Jump to content

Main Page: Difference between revisions

From HPCwiki
← Older edit
Honfi001 (talk | contribs)
Bureaucrats, Administrators
250 edits
VisualWikitext
mNo edit summary
 
(108 intermediate revisions by 7 users not shown)
Line 1: Line 1:
Anunna 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.


= 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 and file transfer]]
* <h3>[[Roadmap]]</h3> How we decide what to work on
* [[Services | Alternative access methods, and extra features and services on Anunna]]
* <h3>[[Cluster Architecture Overview]]</h3> How the cluster is put together
* [[Filesystems | Accessible storage methods on Anunna]]
* <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
*


== 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]] ==
* [[Courses]] that have happened and are happening
* <h3>[[Scheduler Overview (Slurm)]]</h3> How scheduling works
* [[Downtime]] that will affect all users
* <h3>[[Partitions / Queues]]</h3> The available partitions
* [[Meetings]] that may affect the policies of Anunna
* <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


= Other Software =
== [[Software]] ==
* <h3>[[Software Overview]]</h3> The software landscape
* <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


== Cluster Management Software and Scheduler ==
* <h3>Scripting languages</h3>
Anunna uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.
** <h4>[[Python]]</h4> Python modules and environment managers
* [[BCM_on_B4F_cluster | Monitor cluster status with BCM]]
** <h4>[[R]]</h4> R modules, packages, and parallel R jobs
* [[Using_Slurm | Submit jobs with Slurm]]
** <h4>[[Julia]]</h4> Loading Julia, packages, and running it in a job
* [[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>Containers</h3>
** <h4>[[Apptainer]]</h4> Portable, reproducible containers for HPC


* [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]
* <h3>MPI implementations</h3>
* [[Setting local variables]]
** <h4>[[OpenMPI]]</h4> The MPI library Anunna is built around
* [[Installing_R_packages_locally | Installing R packages locally]]
** <h4>[[IntelMPI]]</h4> Intel MPI, with the Intel compilers and MKL
* [[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 ]]
* [[Installing WRF and WPS]]


== Installed software ==
== [[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


* [[Globally_installed_software | Globally installed software]]
== Graphical Interface Applications ==
* [[ABGC_modules | ABGC specific modules]]
* <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


= Useful Notes =  
== [[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


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


* [[Using_environment_modules | Using environment modules]]
== [[For PIs]] ==
* [[Setting local variables]]
* <h3>[[Dos and Don'ts]]</h3> Good and bad practice at a glance
* [[Setting_TMPDIR | Set a custom temporary directory location]]
* <h3>[[Managing Group Members]]</h3> Working with groups
* [[Installing_R_packages_locally | Installing R packages locally]]
* <h3>[[Storage Requests]]</h3> Requesting more storage
* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]
* <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


== Controlling costs ==
== [[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


* [[SACCT | using SACCT to see your costs]]
* <h3>Parallel Workflows</h3>
* [[get_my_bill | using the "get_my_bill" script to estimate costs]]
** <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


== Management ==
== Quick links ==
Project Leader of Anunna is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] and [[User:bexke002 | Stefan Bexkens (Wageningen UR,FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]] of the cluster.


* [[Roadmap | Ambitions regarding innovation, support and administration of Anunna ]]
* [[How to Get Help]] — contact the HPC team
* [[Maintenance Schedule]] — planned downtimes
* [[Glossary of Terms]] — common HPC and Anunna terms explained


= Miscellaneous =
== External links ==
* [[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]]


= See also =
* [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]
* [[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%" |
* [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]
* [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%" |
* [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"