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| The Agrogenomics cluster is a [http://en.wikipedia.org/wiki/High-performance_computing High Performance Compute] (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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| == Rationale and Requirements for a new cluster == | | == Documentation == |
| [[File:Breed4food-logo.jpg|thumb|right|200px|The Breed4Food logo]]
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| The Agrogenomics Cluster was originally conceived as being the 7th pillar of the [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]. While the other six pillars revolve around specific research themes, the Cluster represents a joint infrastructure. The rationale behind the cluster is to enable the increasing computational needs in the field of genetics and genomics research, by creating a joint facility that will generate benefits of scale, thereby reducing cost. In addition, the joint infrastructure is intended to facilitate cross-organisational knowledge transfer. In that capacity, the HPC-Ag acts as a joint (virtual) laboratory where researchers - academic and applied - can benefit from each other's know-how. Lastly, the joint cluster, housed at Wageningen University campus, allows retaining vital and often confidential data sources in a controlled environment, something that cloud services such as Amazon Cloud or others usually can not guarantee.
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| == Process of acquisition and financing == | | === Start here === |
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| [[File:Signing_CatAgro.png|thumb|left|300px|Petra Caessens, manager operations of CAT-AgroFood, signs the contract of the supplier on August 1st, 2013. Next to her Johan van Arendonk on behalf of Breed4Food.]] | | * [[About]] — what Anunna is, how it is built and run, and the policies that apply |
| The Agrogenomics cluster was financed by [http://www.wageningenur.nl/en/Expertise-Services/Facilities/CATAgroFood-3/CATAgroFood-3/News-and-agenda/Show/CATAgroFood-invests-in-a-High-Performance-Computing-cluster.htm CATAgroFood]. The [[B4F_cluster#IT_Workgroup | IT-Workgroup]] formulated a set of requirements that in the end were best met by an offer from [http://www.dell.com/learn/nl/nl/rc1078544/hpcc Dell]. [http://www.clustervision.com ClusterVision] was responsible for installing the cluster at the Theia server centre of FB-ICT.
| | * [[Get Started]] — eligibility, getting an account, and logging in |
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| | * [[Glossary of Terms]] — common HPC and Anunna terms explained |
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| == Architecture of the cluster == | | === Using the cluster === |
| [[Architecture_of_the_HPC | Main Article: Architecture of the Agrogenomics HPC]]
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| [[File:Cluster_scheme.png|thumb|right|600px|Schematic overview of the cluster.]]
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| The new Agrogenomics HPC has a classic cluster architecture: state of the art Parallel File System (PSF), headnodes, compute nodes (of varying 'size'), all connected by superfast network connections (Infiniband). Implementation of the cluster will be done in stages. The initial stage includes a 600TB PFS, 48 slim nodes of 16 cores and 64GB RAM each, and 2 fat nodes of 64 cores and 1TB RAM each. The overall architecture, that include two head nodes in fall-over configuration and an infiniband network backbone, can be easily expanded by adding nodes and expanding the PFS. The cluster management software is designed to facilitate a heterogenous and evolving cluster.
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| == Housing at Theia ==
| | * [[System Access]] — login and compute nodes, filesystems, data transfer |
| [[File:Map_Theia.png|thumb|left|200px|Location of Theia, just outside of Wageningen campus]] | | * [[Scheduling]] — submitting and managing jobs with SLURM |
| The Agrogenomics Cluster is housed at one of two main server centres of WUR-FB-IT, near Wageningen Campus. The building (Theia) may not look like much from the outside (used to function as potato storage) but inside is a modern server centre that includes, a.o., emergency power backup systems and automated fire extinguishers. Many of the server facilities provided by FB-ICT that are used on a daily basis by WUR personnel and students are located there, as is the Agrogenomics Cluster. Access to Theia is evidently highly restricted and can only be granted in the presence of a representative of FB-IT.
| | * [[Software]] — modules, languages, containers, and licensed software |
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| | * [[Storage]] — the storage tiers and how data is kept and protected |
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| | * [[Apps Portal]] — graphical applications and desktops in your browser |
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| | * [[Workflows]] — reproducible, efficient research workflows |
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| | === Help and more === |
| [[File:Cluster2_pic.png|thumb|left|220px|Some components of the cluster after unpacking.]]
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| [[File:Cluster_pic.png|thumb|right|400px|The final configuration after installation.]]
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| == Management ==
| | * [[Training]] — courses, tutorials, and reference material |
| [[HPC_management | Main Article: HPC management]] | | * [[Support]] — getting help, reporting problems, and cluster status |
| | * [[For PIs]] — projects, allocations, and group management for group leaders |
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| Project Leader of the HPC is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:pollm001 | Koen Pollmann (Wageningen UR,FB-IT, Infrastructure)]] and [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]].
| | == Quick links == |
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| == Access Policy ==
| | * [[How to Get Help]] — contact the HPC team |
| [[Access_Policy | Main Article: Access Policy]] | | * [[Tariffs]] — costs of using Anunna |
| | | * [[Maintenance Schedule]] — planned downtimes |
| Access policy is still a work in progress. In principle, all staff and students of the five main partners will have access to the cluster. Access needs to be granted actively (by creation of an account on the cluster by FB-IT reagdring non WUR accounts). 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.
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| == Users ==
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| * [[List_of_users | List of users (alphabetical order)]]
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| * [[Mailinglist | Electronic mail discussion lists]]
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| == Using the HPC-Ag ==
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| === Gaining access to the HPC-Ag ===
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| 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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| === Cluster Management Software and Scheduler ===
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| The HPC-Ag uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.
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| * [[BCM_on_B4F_cluster | Monitor cluster status with BCM]]
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| * [[SLURM_on_B4F_cluster | Submit jobs with Slurm]]
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| * [[SLURM_Compare | Rosetta Stone of Workload Managers]]
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| === Installation of software by users ===
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| * [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]
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| * [[Setting local variables]]
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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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| === Installed software ===
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| * [[Globally_installed_software | Globally installed software]]
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| * [[ABGC_modules | ABGC specific modules]]
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| === 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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| == Miscellaneous ==
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| * [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]
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| * [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]
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| == See also ==
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| * [[Maintenance_and_Management | Maintenance and Management]] | |
| * [[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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