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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.  
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.


== Access Policy ==
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/).
[[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.
== [[About]] ==
* <h3>[[Mission and Governance]]</h3> What Anunna is for and who runs it
* <h3>[[Roadmap]]</h3> How we decide what to work on
* <h3>[[Cluster Architecture Overview]]</h3> How the cluster is put together
* <h3>[[Compute_Hardware_Overview]]</h3> The node types and their hardware
* <h3>[[Storage Systems Overview]]</h3> The storage tiers at a glance
* <h3>[[Tariffs]]</h3> Costs of using Anunna
* <h3>[[Network & Security]]</h3> Interconnect and data-security posture
* <h3>[[History of the Cluster]]</h3> How Anunna came to be
* <h3>[[Sustainability]]</h3> Green-HPC policy and measures
* <h3>[[FAQ]]</h3> Frequently Asked Questions
* <h3>[[Policies and Terms of Use]]</h3> Who may use Anunna and on what terms
*


= Using Anunna =
== [[Get Started]] ==
* [[Tariffs | Costs associated with resource usage]]
* <h3>[[Who Can Access?]]</h3> Eligibility
* <h3>[[Account Application Process]]</h3> How to request an account
* <h3>[[User Responsibilities]]</h3> What is expected of you as a user
* <h3>[[SSH Access]]</h3> Logging in over SSH to the cluster
* <h3>[[Apps Portal]]</h3> Using applications on Anunna through your web browser
* <h3>[[Workflow Migration from Laptop to HPC]]</h3> Moving your work to the cluster from your computer
* <h3>[[Grant_Support_%26_Acknowledgement|Grant support & Acknowledgement]]</h3> Guidance and standard text that can be used in grant proposals, research papers, theses and other publications.


== Gaining access to Anunna==
== [[System Access]] ==
Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP].
* <h3>[[Login Nodes]]</h3> The entry point you connect to
* [[log_in_to_B4F_cluster | Logging into cluster using ssh]]
* <h3>[[Compute Nodes]]</h3> Where your jobs run, and how to reach them
* [[file_transfer | File transfer options]]
* <h3>[[Filesystems]]</h3> The storage tiers
* [[Services | Alternative access methods, and extra features and services on Anunna]]
* <h3>[[Quotas]]</h3> Storage limits and how to check them
* [[Filesystems | Data storage methods on Anunna]]
* <h3>[[Remote Access (VPN, Gateway)]]</h3> Reaching Anunna from off campus
* <h3>[[Data Transfer Methods]]</h3> Moving data to and from Anunna


= Events =
== [[Scheduling|Job Scheduling and Resource Management]] ==
* <h3>[[Scheduler Overview (Slurm)]]</h3> How scheduling works
* <h3>[[Partitions / Queues]]</h3> The available partitions
* <h3>[[Choosing a node (constraints)]]</h3> Targeting particular hardware
* <h3>[[Batch Jobs]]</h3> Submitting a batch script
* <h3>[[Interactive Jobs]]</h3> An interactive shell on a compute node
* <h3>[[Array Jobs]]</h3> Running many similar jobs at once
* <h3>[[Monitoring Jobs]]</h3> Checking on your jobs
* <h3>[[Cancelling Jobs]]</h3> Stopping a job
* <h3>[[Reservations]]</h3> Reserving nodes
* <h3>[[Fair Use Policy]]</h3> Using shared resources considerately


* [[Courses]] that have happened and are happening
== [[Software]] ==
* [[Downtime]] that will affect all users
* <h3>[[Software Overview]]</h3> The software landscape
* [[Meetings]] that may affect the policies of Anunna
* <h3>[[Environment Modules]]</h3> Loading software with modules and buckets
* <h3>[[Installing Personal Software]]</h3> Installing into your own space
* <h3>[[Licensed Software]]</h3> Software that needs a licence


= Software =
* <h3>Scripting languages</h3>
* [[Apptainer]]
** <h4>[[Python]]</h4> Python modules and environment managers
* [[Python]]
** <h4>[[R]]</h4> R modules, packages, and parallel R jobs
* [[R]]  
** <h4>[[Julia]]</h4> Loading Julia, packages, and running it in a job
* [[Julia]]


= Other Software =
* <h3>Containers</h3>
** <h4>[[Apptainer]]</h4> Portable, reproducible containers for HPC


== Cluster Scheduler ==
* <h3>MPI implementations</h3>
Anunna uses Slurm as job scheduler.
** <h4>[[OpenMPI]]</h4> The MPI library Anunna is built around
* [[Using_Slurm | Submit jobs with Slurm]]
** <h4>[[IntelMPI]]</h4> Intel MPI, with the Intel compilers and MKL
* [[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]]


== Installation of software by users ==
== [[Storage]] ==
* <h3>[[Storage Systems Overview]]</h3> The storage tiers at a glance
* <h3>[[Home Directory]]</h3> Your personal space
* <h3>[[Compute Storage]]</h3> The fast Lustre filesystem for active work
* <h3>[[Shared Storage]]</h3> Sharing data within a group
* <h3>[[Backup Policy]]</h3> What is backed up, and what is not
* <h3>[[Archival Storage]]</h3> Long-term storage on tape
* <h3>[[Quotas]]</h3> Storage limits
* <h3>[[Data Lifecycle Policy]]</h3> How data moves from active to archived to removed
* <h3>[[Data storage best practices|Data Storage Best Practices]]</h3> Keeping data safe, tidy, and cheap
* <h3>[[Data Transfer Best Practices]]</h3> Moving data efficiently and reliably
* <h3>[[Handling Sensitive Data (GDPR, etc.)]]</h3> Confidential and personal data


* [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]
== Graphical Interface Applications ==
* [[Setting local variables]]
* <h3>[[Portal Overview]]</h3> What the portal is and how the dashboard is laid out
* [[Installing_R_packages_locally | Installing R packages locally]]
* <h3>[[Running GUI Applications]]</h3> The general way to launch and connect to a graphical application
* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]
* <h3>[[How to Launch a Desktop Session]]</h3> Start a full Linux desktop in your browser
* [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]
* <h3>[[Jupyter]]</h3> Jupyter notebooks
* [[Installing WRF and WPS]]
* <h3>[[RStudio]]</h3> The RStudio IDE for R and Python
* [[Running scripts on a fixed timeschedule (cron)]]
* <h3>[[File Browser]]</h3> Manage your files in the browser
* <h3>[[Shell Access]]</h3> A terminal in the browser
* <h3>[[Jobs Queue Overview]]</h3> See your jobs in the browser


== Installed software ==
== [[Training]] ==
* <h3>[[Training Materials]]</h3> Course slides and self-study resources
* <h3>[[Tutorials]]</h3> Hands-on tutorials
* <h3>[[Workshops]]</h3> Instructor-led courses and their dates


* [[Globally_installed_software | Globally installed software]]
== [[Support]] ==
* [[ABGC_modules | ABGC specific modules]]
* <h3>[[How to Get Help]]</h3> Who to contact and how
* <h3>[[Support Ticket System]]</h3> The WUR support portal
* <h3>[[Reporting Incidents]]</h3> Writing a good problem report
* <h3>[[Known Issues]]</h3> Current problems and workarounds
* <h3>[[Our User community]]</h3> The Anunna user community
* <h3>[[Maintenance Schedule]]</h3> Planned downtimes


= Useful Notes =  
== [[For PIs]] ==
* <h3>[[Dos and Don'ts]]</h3> Good and bad practice at a glance
* <h3>[[Managing Group Members]]</h3> Working with groups
* <h3>[[Storage Requests]]</h3> Requesting more storage
* <h3>[[Resource Allocation Requests]]</h3> Requesting larger or dedicated allocations
* <h3>[[External Collaborator Access]]</h3> Giving access to collaborators outside WUR
* <h3>[[Reporting Usage]]</h3> Tracking your group's usage and costs
* <h3>[[Grant Support & Acknowledgement]]</h3> Facility descriptions and support for funding applications


== Being in control of Environment parameters ==
== [[Workflows]] ==
* <h3>[[Workflow Migration from Laptop to HPC]]</h3> Moving your work to the cluster
* <h3>[[Reproducibility Guidelines]]</h3> Keeping your work reproducible
* <h3>[[Workflow Engines (Snakemake, Nextflow)]]</h3> Managing multi-step pipelines
* <h3>[[Debugging Jobs]]</h3> Working out why a job failed
* <h3>[[Checkpointing]]</h3> Saving and restarting long jobs
* <h3>[[Scheduled tasks (cron)|Scheduled Tasks (cron)]]</h3> Running recurring tasks with scrontab


* [[Using_environment_modules | Using environment modules]]
* <h3>Parallel Workflows</h3>
* [[Setting local variables]]
** <h4>[[Workflows/Parallel-Computing|Parallel Computing]]</h4> What parallel computing means on Anunna, and which type fits your work
* [[Setting_TMPDIR | Set a custom temporary directory location]]
** <h4>[[Workflows/Serial|Serial]]</h4> One program on a single core — the baseline
* [[Installing_R_packages_locally | Installing R packages locally]]
** <h4>[[Workflows/Embarassinly-Parallel|Embarrassingly Parallel]]</h4> Running the same program many times over
* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]
** <h4>[[Workflows/Multi-threaded|Multi-threaded]]</h4> Many cores on one machine, within a single process
** <h4>[[Workflows/Multi-Process|Multi-Process]]</h4> One calculation spread across several machines


== Controlling costs ==
== Quick links ==


* [[SACCT | using SACCT to see your costs]]
* [[How to Get Help]] — contact the HPC team
* [[get_my_bill | using the "get_my_bill" script to estimate costs]]
* [[Maintenance Schedule]] — planned downtimes
* [[Glossary of Terms]] — common HPC and Anunna terms explained


== Management ==
== External links ==
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 ]]
* [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]
 
= 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]]
* [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]
* [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]
* [[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 =
* [[Maintenance_and_Management | Maintenance and Management]]
* [[BCData | BCData]]
* [[Mailinglist | Electronic mail discussion lists]]
* [[About_ABGC | About ABGC]]
* [[Computer_cluster | High Performance Computing @ABGC]]
* [[Lustre_PFS_layout | Lustre Parallel File System layout]]
 
= External links =
{| width="90%"
|- valign="top"
| width="30%" |
* [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]
| width="30%" |
* [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]
* [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]
|}

Latest revision as of 06:49, 31 August 2026

Anunna is a High Performance Computing (HPC) cluster hosted by Wageningen University & Research. It is open to all WUR research groups, and to other organisations and companies running collaborative projects with WUR.

You reach the cluster over SSH at login.anunna.wur.nl, or through your browser at the Apps Portal (https://apps.anunna.wur.nl/).

About

Get Started

System Access

Job Scheduling and Resource Management

Software

  • Scripting languages

    • Python

      Python modules and environment managers

    • R

      R modules, packages, and parallel R jobs

    • Julia

      Loading Julia, packages, and running it in a job

  • Containers

    • Apptainer

      Portable, reproducible containers for HPC

  • MPI implementations

    • OpenMPI

      The MPI library Anunna is built around

    • IntelMPI

      Intel MPI, with the Intel compilers and MKL

Storage

Graphical Interface Applications

Training

Support

For PIs

Workflows

Retrieved from "https://wiki.anunna.wur.nl/index.php?title=Main_Page&oldid=3181"