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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.


= Using Anunna =
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/).
* [[Tariffs | Costs associated with resource usage]]


== Gaining access to Anunna==
== [[About]] ==
Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP].
* <h3>[[Mission and Governance]]</h3> What Anunna is for and who runs it
* [[log_in_to_B4F_cluster | Logging into cluster using ssh]]
* <h3>[[Roadmap]]</h3> How we decide what to work on
* [[file_transfer | File transfer options]]
* <h3>[[Cluster Architecture Overview]]</h3> How the cluster is put together
* [[Services | Alternative access methods, and extra features and services on Anunna]]
* <h3>[[Compute_Hardware_Overview]]</h3> The node types and their hardware
* [[Filesystems | Data storage methods on Anunna]]
* <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
*


== Access Policy ==
== [[Get Started]] ==
[[Access_Policy | Main Article: Access Policy]]
* <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.


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 Anunna 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 Shared Research Facilities or FB-IT.
== [[System Access]] ==
* <h3>[[Login Nodes]]</h3> The entry point you connect to
* <h3>[[Compute Nodes]]</h3> Where your jobs run, and how to reach them
* <h3>[[Filesystems]]</h3> The storage tiers
* <h3>[[Quotas]]</h3> Storage limits and how to check them
* <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


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


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


* [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]
== [[Storage]] ==
* [[Setting local variables]]
* <h3>[[Storage Systems Overview]]</h3> The storage tiers at a glance
* [[Installing_R_packages_locally | Installing R packages locally]]
* <h3>[[Home Directory]]</h3> Your personal space
* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]
* <h3>[[Compute Storage]]</h3> The fast Lustre filesystem for active work
* [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]
* <h3>[[Shared Storage]]</h3> Sharing data within a group
* [[Installing WRF and WPS]]
* <h3>[[Backup Policy]]</h3> What is backed up, and what is not
* [[Running scripts on a fixed timeschedule (cron)]]
* <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


== Installed software ==
== Graphical Interface Applications ==
* <h3>[[Portal Overview]]</h3> What the portal is and how the dashboard is laid out
* <h3>[[Running GUI Applications]]</h3> The general way to launch and connect to a graphical application
* <h3>[[How to Launch a Desktop Session]]</h3> Start a full Linux desktop in your browser
* <h3>[[Jupyter]]</h3> Jupyter notebooks
* <h3>[[RStudio]]</h3> The RStudio IDE for R and Python
* <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


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


= Useful Notes =  
== [[Support]] ==
* <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


== Being in control of Environment parameters ==
== [[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


* [[Using_environment_modules | Using environment modules]]
== [[Workflows]] ==
* [[Setting local variables]]
* <h3>[[Workflow Migration from Laptop to HPC]]</h3> Moving your work to the cluster
* [[Setting_TMPDIR | Set a custom temporary directory location]]
* <h3>[[Reproducibility Guidelines]]</h3> Keeping your work reproducible
* [[Installing_R_packages_locally | Installing R packages locally]]
* <h3>[[Workflow Engines (Snakemake, Nextflow)]]</h3> Managing multi-step pipelines
* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]
* <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


== Controlling costs ==
* <h3>Parallel Workflows</h3>
** <h4>[[Workflows/Parallel-Computing|Parallel Computing]]</h4> What parallel computing means on Anunna, and which type fits your work
** <h4>[[Workflows/Serial|Serial]]</h4> One program on a single core — the baseline
** <h4>[[Workflows/Embarassinly-Parallel|Embarrassingly Parallel]]</h4> Running the same program many times over
** <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


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


== Management ==
* [[How to Get Help]] — contact the HPC team
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.
* [[Maintenance Schedule]] — planned downtimes
* [[Glossary of Terms]] — common HPC and Anunna terms explained


* [[Roadmap | Ambitions regarding innovation, support and administration of Anunna ]]
== External links ==


= Miscellaneous =
* [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]
* [[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"
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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 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"