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| The Agrogenomics cluster is a [http://en.wikipedia.org/wiki/High-performance_computing High Performance Computer] (HPC) infrastructure hosted by [http://www.wageningenur.nl/nl/activiteit/Opening-High-Performance-Computing-cluster-HPC.htm Wageningen University & Research Centre]. It is open for use for all WUR research groups as well as other organizations, including companies, that have collaborative projects with WUR.
| | Anunna is a [http://en.wikipedia.org/wiki/High-performance_computing High Performance Computing] (HPC) cluster hosted by [https://www.wur.nl/ Wageningen University & Research]. It is open to all WUR research groups, and to other organisations and companies running collaborative projects with WUR. |
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| The Agrogenomics HPC was an initiative of the [http://www.breed4food.com/en/breed4food.htm Breed4Food] (B4F) consortium, consisting of the [[About_ABGC | Animal Breeding and Genomics Centre]] (WU-Animal Breeding and Genomics and Wageningen Livestock Research) and four major breeding companies: [http://www.cobb-vantress.com Cobb-Vantress], [https://www.crv4all.nl CRV], [http://www.hendrix-genetics.com Hendrix Genetics], and [http://www.topigs.com TOPIGS]. Currently, in addition to the original partners, the HPC (HPC-Ag) is used by other groups from Wageningen UR (Bioinformatics, Centre for Crop Systems Analysis, Environmental Sciences Group, and Plant Research International) and plant breeding industry (Rijk Zwaan).
| | You reach the cluster over [[SSH Access|SSH]] at <code>login.anunna.wur.nl</code>, or through your browser at the [[Apps Portal]] (https://apps.anunna.wur.nl/). |
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| == Events == | | == Documentation == |
| * [[Courses]] that have happened and are happening
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| * [[Downtime]] that will affect all users
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| * [[Meetings]] that may affect the policies of the HPC
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| == Using the HPC-Ag == | | === Start here === |
| === Gaining access to the HPC-Ag === | |
| Access to the cluster and file transfer are done by [http://en.wikipedia.org/wiki/Secure_Shell ssh-based protocols].
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| * [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]
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| * [[Services | Available features and services on the HPC]]
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| * [[Filesystems | Accessible storage methods on the HPC]]
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| == Access Policy ==
| | * [[About]] — what Anunna is, how it is built and run, and the policies that apply |
| [[Access_Policy | Main Article: Access Policy]] | | * [[Get Started]] — eligibility, getting an account, and logging in |
| | * [[Glossary of Terms]] — common HPC and Anunna terms explained |
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| Access needs to be granted actively (by creation of an account on the cluster by FB-IT). Use of resources is limited by the scheduler. Depending on availability of queues ('partitions') granted to a user, priority to the system's resources is regulated. Note that the use of the HPC-Ag is not free of charge. List price of CPU time and storage, and possible discounts on that list price for your organisation, can be retrieved from CAT-AGRO or FB-ICT.
| | === Using the cluster === |
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| === Cluster Management Software and Scheduler ===
| | * [[System Access]] — login and compute nodes, filesystems, data transfer |
| The HPC-Ag uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.
| | * [[Scheduling]] — submitting and managing jobs with SLURM |
| * [[BCM_on_B4F_cluster | Monitor cluster status with BCM]] | | * [[Software]] — modules, languages, containers, and licensed software |
| * [[SLURM_on_B4F_cluster | Submit jobs with Slurm]] | | * [[Storage]] — the storage tiers and how data is kept and protected |
| * [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']] | | * [[Apps Portal]] — graphical applications and desktops in your browser |
| * [[SLURM_Compare | Rosetta Stone of Workload Managers]] | | * [[Workflows]] — reproducible, efficient research workflows |
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| === Installation of software by users === | | === Help and more === |
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| * [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]] | | * [[Training]] — courses, tutorials, and reference material |
| * [[Setting local variables]] | | * [[Support]] — getting help, reporting problems, and cluster status |
| * [[Installing_R_packages_locally | Installing R packages locally]]
| | * [[For PIs]] — projects, allocations, and group management for group leaders |
| * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]] | |
| * [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]
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| === Installed software === | | == Quick links == |
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| * [[Globally_installed_software | Globally installed software]] | | * [[How to Get Help]] — contact the HPC team |
| * [[ABGC_modules | ABGC specific modules]]
| | * [[Tariffs]] — costs of using Anunna |
| | | * [[Maintenance Schedule]] — planned downtimes |
| === Being in control of Environment parameters ===
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| * [[Using_environment_modules | Using environment modules]]
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| * [[Setting local variables]]
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| * [[Setting_TMPDIR | Set a custom temporary directory location]]
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| * [[Installing_R_packages_locally | Installing R packages locally]]
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| * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]
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| === Controlling costs ===
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| * [[SACCT | using SACCT to see your costs]]
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| * [[get_my_bill | using the "get_my_bill" script to estimate costs]]
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| == Management ==
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| [[HPC_management | Main Article: HPC management]]
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| Project Leader of the HPC is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:lith010 | Jan van Lith (Wageningen UR,FB-IT, Infrastructure)]] and [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]].
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| == Miscellaneous ==
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| * [[Mailinglist | Electronic mail discussion lists]] | |
| * [[History_of_the_Cluster | Historical information on the startup of the HPC]]
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| * [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]
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| * [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]
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| * [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]
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| * [[Manual GitLab | GitLab: Create projects and add scripts]]
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| == See also ==
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| * [[Maintenance_and_Management | Maintenance and Management]] | |
| * [[BCData | BCData]]
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| * [[Mailinglist | Electronic mail discussion lists]]
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| * [[About_ABGC | About ABGC]]
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| * [[Computer_cluster | High Performance Computing @ABGC]]
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| * [[Lustre_PFS_layout | Lustre Parallel File System layout]]
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| == External links == | | == External links == |
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| * [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]
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| * [http://www.wageningenur.nl/en/Expertise-Services/Facilities/CATAgroFood-3/CATAgroFood-3/Our-facilities/Show/High-Performance-Computing-Cluster-HPC.htm CATAgroFood offers a HPC facilty]
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| * [http://www.cobb-vantress.com Cobb-Vantress homepage]
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| | * [https://www.wur.nl/en/Value-Creation-Cooperation/Facilities/Wageningen-Shared-Research-Facilities/Our-facilities/Show/High-Performance-Computing-Cluster-HPC-Anunna.htm Wageningen Shared Research Facilities — HPC] |
| * [https://www.crv4all.nl CRV homepage] | |
| * [http://www.hendrix-genetics.com Hendrix Genetics homepage]
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| * [http://www.topigs.com TOPIGS homepage]
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| * [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]
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| * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]
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