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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 Computer] (HPC) infrastructure hosted by [https://www.wur.nl/en/show/supercomputer-anunna-opens-up-more-opportunities-for-data-storage-and-artificial-intelligence-applications.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.  


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).
== Access Policy ==
 
[[Access_Policy | Main Article: Access Policy]]
== Rationale and Requirements for a new cluster ==
[[File:Breed4food-logo.jpg|thumb|right|200px|The Breed4Food logo]]
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 ==
 
[[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.]]
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.
{{-}}


== Architecture of the cluster ==
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. Note that the use of Anunna is not free of charge.  
[[Architecture_of_the_HPC | Main Article: Architecture of the Agrogenomics HPC]]
[[File:Cluster_scheme.png|thumb|right|600px|Schematic overview of the cluster.]]
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 ==
= Using Anunna =
[[File:Map_Theia.png|thumb|left|200px|Location of Theia, just outside of Wageningen campus]]
* [[Tariffs | Costs associated with resource usage]]
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.
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== Gaining access to Anunna==
[[File:Cluster2_pic.png|thumb|left|220px|Some components of the cluster after unpacking.]]
Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP].
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* [[log_in_to_B4F_cluster | Logging into cluster using ssh]]
[[File:Cluster_pic.png|thumb|right|400px|The final configuration after installation.]]
* [[file_transfer | File transfer options]]
|}
* [[Services | Alternative access methods, and extra features and services on Anunna]]
{{-}}
* [[Filesystems | Data storage methods on Anunna]]
 
== Management ==
[[HPC_management | Main Article: HPC management]]


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]].
== Using Anunna for courses (mainly jupyter notebooks) ==
* [[steps_for_courses | Steps involved to run a course on Anunna]]
= Events =


== Access Policy ==
* [[Courses]] that have happened and are happening
[[Access_Policy | Main Article: Access Policy]]
* [[Downtime]] that will affect all users
* [[Meetings]] that may affect the policies of Anunna


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.
= Software =
* [[Modules]]
* [[Apptainer]]
* [[Python]]
* [[R]]
* [[Julia]]


== Users ==
=Web Apps=


* [[List_of_users | List of users (alphabetical order)]]
*[[Jupyter]]
* [[Mailinglist | Electronic mail discussion lists]]


== Using the HPC-Ag ==
= Other Software =
=== 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].
* [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]


=== Cluster Management Software and Scheduler ===
== Cluster Scheduler ==
The HPC-Ag uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.
Anunna uses Slurm as job scheduler.
* [[BCM_on_B4F_cluster | Monitor cluster status with BCM]]
* [[Using_Slurm | Submit jobs with Slurm]]
* [[SLURM_on_B4F_cluster | Submit jobs with Slurm]]
* [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']]
* [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']]
* [[SLURM_Compare | Rosetta Stone of Workload Managers]]
* [[SLURM_Compare | Rosetta Stone of Workload Managers]]


=== Installation of software by users ===
== Installation of software by users ==


* [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]
* [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]
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* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]
* [[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 ]]
* [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]
* [[Installing WRF and WPS]]
* [[Running scripts on a fixed timeschedule (cron)]]


=== Installed software ===
== Installed software ==


* [[Globally_installed_software | Globally installed software]]
* [[Globally_installed_software | Globally installed software]]
* [[ABGC_modules | ABGC specific modules]]
* [[ABGC_modules | ABGC specific modules]]


=== Being in control of Environment parameters ===
= Useful Notes =
 
== Being in control of Environment parameters ==


* [[Using_environment_modules | Using environment modules]]
* [[Using_environment_modules | Using environment modules]]
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* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]
* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]


=== Controlling costs ===
== Controlling costs ==


* [[SACCT | using SACCT to see your costs]]
* [[SACCT | using SACCT to see your costs]]
* [[get_my_bill | using the "get_my_bill" script to estimate costs]]
* [[get_my_bill | using the "get_my_bill" script to estimate costs]]


== Miscellaneous ==
== Management ==
Product Owner of Anunna is Alexander van Ittersum (Wageningen UR,FB-IT, C&PS). [[User: prins089 | Fons Prinsen (Wageningen UR, FB-IT, C&PS)]] is responsible for [[Maintenance_and_Management | Maintenance and Management]] of the cluster.
 
* [[Roadmap | Ambitions regarding innovation, support and administration of Anunna ]]
 
= Miscellaneous =
* [[Mailinglist | Electronic mail discussion lists]]
* [[History_of_the_Cluster | Historical information on the startup of Anunna]]
* [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]
* [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]
* [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]
* [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]
* [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]
* [[Manual GitLab | GitLab: Create projects and add scripts]]
* [[Manual GitLab | GitLab: Create projects and add scripts]]
* [[Monitoring_executions | Monitoring job execution]]
* [[Shared_folders | Working with shared folders in the Lustre file system]]
* [[Old_binaries | Running older binaries on the updated OS]]


== See also ==
= See also =
* [[Maintenance_and_Management | Maintenance and Management]]
* [[Maintenance_and_Management | Maintenance and Management]]
* [[BCData | BCData]]
* [[BCData | BCData]]
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* [[Lustre_PFS_layout | Lustre Parallel File System layout]]
* [[Lustre_PFS_layout | Lustre Parallel File System layout]]


== 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]
* [https://www.wur.nl/en/Value-Creation-Cooperation/Facilities/Wageningen-Shared-Research-Facilities/Our-facilities/Show/High-Performance-Computing-Cluster-HPC-Anunna.htm SRF offers a HPC facilty]
* [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]
* [http://www.cobb-vantress.com Cobb-Vantress homepage]
 
| width="30%" |
* [https://www.crv4all.nl CRV homepage]
* [http://www.hendrix-genetics.com Hendrix Genetics homepage]
* [http://www.topigs.com TOPIGS homepage]
| width="30%" |
| width="30%" |
* [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]
* [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]
* [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]
* [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]
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Latest revision as of 09:51, 1 November 2024

Anunna is a High Performance Computer (HPC) infrastructure hosted by 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.

Access Policy

Main Article: Access Policy

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. Note that the use of Anunna is not free of charge.

Using Anunna

Gaining access to Anunna

Access to the cluster and file transfer are traditionally done via SSH and SFTP.

Using Anunna for courses (mainly jupyter notebooks)

Events

  • Courses that have happened and are happening
  • Downtime that will affect all users
  • Meetings that may affect the policies of Anunna

Software

Web Apps

Other Software

Cluster Scheduler

Anunna uses Slurm as job scheduler.

Installation of software by users

Installed software

Useful Notes

Being in control of Environment parameters

Controlling costs

Management

Product Owner of Anunna is Alexander van Ittersum (Wageningen UR,FB-IT, C&PS). Fons Prinsen (Wageningen UR, FB-IT, C&PS) is responsible for Maintenance and Management of the cluster.

Miscellaneous

See also

External links

Retrieved from "https://wiki.anunna.wur.nl/index.php?title=Main_Page&oldid=2408"