computer */

__TOC__
==Introduction==
You'll need to make a secure remote connection from your local computer to Viper.

'''Important:''' To use Viper off campus a VPN is required. For more information on 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 (''port 22 if required'')
[[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''>@viperlogin.hpc.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 on the screen.

[[File:mac_getting_connected2.png]]

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

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

==Navigation==

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

Training/Getting Connected

2024-08-20T11:04:17Z

Pysdlb: /* Connecting to Viper from a Linux Computer */

__TOC__
==Introduction==
You'll need to make a secure remote connection from your local computer to Viper.

'''Important:''' To use Viper off campus a VPN is required. For more information on 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 (''port 22 if required'')
[[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''>@viperlogin.hpc.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 on the screen.

[[File:mac_getting_connected2.png]]

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

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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]]

==Navigation==

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

Training/Getting Connected

2024-08-20T11:03:57Z

Pysdlb: /* Connecting to Viper from an Apple Mac */

__TOC__
==Introduction==
You'll need to make a secure remote connection from your local computer to Viper.

'''Important:''' To use Viper off campus a VPN is required. For more information on 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 (''port 22 if required'')
[[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''>@viperlogin.hpc.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 on 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]]

==Navigation==

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

Quickstart/Using Modules

2024-08-20T10:53:03Z

Pysdlb:

==What are modules?==
Viper uses a module environment to provide access to applications, tools and libraries. Modules allow us to provide multiple versions of applications and libraries without causing conflicts. By loading a module, your environment is configured to allow you to use your chosen application by setting required paths and environment variables. Modules can be loaded and unloaded dynamically, giving you full control over your working environment.

The following commands allow you to find out what modules are available on Viper, find out more information about them and control which modules you load.

'''Loading a module means it will be active for that session only, changing node (for example moving to an interactive session) requires modules to be reloaded.'''

==module avail==
To see a full list of applications and libraries that are available to use on Viper, you should run '''module avail''' as shown below (showing only a few of the hundreds of modules that are available):
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ module avail

--------------------------------------------- /usr/share/Modules/modulefiles ---------------------------------------------------------------------------------------
dot module-git module-info modules null use.own

--------------------------------------------- /trinity/clustervision/CentOS/7/modulefiles/apps ------------------------------------------------------------------------------
abyss/1.5.2/gcc-5.2.0 centrifuge/1.0.4 hyphy/2.2.7/gcc-6.3.0/openmpi-2.0.2 orca/4.0.0 STAR/2.6.1
albacore/1.2.6 cp2k/3.0 hypre/intel/2.10.0b orca/4.0.1 starccm+/11.02.010
ansys/v170 cp2k/6.1.0/gcc-7.3.0/intelmpi-2018 idl/8.4 orca/4.1.0/openmpi212 starccm+/12.04.011
ansys/v172 cp2k/6.1.0/gcc-7.3.0/openmpi-3.0.0 image-magic/7.0.7/mpich-3.2/gcc-5.2.0 orca/4.1.0/openmpi313 starccm+/12.06.011

</pre>

If you want to use a specific application, you can find which versions are available by running '''module avail modulename''', e.g.:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ module avail gcc

-------------------------------------------- /trinity/clustervision/CentOS/7/modulefiles/development ---------------------------------------------------------------------------
gcc/4.9.3(default) gcc/5.2.0 gcc/6.3.0 gcc/7.3.0 gcc/8.2.0

</pre>

In this case, the (default) indicates that '''gcc/4.9.3''' is the default GCC module.

== module add ==

To add a module you use '''module add modulename'''. In most cases, running this command will not display anything and will just return you back to the Linux command prompt.

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

If you want to add a specific version of a module then you should include the version number, for example:

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ module add gcc/8.2.0
</pre>

Without putting a version in, you will either load the highest alphanumeric version or the default if one is set.

Note: '''module load''' and '''module add''' are the same.

== module list ==
To see what modules you have loaded, run '''module list'''
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ module list
Currently Loaded Modulefiles:
1) gcc/8.2.0
</pre>

== module delete ==

To remove a loaded module and all environment configurations that the module has set, run '''module delete modulename'''. Running this command will not display anything and will just return you to the Linux command prompt.

Note: module delete, module unload, module del and module rm are the same.

== module purge ==

To remove all loaded modules and return your environment to are vanilla state, run '''module purge'''. Running this command will not display anything and will just return you to the Linux command prompt.

==What modules are available?==
[[Modules| Modules Available]]

[[Applications/Special Licenses| Modules requiring special licenses]]

[[Modules #Test Modules| Test Modules]]

[[Main Page #Quickstart| Back]] / [[Quickstart/Interactive| Next (Interactive Sessions)]]

Quickstart/Connect

2024-08-20T10:51:25Z

Pysdlb: /* Connecting on a Windows PC */

To connect to Viper off campus a VPN is required. If you do not have access to the VPN you can request access through the [https://hull.service-now.com/ Support Portal].

Jump ahead to your operating system: [[#Connecting on a Windows PC| Windows]] / [[#Connecting on Mac| Mac]] / [[#Connecting on Linux| Linux]]

If this is your first time connecting please note that you may see an error message in .XAuthority, this is normal and you can ignore it.
==Connecting on a Windows PC==
To connect to Viper from a Windows PC an application that allows SSH connections must be installed. We recommend MobaXterm.

'''Installing MobaXterm'''

1. Visit [https://mobaxterm.mobatek.net/download-home-edition.html MobaXterm Website]

2. Complying with the license agreement download the ''portable version''

[[File:Mobaxtermportable.png| none|link=https://mobaxterm.mobatek.net/download-home-edition.html]]

3. Unzip the file

4. Double-click MobaXterm_Personal_24.2 (or later)

'''Using MobaXterm To Connect'''

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: '''viperlogin.hpc.hull.ac.uk''' (''port 22 if required'')

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

<pre>
password:
</pre>

8. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

==Connecting on Mac==
1. Go to Applications -> Utilities and open Terminal

2. Type ssh -Y <''yourusername''>@viperlogin.hpc..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 on the screen.

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

==Connecting on Linux==
1. Open a Terminal application

2. Type '''ssh -Y <''yourusername''>@viperlogin.hpc.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

<pre>
password:
</pre>

5. If you have connected successfully you will see the following:
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$
</pre>

[[Main Page#Quickstart| Back]] / [[Quickstart/Linux Command Line| Next (Linux Command Line)]]

File:Mobaxtermportable.png

2024-08-20T10:41:38Z

Pysdlb: