HPCwiki - User contributions [en]

Using the Shell

2026-06-19T20:35:32Z

Haars0011: Orphan fix: redirect old/junk page to Shell Access (via update-page on MediaWiki MCP Server)

#REDIRECT [[Shell Access]]

SSH Access

2026-06-19T20:35:29Z

Haars0011: Link Create shortcut log-in command from See also (orphan fix) (via update-page on MediaWiki MCP Server)

This page explains how to connect to Anunna over SSH. Once you are logged in, see [[Login Nodes]] for what the login nodes are for, and [[Policies and Terms of Use]] for the rules that apply.

== Connecting ==

You log in to Anunna using the Secure Shell protocol (SSH) on the default port (TCP 22). The address of the login server is:

login.anunna.wur.nl

You are automatically redirected to a currently valid login server. An SSH client is built in on Linux and macOS; on Windows you usually install one, such as [http://www.chiark.greenend.org.uk/~sgtatham/putty/ PuTTY] or MobaXTerm.

Note that access may be restricted to certain IP ranges, and SSH may be blocked where port 22 is closed by a firewall. (For example, WUR FB-IT does not allow port 22 over WiFi to certain systems.)

'''The login server is an access point only — it is not for CPU- or memory-intensive work.''' Anything beyond light, interactive use belongs in a job; see [[Login Nodes]] and [[Scheduler Overview (Slurm)]].

=== Linux and macOS ===

An SSH client is available from any Linux or macOS terminal:

<syntaxhighlight lang="bash">
ssh <username>@login.anunna.wur.nl
</syntaxhighlight>

If the connection is refused, check your firewall settings — SSH needs port 22 open.

=== Windows ===

On Windows you connect with an SSH client such as '''MobaXTerm''' or '''PuTTY'''. In either case, set the remote host to <code>login.anunna.wur.nl</code> and enter your username (not your email address) and WUR password. No characters appear while you type your password — this is normal.

For key-based login, generate an SSH key pair with the client's key generator (MobaKeygen in MobaXTerm, or PuTTYgen for PuTTY), protect it with a passphrase, and add the public key to <code>~/.ssh/authorized_keys</code> on Anunna. PuTTY users can hold the key in Pageant so they do not have to type the passphrase each time. See the [http://www.chiark.greenend.org.uk/~sgtatham/putty/ PuTTY homepage] for full instructions.

== Logging in without a password ==

You can configure SSH to log in without typing your password each time; see [[ssh_without_password|SSH without password]].

== Connecting to a compute node ==

To open a shell or a direct connection on a compute node where your job is running, see [[Compute Nodes]].

== See also ==
* [[Login Nodes]]
* [[Compute Nodes]]
* [[Data Transfer Methods]]
* [[Create shortcut log-in command]] — SSH aliases and ~/.ssh/config shortcuts
* [[ssh_without_password|SSH without password]]
* [[Scheduler Overview (Slurm)]]

== External links ==
* [http://en.wikipedia.org/wiki/Secure_Shell Secure Shell on Wikipedia]
* [http://www.chiark.greenend.org.uk/~sgtatham/putty/ PuTTY homepage]

Software Overview

2026-06-19T20:35:28Z

Haars0011: Link ABGC/JBrowse from See also (orphan fix) (via update-page on MediaWiki MCP Server)

Anunna offers software in several ways, depending on whether you need a ready-made package, your own custom setup, or a commercial product. This page is a map of the options and points to the page that covers each in detail.

== Pre-installed software: modules ==

Most software on the cluster is provided as [[Environment Modules | environment modules]], organised into yearly "buckets". Load a bucket and then the software you need — the module sets up your environment so the right versions of the program and its dependencies are available. Use <code>module key <name></code> to search for a package, and request additions through [[Requesting New Software]].

== Languages ==

The common scientific languages have their own pages covering the provided modules, how to manage packages, and how to run them in jobs and notebooks:

* [[Python]] — modules, virtual environments, Miniforge, and Jupyter kernels.
* [[R]] — modules, local package libraries, batch jobs, and parallel R.
* [[Julia]] — modules and package management.

== Your own software ==

If a package is not available as a module, you have a few options:

* [[Installing Personal Software]] — shell configuration, environment variables, and installing small tools into your own space.
* [[Apptainer]] — package an application and all its dependencies into a portable container. This is the most reproducible way to bring in software that is awkward to install directly.

== Commercial and licensed software ==

Some packages are commercial and restricted to eligible users — see [[Licensed Software]] for what is available and how to get access.

== Graphical applications ==

Several applications are available through your web browser via the Apps Portal, without using the command line — see [[General overview | the Apps Portal overview]].

== Requesting new software ==

If what you need is not available anywhere above, [[Requesting New Software | submit a software request]].

== See also ==

* [[Environment Modules]]
* [[Installing Personal Software]]
* [[Licensed Software]]
* [[Requesting New Software]]
* [[ABGC/JBrowse]] — setting up JBrowse (ABGC genome browser)

Environment Modules

2026-06-19T20:35:23Z

Haars0011: Link ABGC/Modules from See also (orphan fix) (via update-page on MediaWiki MCP Server)

Anunna provides software through '''environment modules''', managed with [https://lmod.readthedocs.io/ Lmod]. A module configures your shell — and the environment of your jobs — so that a chosen application and the right version of its dependencies are available. Because each module lives in its own self-contained tree, modules let several otherwise-conflicting programs and several versions of the same program coexist on the cluster without clashing.

== Software buckets ==

Modules on Anunna are organised into '''buckets'''. Each bucket is a snapshot of a particular compiler-and-toolchain generation; all the software in a bucket is built with the same compiler. This matters because mixing software built with different compilers in one job can cause conflicts, errors, or silently wrong results — so keeping a job's software within a single bucket keeps it consistent.

The buckets currently available are:

* '''legacy''' — old software that is no longer maintained or updated but is still used in active research.
* '''2023''' — software built with the 2023 compilers and toolchain. One version of each package.
* '''2024''' — software built with the 2024 compilers and toolchain. One version of each package.
* '''utilities''' — software that does not depend on a specific compiler or toolchain (for example [[Apptainer]]).
* '''groups''' — module files contributed by groups inside and outside WUR.
* '''GPU''' — CUDA, cuDNN, and related packages that are independent of toolchains.

A bucket has to be loaded before its modules become visible. To use the 2023 bucket:

<syntaxhighlight lang="bash">
module load 2023
</syntaxhighlight>

After this, <code>module avail</code> shows the expanded list of modules from that bucket.

The modules are built with [https://easybuild.io/ EasyBuild], which uses publicly shared recipes called easyconfigs. Their [https://github.com/easybuilders/easybuild-easyconfigs/tree/develop/easybuild/easyconfigs repository] is a good place to check what software is available upstream.

== Requesting modules ==

If a module you need is not available, submit a software request at [https://ideas.anunna.wur.nl https://ideas.anunna.wur.nl]. There you can follow the progress of your request and upvote requests from other users — the more upvotes, the sooner it is prioritised.

== Listing modules ==

Three commands list the available modules in increasing detail. <code>overview</code> gives a top-level view — just the software names and how many versions exist. <code>avail</code> lists the individual versions. <code>spider</code> gives a verbose list with a description of each.

<syntaxhighlight lang="bash">
module overview
module avail
module spider
</syntaxhighlight>

== Searching for modules ==

The same three commands search when you pass a module name as an argument, again at increasing levels of detail:

<syntaxhighlight lang="bash">
module overview <nameOfModule>
module avail <nameOfModule>
module spider <nameOfModule>
</syntaxhighlight>

=== Searching by keyword ===

You can also search for a keyword inside modules with <code>module key</code>. This is useful for finding which module contains a specific Python or R extension — there are bundle modules for both languages that list their extensions, and Lmod searches the module descriptions too.

<syntaxhighlight lang="bash">
module key <keyword>
</syntaxhighlight>

For example, to find which module provides the R package <code>terra</code>, first load a bucket, then search:

<syntaxhighlight lang="bash">
module load 2023
module key terra
</syntaxhighlight>

which yields:

<syntaxhighlight lang="text">
The following modules match your search criteria: "terra"
--------------------------------------------------------------------------------------------------------

R-bundle-CRAN: R-bundle-CRAN/2023.12-foss-2023a
Bundle of R packages from CRAN

--------------------------------------------------------------------------------------------------------
</syntaxhighlight>

So you would load <code>R-bundle-CRAN/2023.12-foss-2023a</code> to get the <code>terra</code> package.

== Loading modules ==

Load a module by name:

<syntaxhighlight lang="bash">
module load <moduleName>
</syntaxhighlight>

For example, to load Python from the 2023 bucket:

<syntaxhighlight lang="bash">
module load 2023
module load Python/3.11.3
</syntaxhighlight>

'''Specify the version''' you load, as in the example. It is good practice for consistency and reproducibility — if you omit the version, Lmod picks whatever the current default is, and that default can change over time. Naming the exact version in a submit script also turns the script into documentation of the environment it ran in. When you load a module, its dependencies are loaded automatically.

=== Listing loaded modules ===

<syntaxhighlight lang="bash">
module list
</syntaxhighlight>

Following the example above, after loading the 2023 bucket and <code>Python/3.11.3</code>, the list shows the module plus the dependencies pulled in with it:

<syntaxhighlight lang="text">
user001@login201:~$ module list

Currently Loaded Modules:
1) slurm/24.05.1 (S) 5) binutils/2.40-GCCcore-12.3.0 9) Tcl/8.6.13-GCCcore-12.3.0 13) OpenSSL/1.1
2) 2023 6) bzip2/1.0.8-GCCcore-12.3.0 10) SQLite/3.42.0-GCCcore-12.3.0 14) Python/3.11.3-GCCcore-12.3.0
3) GCCcore/12.3.0 7) ncurses/6.4-GCCcore-12.3.0 11) XZ/5.4.2-GCCcore-12.3.0
4) zlib/1.2.13-GCCcore-12.3.0 8) libreadline/8.2-GCCcore-12.3.0 12) libffi/3.4.4-GCCcore-12.3.0

Where:
S: Module is Sticky, requires --force to unload or purge
</syntaxhighlight>

The <code>slurm</code> module is loaded by default and marked '''Sticky''' (<code>S</code>) — it survives a normal unload or purge.

== Removing and switching modules ==

Unload a single module:

<syntaxhighlight lang="bash">
module unload Python/3.11.3
</syntaxhighlight>

This unloads only the named module, not its dependencies. To swap one module for another in a single step:

<syntaxhighlight lang="bash">
module switch <oldModule> <newModule>
</syntaxhighlight>

Some modules refuse to load alongside others — for example, two Java modules cannot be loaded at once. Attempting it produces a conflict message:

<syntaxhighlight lang="text">
Module 'foo/2' conflicts with the currently loaded module(s) 'foo/1'
</syntaxhighlight>

When you see this, unload or switch rather than trying to stack the two modules.

To clear the whole environment, use <code>purge</code>:

<syntaxhighlight lang="bash">
module purge
</syntaxhighlight>

Sticky modules such as <code>slurm</code> survive a plain purge:

<syntaxhighlight lang="text">
user001@login201:~$ module purge
The following modules were not unloaded:
(Use "module --force purge" to unload all):

1) slurm/24.05.1
</syntaxhighlight>

Putting <code>module purge</code> (or <code>module reset</code>) near the top of a job script is good practice: it clears anything that might have been loaded by mistake, so the job starts from a known-clean environment.

== See also ==

* [[Installing Personal Software]]
* [[Batch Jobs]]
* [[Python]]
* [[R]]
* [[Apptainer]]
* [[ABGC/Modules]] — group-specific modules for ABGC

== External links ==

* [https://lmod.readthedocs.io/ Lmod documentation]
* [https://easybuild.io/ EasyBuild]
* [https://github.com/easybuilders/easybuild-easyconfigs/tree/develop/easybuild/easyconfigs EasyBuild easyconfigs repository]

About

2026-06-19T20:35:20Z

Haars0011: Link History pages into the About hub (orphan fix) (via update-page on MediaWiki MCP Server)

An overview of the Anunna HPC facility: what it is, how it is built and run, and the policies that apply.

== In this section ==

* [[Mission and Governance]] — what Anunna is for and who runs it
* [[Cluster Architecture Overview]] — how the cluster is put together
* [[Compute Hardware Overview]] — the node types and their hardware
* [[Storage Systems Overview]] — the storage tiers at a glance
* [[Network & Security]] — interconnect and data-security posture
* [[Sustainability]] — green-HPC policy and measures
* [[Policies and Terms of Use]] — who may use Anunna and on what terms
* [[FAQ]] — frequently asked questions
* [[Roadmap]] — where Anunna is heading
* [[History/Origins|History of the cluster]] — how Anunna came to be

Main Page

2026-06-19T12:28:24Z

Haars0011: IA migration: rewrite Main Page as the section-landing front door for the new 11-section IA (via update-page on MediaWiki MCP Server)

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.

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/).

== Documentation ==

=== Start here ===

* [[About]] — what Anunna is, how it is built and run, and the policies that apply
* [[Get Started]] — eligibility, getting an account, and logging in
* [[Glossary of Terms]] — common HPC and Anunna terms explained

=== Using the cluster ===

* [[System Access]] — login and compute nodes, filesystems, data transfer
* [[Scheduling]] — submitting and managing jobs with SLURM
* [[Software]] — modules, languages, containers, and licensed software
* [[Storage]] — the storage tiers and how data is kept and protected
* [[Apps Portal]] — graphical applications and desktops in your browser
* [[Workflows]] — reproducible, efficient research workflows

=== Help and more ===

* [[Training]] — courses, tutorials, and reference material
* [[Support]] — getting help, reporting problems, and cluster status
* [[For PIs]] — projects, allocations, and group management for group leaders

== Quick links ==

* [[How to Get Help]] — contact the HPC team
* [[Tariffs]] — costs of using Anunna
* [[Maintenance Schedule]] — planned downtimes

== External links ==

* [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]

Wiki TODO

2026-06-19T12:23:20Z

Haars0011: Add Handling Sensitive Data + Grant Support Documentation tasks (via update-page on MediaWiki MCP Server)

This page lists Anunna documentation that has been published but still needs current or authoritative information filled in. The pages below are usable as they stand, but each contains placeholders — marked in the page source with <code></code> comments — where someone with current operational knowledge needs to add or confirm details.

To pick up a task: open the page, find the <code>TODO</code> comment(s) in its source, add the information, and remove the item from this list.

== Hardware and network ==

* '''[[Cluster Architecture Overview]]''' — confirm the current interconnect (Omnipath and/or InfiniBand) and topology; add a current architecture diagram (the old schematics were out of date and were removed).
* '''[[Compute Hardware Overview]]''' — fill in the per-node specifications: number of CPU nodes, cores and memory per node, CPU model(s), and whether there are high-memory "fat" nodes; number of NVIDIA GPU nodes, GPUs per node, and host CPU/memory; AMD GPU model and node details.
* '''[[Network & Security]]''' — confirm the interconnect (as above) and document the data-security posture: how data is protected at rest and in transit, access control, handling of confidential or personal data, and backup/retention.
* '''[[Performance Optimization/Multiple nodes (MPI)]]''' — confirm the recommended MPI library and module names, any required <code>srun --mpi=...</code> plugin flag, and whether specific interconnect/fabric tuning is needed. The old mvapich2 + InfiniBand (ib0) example was Breed4Food-era and was removed.

== Storage ==

* '''[[Quotas]]''' — document the Lustre quota model (per-user or per-group, and the default sizes for /lustre/backup, /lustre/nobackup, /lustre/scratch), the command(s) users run to check their current usage, and how to request more space. Only the home-directory quota (200 GB) is currently documented.
* '''[[Archival Storage]]''' — clarify how the manual iRODS/itape workflow relates to Tapeworm, now that Tapeworm manages archival from /archive to tape automatically: is itape still the recommended way to push data to tape, or is iRODS now used mainly for retrieving archived datasets?
* '''[[Data Lifecycle Policy]]''' — add the formal data-retention policy if one exists: how long different data is kept, any maximum retention, and what happens to data when an account or project closes.

== Software and workflows ==

* '''[[Workflow Engines (Snakemake, Nextflow)]]''' — confirm the recommended way to run Snakemake on Anunna (the documented profile is the older Snakemake <8 style; Snakemake 8+ uses the <code>--executor slurm</code> plugin), and write the Nextflow section (loading/installing Nextflow, the SLURM executor configuration, and a minimal example).
* '''[[Conda for teaching]]''' — modernise for current Anunna: the page still describes the old Bright <code>/cm/shared</code> paths and tcl modulefiles. Replace with a Miniforge environment on Lustre and the current course-kernel route (kernel registered at notebook.anunna.wur.nl; see [[Steps for courses]]).
* '''[[Julia]]''' — confirm the exact Julia module name(s) and version(s) available in the current buckets.

== Support and operations ==

* '''[[Maintenance Schedule]]''' — confirm where planned-maintenance dates are announced (Apps Portal message of the day, mailing list, Teams) and add the next scheduled downtime, or a link to a live maintenance schedule. Only the general cadence (roughly April/May and October) is documented.
* '''[[System Status Page]]''' — add the Anunna status / health dashboard URL, or confirm whether such a dashboard exists.
* '''[[Reporting Usage]]''' — document the reports.anunna.wur.nl usage and cost dashboard: what reports it offers, who can see what (your own usage versus your group's), and how to read them.
* '''[[Managing Group Members]]''' — confirm how a PI adds or removes members from their Anunna group (self-service, via the AD group owner, or via the administrators) and document the steps.
* '''[[Project Creation]]''' — document the project / billing-account creation process: how a PI requests one, how a commitment is agreed, and who can be added.
* '''[[Storage Requests]]''' — confirm whether storage requests use a dedicated form or the general HPC (Anunna) support service, and any approval or group-owner requirements.
* '''[[Remote Access (VPN, Gateway)]]''' — link the official WUR VPN setup instructions, and document any Anunna-specific gateway or jump-host arrangements.
* '''[[Resource Allocation Requests]]''' — document the resource-allocation process: what can be requested (extra priority/QoS, dedicated nodes, GPU allocations), how it relates to a group commitment, who approves it, and lead times.
* '''[[External Collaborator Access]]''' — document the external-collaborator process: sponsorship and approval, any data/security agreement, account duration and renewal, and access scope.

== Policy and governance ==

* '''[[Mission and Governance]]''' — confirm and document the current governance bodies (for example a steering group and user group) and their membership. The previous roster was from the Breed4Food era and was removed.
* '''[[Roadmap]]''' — add the current roadmap, or link the latest roadmap document. The 2019–2020 version was removed.
* '''[[Sustainability]]''' — add the sustainability / green-HPC policy and any concrete measures: energy sourcing, cooling, hardware lifecycle, and institutional targets.
* '''[[Policies and Terms of Use]]''' — supply the formal terms of use / acceptable-use policy (data ownership and responsibilities, security obligations, consequences of misuse) and confirm the current account-request route and per-group access contacts. The previous access-contact list was from the Breed4Food era and was removed.
* '''[[Account Application Process]]''' — confirm whether WUR users request an Anunna account through the general "HPC (Anunna)" support service or a dedicated account-request form, and what details are needed (group/affiliation, sponsor, intended use).
* '''[[User's group]]''' — document any formal user representation: regular user meetings, how users feed back into decisions, and how that relates to the governance bodies. Currently only the Anunna Users Teams community is documented.
* '''[[Handling Sensitive Data (GDPR, etc.)]]''' — document Anunna's posture on confidential and personal data / GDPR: which data categories may be processed, any data-processing agreements or approvals, protection at rest and in transit, and who to contact for a data-protection assessment.
* '''[[Grant Support Documentation]]''' — provide grant-support material: a standard facility description for funding applications, the acknowledgement text to cite Anunna in publications, cost/quotation support, and who to contact for a letter of support.

== Nice to have ==

* '''[[FAQ]]''' — extend with the questions the HPC team is asked most often (for example quota limits, GPU access, course accounts, data transfer).

== See also ==

* [[Support]]

Wiki TODO

2026-06-19T12:23:08Z

Haars0011: Add Remote Access / Resource Allocation Requests / External Collaborator Access tasks (via update-page on MediaWiki MCP Server)

This page lists Anunna documentation that has been published but still needs current or authoritative information filled in. The pages below are usable as they stand, but each contains placeholders — marked in the page source with <code></code> comments — where someone with current operational knowledge needs to add or confirm details.

To pick up a task: open the page, find the <code>TODO</code> comment(s) in its source, add the information, and remove the item from this list.

== Hardware and network ==

* '''[[Cluster Architecture Overview]]''' — confirm the current interconnect (Omnipath and/or InfiniBand) and topology; add a current architecture diagram (the old schematics were out of date and were removed).
* '''[[Compute Hardware Overview]]''' — fill in the per-node specifications: number of CPU nodes, cores and memory per node, CPU model(s), and whether there are high-memory "fat" nodes; number of NVIDIA GPU nodes, GPUs per node, and host CPU/memory; AMD GPU model and node details.
* '''[[Network & Security]]''' — confirm the interconnect (as above) and document the data-security posture: how data is protected at rest and in transit, access control, handling of confidential or personal data, and backup/retention.
* '''[[Performance Optimization/Multiple nodes (MPI)]]''' — confirm the recommended MPI library and module names, any required <code>srun --mpi=...</code> plugin flag, and whether specific interconnect/fabric tuning is needed. The old mvapich2 + InfiniBand (ib0) example was Breed4Food-era and was removed.

== Storage ==

* '''[[Quotas]]''' — document the Lustre quota model (per-user or per-group, and the default sizes for /lustre/backup, /lustre/nobackup, /lustre/scratch), the command(s) users run to check their current usage, and how to request more space. Only the home-directory quota (200 GB) is currently documented.
* '''[[Archival Storage]]''' — clarify how the manual iRODS/itape workflow relates to Tapeworm, now that Tapeworm manages archival from /archive to tape automatically: is itape still the recommended way to push data to tape, or is iRODS now used mainly for retrieving archived datasets?
* '''[[Data Lifecycle Policy]]''' — add the formal data-retention policy if one exists: how long different data is kept, any maximum retention, and what happens to data when an account or project closes.

== Software and workflows ==

* '''[[Workflow Engines (Snakemake, Nextflow)]]''' — confirm the recommended way to run Snakemake on Anunna (the documented profile is the older Snakemake <8 style; Snakemake 8+ uses the <code>--executor slurm</code> plugin), and write the Nextflow section (loading/installing Nextflow, the SLURM executor configuration, and a minimal example).
* '''[[Conda for teaching]]''' — modernise for current Anunna: the page still describes the old Bright <code>/cm/shared</code> paths and tcl modulefiles. Replace with a Miniforge environment on Lustre and the current course-kernel route (kernel registered at notebook.anunna.wur.nl; see [[Steps for courses]]).
* '''[[Julia]]''' — confirm the exact Julia module name(s) and version(s) available in the current buckets.

== Support and operations ==

* '''[[Maintenance Schedule]]''' — confirm where planned-maintenance dates are announced (Apps Portal message of the day, mailing list, Teams) and add the next scheduled downtime, or a link to a live maintenance schedule. Only the general cadence (roughly April/May and October) is documented.
* '''[[System Status Page]]''' — add the Anunna status / health dashboard URL, or confirm whether such a dashboard exists.
* '''[[Reporting Usage]]''' — document the reports.anunna.wur.nl usage and cost dashboard: what reports it offers, who can see what (your own usage versus your group's), and how to read them.
* '''[[Managing Group Members]]''' — confirm how a PI adds or removes members from their Anunna group (self-service, via the AD group owner, or via the administrators) and document the steps.
* '''[[Project Creation]]''' — document the project / billing-account creation process: how a PI requests one, how a commitment is agreed, and who can be added.
* '''[[Storage Requests]]''' — confirm whether storage requests use a dedicated form or the general HPC (Anunna) support service, and any approval or group-owner requirements.
* '''[[Remote Access (VPN, Gateway)]]''' — link the official WUR VPN setup instructions, and document any Anunna-specific gateway or jump-host arrangements.
* '''[[Resource Allocation Requests]]''' — document the resource-allocation process: what can be requested (extra priority/QoS, dedicated nodes, GPU allocations), how it relates to a group commitment, who approves it, and lead times.
* '''[[External Collaborator Access]]''' — document the external-collaborator process: sponsorship and approval, any data/security agreement, account duration and renewal, and access scope.

== Policy and governance ==

* '''[[Mission and Governance]]''' — confirm and document the current governance bodies (for example a steering group and user group) and their membership. The previous roster was from the Breed4Food era and was removed.
* '''[[Roadmap]]''' — add the current roadmap, or link the latest roadmap document. The 2019–2020 version was removed.
* '''[[Sustainability]]''' — add the sustainability / green-HPC policy and any concrete measures: energy sourcing, cooling, hardware lifecycle, and institutional targets.
* '''[[Policies and Terms of Use]]''' — supply the formal terms of use / acceptable-use policy (data ownership and responsibilities, security obligations, consequences of misuse) and confirm the current account-request route and per-group access contacts. The previous access-contact list was from the Breed4Food era and was removed.
* '''[[Account Application Process]]''' — confirm whether WUR users request an Anunna account through the general "HPC (Anunna)" support service or a dedicated account-request form, and what details are needed (group/affiliation, sponsor, intended use).
* '''[[User's group]]''' — document any formal user representation: regular user meetings, how users feed back into decisions, and how that relates to the governance bodies. Currently only the Anunna Users Teams community is documented.

== Nice to have ==

* '''[[FAQ]]''' — extend with the questions the HPC team is asked most often (for example quota limits, GPU access, course accounts, data transfer).

== See also ==

* [[Support]]

For PIs

2026-06-19T12:22:23Z

Haars0011: Add Resource Allocation Requests / External Collaborator Access / Grant Support Documentation to the For PIs hub (via update-page on MediaWiki MCP Server)

Information for group leaders, PIs, and teachers running projects and courses on Anunna.

== In this section ==

* [[Dos and Don'ts]] — good and bad practice at a glance
* [[Project Creation]] — setting up a project / billing account
* [[Managing Group Members]] — working with groups
* [[Storage Requests]] — requesting more storage
* [[Resource Allocation Requests]] — requesting larger or dedicated allocations
* [[External Collaborator Access]] — giving access to collaborators outside WUR
* [[Reporting Usage]] — tracking your group's usage and costs
* [[Grant Support Documentation]] — facility descriptions and support for funding applications

== See also ==
* [[Steps for courses]] — running a course on Anunna
* [[Conda for teaching]] — setting up a course software environment

Storage

2026-06-19T12:22:20Z

Haars0011: Add Handling Sensitive Data to the Storage hub (via update-page on MediaWiki MCP Server)

Anunna's storage areas, what each is for, and how data is kept and protected.

== In this section ==

* [[Storage Systems Overview]] — the storage tiers at a glance
* [[Home Directory]] — your personal space
* [[Compute Storage]] — the fast Lustre filesystem for active work
* [[Shared Storage]] — sharing data within a group
* [[Backup Policy]] — what is backed up, and what is not
* [[Archival Storage]] — long-term storage on tape
* [[Quotas]] — storage limits
* [[Data Lifecycle Policy]] — how data moves from active to archived to removed
* [[Data storage best practices]] — keeping data safe, tidy, and cheap
* [[Data Transfer Best Practices]] — moving data efficiently and reliably
* [[Handling Sensitive Data (GDPR, etc.)]] — confidential and personal data

== See also ==
* [[Data Transfer Methods]]

System Access

2026-06-19T12:22:17Z

Haars0011: Add Remote Access (VPN, Gateway) to the System Access hub (via update-page on MediaWiki MCP Server)

How to reach and use the different parts of the cluster: the nodes you connect to, the filesystems, and how to move data in and out.

== In this section ==

* [[Login Nodes]] — the entry point you connect to
* [[Compute Nodes]] — where your jobs run, and how to reach them
* [[Storage Systems Overview|File systems]] — the storage tiers
* [[Quotas]] — storage limits and how to check them
* [[Remote Access (VPN, Gateway)]] — reaching Anunna from off campus
* [[Data Transfer Methods]] — moving data to and from Anunna

== See also ==
* [[SSH Access]]
* [[Storage Systems Overview]]

Grant Support Documentation

2026-06-19T12:21:03Z

Haars0011: IA migration §11: new Grant Support Documentation skeleton (P2.31) (via create-page on MediaWiki MCP Server)

When you apply for research funding, you may need to describe Anunna as a computing resource, or include cost estimates and letters of support. This page collects what is available.



For costs to budget with, see [[Tariffs]] and [[Reporting Usage]]. For a description of the facility, see [[Cluster Architecture Overview]] and [[Compute Hardware Overview]].

== See also ==
* [[Tariffs]]
* [[Cluster Architecture Overview]]
* [[Compute Hardware Overview]]
* [[How to Get Help]]

External Collaborator Access

2026-06-19T12:21:00Z

Haars0011: IA migration §11: new External Collaborator Access skeleton (P2.30) (via create-page on MediaWiki MCP Server)

You can give collaborators from outside WUR access to Anunna for a joint project. This page covers how.

== Giving a collaborator access ==

External collaborators need an Anunna account, requested the same way as for any external user — see [[Account Application Process]] (the external-user route). As the WUR contact, you will usually need to sponsor the request and name the project.

Once they have an account, share data and resources with them by adding them to your group — see [[Managing Group Members]] and [[Shared Storage]].



== See also ==
* [[Account Application Process]]
* [[Who Can Access?]]
* [[Managing Group Members]]
* [[How to Get Help]]

Resource Allocation Requests

2026-06-19T12:20:57Z

Haars0011: IA migration §11: new Resource Allocation Requests skeleton (P2.29) (via create-page on MediaWiki MCP Server)

Beyond the resources your account can use by default, you can request larger or dedicated allocations — for example a bigger share of the cluster for a project, or priority around a deadline.

== Requesting an allocation ==

To request additional compute resources or a dedicated allocation, contact the HPC team through [[How to Get Help]].

For short-term exclusive access to specific nodes, see [[Reservations]]. Storage allocations are handled separately — see [[Storage Requests]].



== See also ==
* [[Reservations]]
* [[Storage Requests]]
* [[Project Creation]]
* [[How to Get Help]]

Handling Sensitive Data (GDPR, etc.)

2026-06-19T12:20:53Z

Haars0011: IA migration §6: new Handling Sensitive Data skeleton (P2.16) (via create-page on MediaWiki MCP Server)

Working with confidential or personal data on Anunna brings extra responsibilities, both yours and the facility's. This page is a starting point; for anything involving personal data, follow WUR's data-protection policy.

== Your responsibilities ==

* Only put sensitive data on Anunna if you are permitted to, and keep it to the minimum needed.
* Control who can access it — use group permissions carefully (see [[Shared Storage]] and [[Managing Group Members]]).
* Know what is backed up, and where data goes when it is archived (see [[Backup Policy]] and [[Data Lifecycle Policy]]).



== See also ==
* [[Policies and Terms of Use]]
* [[Network & Security]]
* [[Backup Policy]]
* [[How to Get Help]]

Remote Access (VPN, Gateway)

2026-06-19T12:20:48Z

Haars0011: IA migration §3: new Remote Access (VPN, Gateway) skeleton (P2.7) (via create-page on MediaWiki MCP Server)

Some ways of reaching Anunna require you to be on the WUR network (WURnet). From off campus, you connect through the WUR VPN.

== When you need the VPN ==

* [[SSH Access|SSH]] and the [[Portal Overview|Apps Portal]] are reachable directly over the internet, though access may be restricted to certain IP ranges (see [[SSH Access]]).
* Some services are only available inside WURnet — for example the [[Data Transfer Methods|CIFS/Samba mounts]]. From off campus, connect to the WUR VPN first.

== Connecting to the WUR VPN ==

The WUR VPN is provided by WUR IT, not by the Anunna team.



== See also ==
* [[SSH Access]]
* [[Data Transfer Methods]]
* [[How to Get Help]]

Wiki TODO

2026-06-19T12:18:32Z

Haars0011: Add Julia module-name task (via update-page on MediaWiki MCP Server)

This page lists Anunna documentation that has been published but still needs current or authoritative information filled in. The pages below are usable as they stand, but each contains placeholders — marked in the page source with <code></code> comments — where someone with current operational knowledge needs to add or confirm details.

To pick up a task: open the page, find the <code>TODO</code> comment(s) in its source, add the information, and remove the item from this list.

== Hardware and network ==

* '''[[Cluster Architecture Overview]]''' — confirm the current interconnect (Omnipath and/or InfiniBand) and topology; add a current architecture diagram (the old schematics were out of date and were removed).
* '''[[Compute Hardware Overview]]''' — fill in the per-node specifications: number of CPU nodes, cores and memory per node, CPU model(s), and whether there are high-memory "fat" nodes; number of NVIDIA GPU nodes, GPUs per node, and host CPU/memory; AMD GPU model and node details.
* '''[[Network & Security]]''' — confirm the interconnect (as above) and document the data-security posture: how data is protected at rest and in transit, access control, handling of confidential or personal data, and backup/retention.
* '''[[Performance Optimization/Multiple nodes (MPI)]]''' — confirm the recommended MPI library and module names, any required <code>srun --mpi=...</code> plugin flag, and whether specific interconnect/fabric tuning is needed. The old mvapich2 + InfiniBand (ib0) example was Breed4Food-era and was removed.

== Storage ==

* '''[[Quotas]]''' — document the Lustre quota model (per-user or per-group, and the default sizes for /lustre/backup, /lustre/nobackup, /lustre/scratch), the command(s) users run to check their current usage, and how to request more space. Only the home-directory quota (200 GB) is currently documented.
* '''[[Archival Storage]]''' — clarify how the manual iRODS/itape workflow relates to Tapeworm, now that Tapeworm manages archival from /archive to tape automatically: is itape still the recommended way to push data to tape, or is iRODS now used mainly for retrieving archived datasets?
* '''[[Data Lifecycle Policy]]''' — add the formal data-retention policy if one exists: how long different data is kept, any maximum retention, and what happens to data when an account or project closes.

== Software and workflows ==

* '''[[Workflow Engines (Snakemake, Nextflow)]]''' — confirm the recommended way to run Snakemake on Anunna (the documented profile is the older Snakemake <8 style; Snakemake 8+ uses the <code>--executor slurm</code> plugin), and write the Nextflow section (loading/installing Nextflow, the SLURM executor configuration, and a minimal example).
* '''[[Conda for teaching]]''' — modernise for current Anunna: the page still describes the old Bright <code>/cm/shared</code> paths and tcl modulefiles. Replace with a Miniforge environment on Lustre and the current course-kernel route (kernel registered at notebook.anunna.wur.nl; see [[Steps for courses]]).
* '''[[Julia]]''' — confirm the exact Julia module name(s) and version(s) available in the current buckets.

== Support and operations ==

* '''[[Maintenance Schedule]]''' — confirm where planned-maintenance dates are announced (Apps Portal message of the day, mailing list, Teams) and add the next scheduled downtime, or a link to a live maintenance schedule. Only the general cadence (roughly April/May and October) is documented.
* '''[[System Status Page]]''' — add the Anunna status / health dashboard URL, or confirm whether such a dashboard exists.
* '''[[Reporting Usage]]''' — document the reports.anunna.wur.nl usage and cost dashboard: what reports it offers, who can see what (your own usage versus your group's), and how to read them.
* '''[[Managing Group Members]]''' — confirm how a PI adds or removes members from their Anunna group (self-service, via the AD group owner, or via the administrators) and document the steps.
* '''[[Project Creation]]''' — document the project / billing-account creation process: how a PI requests one, how a commitment is agreed, and who can be added.
* '''[[Storage Requests]]''' — confirm whether storage requests use a dedicated form or the general HPC (Anunna) support service, and any approval or group-owner requirements.

== Policy and governance ==

* '''[[Mission and Governance]]''' — confirm and document the current governance bodies (for example a steering group and user group) and their membership. The previous roster was from the Breed4Food era and was removed.
* '''[[Roadmap]]''' — add the current roadmap, or link the latest roadmap document. The 2019–2020 version was removed.
* '''[[Sustainability]]''' — add the sustainability / green-HPC policy and any concrete measures: energy sourcing, cooling, hardware lifecycle, and institutional targets.
* '''[[Policies and Terms of Use]]''' — supply the formal terms of use / acceptable-use policy (data ownership and responsibilities, security obligations, consequences of misuse) and confirm the current account-request route and per-group access contacts. The previous access-contact list was from the Breed4Food era and was removed.
* '''[[Account Application Process]]''' — confirm whether WUR users request an Anunna account through the general "HPC (Anunna)" support service or a dedicated account-request form, and what details are needed (group/affiliation, sponsor, intended use).
* '''[[User's group]]''' — document any formal user representation: regular user meetings, how users feed back into decisions, and how that relates to the governance bodies. Currently only the Anunna Users Teams community is documented.

== Nice to have ==

* '''[[FAQ]]''' — extend with the questions the HPC team is asked most often (for example quota limits, GPU access, course accounts, data transfer).

== See also ==

* [[Support]]

Wiki TODO

2026-06-19T12:18:22Z

Haars0011: Add Data Lifecycle Policy task (via update-page on MediaWiki MCP Server)

This page lists Anunna documentation that has been published but still needs current or authoritative information filled in. The pages below are usable as they stand, but each contains placeholders — marked in the page source with <code></code> comments — where someone with current operational knowledge needs to add or confirm details.

To pick up a task: open the page, find the <code>TODO</code> comment(s) in its source, add the information, and remove the item from this list.

== Hardware and network ==

* '''[[Cluster Architecture Overview]]''' — confirm the current interconnect (Omnipath and/or InfiniBand) and topology; add a current architecture diagram (the old schematics were out of date and were removed).
* '''[[Compute Hardware Overview]]''' — fill in the per-node specifications: number of CPU nodes, cores and memory per node, CPU model(s), and whether there are high-memory "fat" nodes; number of NVIDIA GPU nodes, GPUs per node, and host CPU/memory; AMD GPU model and node details.
* '''[[Network & Security]]''' — confirm the interconnect (as above) and document the data-security posture: how data is protected at rest and in transit, access control, handling of confidential or personal data, and backup/retention.
* '''[[Performance Optimization/Multiple nodes (MPI)]]''' — confirm the recommended MPI library and module names, any required <code>srun --mpi=...</code> plugin flag, and whether specific interconnect/fabric tuning is needed. The old mvapich2 + InfiniBand (ib0) example was Breed4Food-era and was removed.

== Storage ==

* '''[[Quotas]]''' — document the Lustre quota model (per-user or per-group, and the default sizes for /lustre/backup, /lustre/nobackup, /lustre/scratch), the command(s) users run to check their current usage, and how to request more space. Only the home-directory quota (200 GB) is currently documented.
* '''[[Archival Storage]]''' — clarify how the manual iRODS/itape workflow relates to Tapeworm, now that Tapeworm manages archival from /archive to tape automatically: is itape still the recommended way to push data to tape, or is iRODS now used mainly for retrieving archived datasets?
* '''[[Data Lifecycle Policy]]''' — add the formal data-retention policy if one exists: how long different data is kept, any maximum retention, and what happens to data when an account or project closes.

== Software and workflows ==

* '''[[Workflow Engines (Snakemake, Nextflow)]]''' — confirm the recommended way to run Snakemake on Anunna (the documented profile is the older Snakemake <8 style; Snakemake 8+ uses the <code>--executor slurm</code> plugin), and write the Nextflow section (loading/installing Nextflow, the SLURM executor configuration, and a minimal example).
* '''[[Conda for teaching]]''' — modernise for current Anunna: the page still describes the old Bright <code>/cm/shared</code> paths and tcl modulefiles. Replace with a Miniforge environment on Lustre and the current course-kernel route (kernel registered at notebook.anunna.wur.nl; see [[Steps for courses]]).

== Support and operations ==

* '''[[Maintenance Schedule]]''' — confirm where planned-maintenance dates are announced (Apps Portal message of the day, mailing list, Teams) and add the next scheduled downtime, or a link to a live maintenance schedule. Only the general cadence (roughly April/May and October) is documented.
* '''[[System Status Page]]''' — add the Anunna status / health dashboard URL, or confirm whether such a dashboard exists.
* '''[[Reporting Usage]]''' — document the reports.anunna.wur.nl usage and cost dashboard: what reports it offers, who can see what (your own usage versus your group's), and how to read them.
* '''[[Managing Group Members]]''' — confirm how a PI adds or removes members from their Anunna group (self-service, via the AD group owner, or via the administrators) and document the steps.
* '''[[Project Creation]]''' — document the project / billing-account creation process: how a PI requests one, how a commitment is agreed, and who can be added.
* '''[[Storage Requests]]''' — confirm whether storage requests use a dedicated form or the general HPC (Anunna) support service, and any approval or group-owner requirements.

== Policy and governance ==

* '''[[Mission and Governance]]''' — confirm and document the current governance bodies (for example a steering group and user group) and their membership. The previous roster was from the Breed4Food era and was removed.
* '''[[Roadmap]]''' — add the current roadmap, or link the latest roadmap document. The 2019–2020 version was removed.
* '''[[Sustainability]]''' — add the sustainability / green-HPC policy and any concrete measures: energy sourcing, cooling, hardware lifecycle, and institutional targets.
* '''[[Policies and Terms of Use]]''' — supply the formal terms of use / acceptable-use policy (data ownership and responsibilities, security obligations, consequences of misuse) and confirm the current account-request route and per-group access contacts. The previous access-contact list was from the Breed4Food era and was removed.
* '''[[Account Application Process]]''' — confirm whether WUR users request an Anunna account through the general "HPC (Anunna)" support service or a dedicated account-request form, and what details are needed (group/affiliation, sponsor, intended use).
* '''[[User's group]]''' — document any formal user representation: regular user meetings, how users feed back into decisions, and how that relates to the governance bodies. Currently only the Anunna Users Teams community is documented.

== Nice to have ==

* '''[[FAQ]]''' — extend with the questions the HPC team is asked most often (for example quota limits, GPU access, course accounts, data transfer).

== See also ==

* [[Support]]

Storage

2026-06-19T12:17:06Z

Haars0011: Add the new storage best-practices / lifecycle pages to the Storage section hub (via update-page on MediaWiki MCP Server)

Software

2026-06-19T12:17:04Z

Haars0011: Add Julia to the Software section hub (via update-page on MediaWiki MCP Server)

The software available on Anunna and how to use, install, and manage it.

== In this section ==

* [[Software Overview]] — the software landscape
* [[Environment Modules]] — loading software with modules and buckets
* [[Installing Personal Software]] — installing into your own space
* [[Python]] — Python (modules, Miniforge, virtual environments)
* [[R]] — R and R libraries
* [[Julia]] — Julia
* [[Apptainer]] — containers
* [[Licensed Software]] — software that needs a licence

Data Lifecycle Policy

2026-06-19T12:15:53Z

Haars0011: IA migration §6: new Data Lifecycle Policy (P2.13) (via create-page on MediaWiki MCP Server)

Data on Anunna moves through a lifecycle: active working data, data you keep but no longer actively use, and data that is no longer needed. Managing that lifecycle keeps storage available and costs under control.

== Active data ==

While you are working on it, data lives on the fast [[Compute Storage|Lustre]] filesystem. Temporary working data on <code>/lustre/scratch</code> is not kept indefinitely — it may be purged automatically once the filesystem fills up (see [[Compute Storage]] and [[Backup Policy]]).

== Archiving data you keep ==

When you are finished with data but want to keep it, move it to [[Archival Storage|archival storage]]. Datasets there that are no longer actively used are moved to long-term tape archive automatically by the [[Archival Storage#Tapeworm|Tapeworm]] service, freeing the warm storage tier.

== Removing data ==

Delete intermediate and temporary data you no longer need — it keeps the cluster usable and your costs down. Remember that [[Backup Policy|backups]] are limited, so be sure before you delete.



== See also ==
* [[Storage Systems Overview]]
* [[Archival Storage]]
* [[Backup Policy]]
* [[Data storage best practices]]

Data Transfer Best Practices

2026-06-19T12:15:48Z

Haars0011: IA migration §6: new Data Transfer Best Practices (P2.15) (via create-page on MediaWiki MCP Server)

Guidance for moving data to and from Anunna efficiently and reliably. For the tools themselves, see [[Data Transfer Methods]].

== Choose the right tool ==

* For command-line transfers, prefer <code>rsync</code> over <code>scp</code> for anything large or repeated — it resumes and only copies what has changed.
* The browser-based [[File Browser]] is fine for small files, but not for large or many-file transfers; use rsync, scp, or an SFTP client (WinSCP, FileZilla) instead.

== Transfer to the right place ==

* Transfer compute data directly to [[Compute Storage|Lustre]], not to your home directory.
* Use the correct group path under <code>/lustre</code> — see [[Compute Storage]].

== Make transfers reliable ==

* For long transfers, run them inside a persistent session (<code>screen</code> or <code>tmux</code>) so they survive a dropped connection.
* Verify that large transfers completed before deleting the source — <code>rsync</code> reports this, or compare checksums.
* Resume an interrupted transfer with <code>rsync</code> rather than starting over.

== Be considerate ==

* Transfers run on the [[Login Nodes|login nodes]], which are shared — very large transfers can load them, so be mindful of other users.

== See also ==
* [[Data Transfer Methods]]
* [[Compute Storage]]
* [[Data storage best practices]]

Data storage best practices

2026-06-19T12:15:43Z

Haars0011: IA migration §6: new Data storage best practices (P2.14) (via create-page on MediaWiki MCP Server)

A few practices that keep your data safe, your costs down, and the cluster fast for everyone. For the storage areas themselves, see [[Storage Systems Overview]].

== Put data in the right place ==

* Keep active compute data on [[Compute Storage|Lustre]] (<code>/lustre/nobackup</code> by default), not in your [[Home Directory|home directory]].
* Keep programs, scripts, and configuration — small, important files — in your home directory.
* Move data you have finished with, but want to keep, to [[Archival Storage|archival storage]].

== Protect what matters ==

* Know what is backed up and what is not — see [[Backup Policy]]. Treat <code>/lustre/nobackup</code> and <code>/lustre/scratch</code> as expendable.
* Keep your own copy of anything you cannot regenerate.

== Keep it tidy and cheap ==

* Clean up <code>/lustre/scratch</code> and node-local <code>/tmp</code> when you are done — scratch may be purged automatically, and storage is charged per TB (see [[Tariffs]]).
* Delete intermediate files you no longer need.
* Compress large datasets that you are keeping but rarely touch.

== Work efficiently ==

* Avoid creating very many tiny files; Lustre performs best with fewer, larger files.
* Do not run heavy I/O (including writing logs) against your home directory — use Lustre.

== See also ==
* [[Storage Systems Overview]]
* [[Backup Policy]]
* [[Quotas]]
* [[Archival Storage]]
* [[Data Transfer Best Practices]]

Julia

2026-06-19T12:15:37Z

Haars0011: IA migration §5: new Julia page (P2.11) (via create-page on MediaWiki MCP Server)

[https://julialang.org/ Julia] is a high-level, high-performance language for technical computing. This page covers using Julia on Anunna.

== Loading Julia ==

Julia is provided through the module system. Load a [[Environment Modules|bucket]] first, then Julia:

<syntaxhighlight lang="bash">
module load 2024
module load Julia
</syntaxhighlight>

To see which versions are available, use <code>module spider Julia</code> (see [[Environment Modules]]).



== Packages ==

Julia manages its own packages with the built-in package manager (<code>Pkg</code>). By default packages install into your home directory under <code>~/.julia</code>. Because [[Home Directory|home]] is small and not meant for heavy I/O, point Julia's depot at a larger [[Compute Storage|Lustre]] location by setting <code>JULIA_DEPOT_PATH</code> before starting Julia:

<syntaxhighlight lang="bash">
export JULIA_DEPOT_PATH=/lustre/nobackup/<group>/<user>/julia_depot
</syntaxhighlight>

Then add packages from the Julia REPL:

<syntaxhighlight lang="julia">
import Pkg
Pkg.add("DataFrames")
</syntaxhighlight>

== Running Julia in a job ==

Run Julia scripts as batch jobs through the scheduler — see [[Batch Jobs]]. For interactive work, start an [[Interactive Jobs|interactive job]] first.

To use multiple cores, start Julia with the <code>-t</code> (threads) option, or use Julia's distributed/parallel facilities — see [[Performance Optimization/Multiple CPUs]]:

<syntaxhighlight lang="bash">
julia -t $SLURM_CPUS_PER_TASK myscript.jl
</syntaxhighlight>

== See also ==
* [[Software Overview]]
* [[Environment Modules]]
* [[Jupyter]]
* [[Installing Personal Software]]

Main Page/Tutorials/Apptainer

2026-06-19T12:07:20Z

Haars0011: IA migration P3.13: redirect to Tutorials (via update-page on MediaWiki MCP Server)

#REDIRECT [[Tutorials]]

Main Page/Tutorials

2026-06-19T12:07:19Z

Haars0011: IA migration P3.12: redirect to Tutorials (via update-page on MediaWiki MCP Server)

#REDIRECT [[Tutorials]]

History of the Cluster

2026-06-19T12:04:29Z

Haars0011: Haars0011 moved page History of the Cluster to History/Origins: IA migration 1b/P3.11: relocate History of the Cluster → History/Origins (historical sub-page; leaving redirect) (via move-page on MediaWiki MCP Server)

#REDIRECT [[History/Origins]]

History/Origins

2026-06-19T12:04:29Z

== Rationale and Requirements for a new cluster ==
[[File:Breed4food-logo.jpg|thumb|right|200px|The Breed4Food logo]]
Anunna; previously called '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.
{{-}}

== 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 ==
[[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.
{{-}}

B4F cluster

2026-06-19T12:04:27Z

Haars0011: Haars0011 moved page B4F cluster to History/B4F cluster: IA migration 1b/P3.10: relocate B4F cluster → History/B4F cluster (historical sub-page; leaving redirect) (via move-page on MediaWiki MCP Server)

#REDIRECT [[History/B4F cluster]]

History/B4F cluster

2026-06-19T12:04:27Z

= Historical =
This page contains historical information about the WUR HPC Cluster as of 2013.

== B4F Cluster ==
The [http://www.breed4food.com/en/breed4food.htm Breed4Food] (B4F) cluster is a joint [http://en.wikipedia.org/wiki/High-performance_computing High Performance Compute] (HPC) infrastructure 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].

== Rationale and Requirements for a new cluster ==
[[File:Breed4food-logo.jpg|thumb|right|200px|The Breed4Food logo]]
The B4F Cluster is, in a way, 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 B4F Cluster 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.

{{-}}

== 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 B4F 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 ==

[[File:Cluster_scheme.png|thumb|right|600px|Schematic overview of the cluster.]]
The new B4F HPC has a classic cluster architecture: state of the art Parallel File System (PSF), headnodes, compute nodes (of varying 'size'), all connected by superfast internet 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.
{{-}}
=== Nodes ===
The cluster consists of a bunch of separate machines that each has its own operating system. The default operating system throughout the cluster is RHEL6. The cluster has two master nodes in a redundant configuration, which means that if one crashes, the other will take over seamlessly. Various other nodes exist to support the two main file systems (the Lustre parallel file system and the NFS file system). The actual computations are done on the worker nodes or compute nodes. The cluster is configured in a heterogeneous fashion: it consists of 48 so called 'slim nodes', that each have 16 cores and 64GB of RAM (called 'node001' through 'node060'; note that not all node names map to physical nodes), and two so called 'fat nodes' that each have 64 cores and 1TB of RAM ('fat001' and 'fat002').

Information from the Cluster Management Portal, as it appeared on November 23, 2013:
<code>DEVICE INFORMATION
Hostname State Memory Cores CPU Speed GPU NICs IB Category
master1, master2 UP 67.6 GiB 16 Intel(R) Xeon(R) CPU E5-2660 0+ 2199 MHz 5 1
node001..node042, node049..node054 UP 67.6 GiB 16 Intel(R) Xeon(R) CPU E5-2660 0+ 1200 MHz 3 1 default
node043..node048, node055..node060 DOWN N/A N/A N/A N/A N/A N/A N/A default
mds01, mds02 UP 16.8 GiB 8 Intel(R) Xeon(R) CPU E5-2609 0+ 2400 MHz 5 1 mds
storage01 UP 67.6 GiB 32 Intel(R) Xeon(R) CPU E5-2660 0+ 2200 MHz 5 1 oss
storage02..storage06 UP 67.6 GiB 32 Intel(R) Xeon(R) CPU E5-2660 0+ 2199 MHz 5 1 oss
nfs01 UP 67.6 GiB 8 Intel(R) Xeon(R) CPU E5-2609 0+ 2400 MHz 7 1 login
fat001, fat002 UP 1.0 TiB 64 AMD Opteron(tm) Processor 6376 2299 MHz 5 1 fat </code>

Main cluster node configuration:
* Master nodes: 2 PowerEdge R720 master nodes in a failover configuration
* The NFS server is a PowerEdge R720XD, which will share some applications and databases with machines in the cluster, for which the parallel file system is not the ideal solution. The NFS node will also act as a login node, where users log in and compile applications and submit jobs.
* 50 compute nodes
** 12x Dell PowerEdge C6000 enclosures, each containing four nodes
** 48x Dell PowerEdge C6220; 16 Intel Xeon cores, 64GB RAM each
** 2x Dell R815; 64 AMD Opteron cores, 1TB RAM each
Hyperthreading is disabled in compute nodes.

=== Filesystems ===

[[File:Storage_pic.png|thumb|right|300px|Schematic overview of storage components of the B4F cluster.]]
The B4F Cluster has two primary file systems, each with different properties and purposes.
==== Parallel File System: Lustre ====
At the base of the cluster is an ultrafast file system, a so called [http://en.wikipedia.org/wiki/Parallel_file_system Parallel File System] (PFS). The current size of the PFS is around 600TB. The PFS implemented in the B4F Cluster is called [http://en.wikipedia.org/wiki/Lustre_(file_system) Lustre]. Lustre has become very popular in recent years due to the fact that it is very feature rich, deemed very stable, and is Open Source. Lustre nowadays is the default option for PFS in Dell clusters as well as clusters sold by other vendors. The PFS is mounted on all head nodes and worker nodes of the cluster, providing a seamless integration between compute and data infrastructure. The strength of a PFS is speed - the total I/O should be up to 15GB/s. by design. With a very large number of compute nodes - and with very high volumes of data - these high read-write speeds that the PSF can provide are necessary. The Lustre filesystem is divided in [[Lustre_PFS_layout | several partitions]], each differing in persistence and backup features. The Lustre PSF is meant to store (shared) data that is likely to be used for analysis in the near future. Personal analysis scripts, software, or additional small data files can be stored in the $HOME directory of each of the users.

The hardware components of the PFS:
* 2x Dell PowerEdge R720
* 1x Dell PowerVault MD3220
* 6x Dell PowerEdge R620
* 6x Dell PowerVault MD3260

==== Network File System (NFS): $HOME dirs ====
Each user will have his/her own home directory. The path of the home directory will be:

/home/[name partner]/[username]

/home lives on a so called [http://en.wikipedia.org/wiki/Network_File_System Network File System], or NFS. The NFS is separate from the PFS and is far more limited in I/O (read/write speeds, latency, etc) than the PFS. This means that it is not meant to store large datavolumes that require high data transfer or small latency. Compared to the Lustre PFS (600TB in size), the size of the NFS is small in comparison - only 20TB. The /home partition will be backed up daily. The amount of space that can be allocated is limited per user. Personal quota and total use per user can be found using:

<pre>
quota
</pre>

The NFS is supported through the NFS server that also serves as access point to the cluster.

Hardware components of the NFS:
* 1x Dell PowerEdge R720XD
* 1x Dell PowerVault MD3220

=== Network ===
The various components - head-nodes, worker nodes, and most importantly, the Lustre PFS - are all interconnected by an ultra-high speed network connection called [http://en.wikipedia.org/wiki/Infiniband InfiniBand]. A total of 7 InifiniBand switches are configured in a [http://en.wikipedia.org/wiki/Fat_tree fat tree] configuration.

== Housing at Theia ==
[[File:Map_Theia.png|thumb|left|200px|Location of Theia, just outside of Wageningen campus]]
The B4F Cluster is housed at the main server centre of WUR-FB-ICT, 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 B4F Cluster. Access to Theia is evidently highly restricted and can only be granted in the presence of a representative of FB-ICT.
{{-}}
{| width="90%"
|- valign="top"
| width="10%" |

| width="30%" |
[[File:Cluster2_pic.png|thumb|left|220px|Some components of the cluster after unpacking.]]
| width="70%" |
[[File:Cluster_pic.png|thumb|right|400px|The final configuration after installation.]]
|}
{{-}}

== Management ==

=== Project Leader ===
* Stephen Janssen (Wageningen UR, FB-IT, Service Management)

=== Daily Project Management ===
* [[User:pollm001 | Koen Pollmann (Wageningen UR, FB-IT, Infrastructure)]]
* Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)
[[Maintenance_and_Management | Maintenance and Management]]

=== Steering Group ===
Ensures that the HPC generates enough revenues and meets the needs of the users. This includes setting fees, developing contracts, attracting new users, decisions on investments in the HPC and communication.
* Frido Hamoen (CRV, on behalf of Breed4Food industrial partners, replaced Alfred de Vries in August)
* Petra Caessens (CAT-AgroFood)
* Wojtek Sablik (Wageningen UR, FB-IT, Infrastructure)
* Edda Neuteboom (CAT_AgroFood, secretariat)
* Martien Groenen (Wageningen UR, chair, replaced Johan van Arendonk).

=== IT Workgroup ===
[[File:Image_(1).jpeg|thumb|right|380px|(part of) the IT working group in front of the B4F Cluster]]
Is responsible for the technical performance of the HPC. The IT-workgroup has been involved in the design of the HPC and the selection of the supplier. They will support the technical management of the HPC and share experiences to ensure that the HPC meets the needs of its users. The IT-workgroup will advise the steering group on investments in software and hardware.
* Stephen Janssen (Wageningen UR, FB-IT, Service Management)
* [[User:pollm001 | Koen Pollmann (Wageningen UR, FB-IT, Infrastructure)]]
* Gwen Dawes (Wageningen UR, FB-IT, Infrastructure, replaced Andre ten Böhmer)
* Wes Barris (Cobb)
* Ton Dings (Hendrix Genetics)
* Henk van Dongen (Topigs)
* Harry Dijkstra (CRV)
* Mario Calus (ABGC-WLR)
* Hendrik-Jan Megens (ABGC-ABG)
{{-}}

=== User Group ===
The User Group ultimately is the most important of all groups, because it encompasses the users for which the infrastructure was built. In addition, successful use of the cluster will rely on an active community of users that is willing to share knowledge and best practices, including maintenance and expansion of this Wiki. Regular User Group meetings will be held in the future [frequency to be determined] to facilitate this process.

== Access Policy ==
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-ICT). 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.

=== Contact Persons ===
A request to access the cluster needs to be directed to one of the following persons (please refer to appropriate partner):

==== Cobb-Vantress ====
* Wes Barris
* Jun Chen

==== ABGC ====
===== Animal Breeding and Genetics =====
* [[User:Hulze001 |Alex Hulzebosch]]
* [[User:Hjmegens | Hendrik-Jan Megens]]

===== Wageningen Livestock Research =====
* Mario Calus
* Ina Hulsegge
==== CRV ====
* Frido Hamoen
* Chris Schrooten
==== Hendrix Genetics ====
* Ton Dings
* Abe Huisman
* Addie Vereijken
==== Topigs ====
* Henk van Dongen
* Egiel Hanenbarg
* Naomi Duijvensteijn

== Using the B4F Cluster ==
=== Gaining access to the B4F Cluster ===
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 ===
The B4F cluster uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.
* [[BCM_on_B4F_cluster | Monitor cluster status with BCM]]
* [[SLURM_on_B4F_cluster | Submit jobs with Slurm]]

=== Installation of software by users ===

* [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]
* [[Setting local variables]]
* [[Installing_R_packages_locally | Installing R packages locally]]
* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]

== See also ==
* [[Maintenance_and_Management | Maintenance and Management]]
* [[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="45%" |
* [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/News-and-agenda/Show/CATAgroFood-invests-in-a-High-Performance-Computing-cluster.htm CATAgroFood invests in HPC]
* [http://www.cobb-vantress.com Cobb-Vantress homepage]
| width="45%" |
* [https://www.crv4all.nl CRV homepage]
* [http://www.hendrix-genetics.com Hendrix Genetics homepage]
* [http://www.topigs.com TOPIGS homepage]
|}

JBrowse

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Haars0011: Haars0011 moved page JBrowse to ABGC/JBrowse: IA migration 1b/P3.9: relocate JBrowse → ABGC/JBrowse (group sub-page; leaving redirect) (via move-page on MediaWiki MCP Server)

#REDIRECT [[ABGC/JBrowse]]

ABGC/JBrowse

2026-06-19T12:04:26Z

Haars0011: Haars0011 moved page JBrowse to ABGC/JBrowse: IA migration 1b/P3.9: relocate JBrowse → ABGC/JBrowse (group sub-page; leaving redirect) (via move-page on MediaWiki MCP Server)

=== Typical commands used to set up a JBrowse ===

Author: Martijn Derks

* JBrowse is available for multiple species:
** https://jbrowse.hpcagrogenomics.wur.nl/pig/
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/
** https://jbrowse.hpcagrogenomics.wur.nl/Cyprinus_carpio/
* Users are free to add usefull commands to this tutorial

=== Install JBrowse ===

Download the latest JBrowse here: http://jbrowse.org/

Make a directory in <code>/shared/apps/jbrowse/</code> for your species of interested (e.g. <code>mkdir Cyprinus_carpio</code>). Move the downloaded JBrowse source files there. All further procedures detailed in this Wiki page assume working from that directory (NOTE: if your species of interest is already there, contact the maintainer of that JBrowse instance).
Run the setup script to install perl dependencies and required modules

<pre>
unzip JBrowse-1.12.0.zip
mv JBrowse-1.12.0/* $PWD
./setup.sh
</pre>

=== Add reference sequence ===

Example code for chicken genome

<pre>
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa
</pre>

To remove tracks use following command:

<pre>
bin/remove-track.pl -D --trackLabel 'trackname'
</pre>

===Add annotation files (GFF/BED)===

Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html

Add gene features:

<pre>
bin/flatfile-to-json.pl --key "Genes" --type gene --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3
</pre>

Add corresponding transcripts:

<pre>
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3
</pre>

===Alignment tracks (BAM)===

You can load single BAM-files by following command:
<pre>
bin/add-bam-track --label <label> --bam_url <url>
</pre>

To load multiple BAM files present in a certain directory use:
<pre>

for bam in /<dir>*.bam; do
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files
ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files
tissue=`echo $bam | rev | cut -c 5- | cut -d'/' -f1 | rev` ## USe the name of the file without .bam as trackLabel

## Add BAM in alignment mode (Alignments2)
echo '{
"label" : "'${tissue}'_alignment",
"key" : "'${tissue}'_alignment",
"storeClass" : "JBrowse/Store/SeqFeature/BAM",
"urlTemplate" : "../track_symlinks/'${tissue}'",
"category" : "3. RNA-seq alignments",
"type" : "Alignments2"
}' | bin/add-track-json.pl data/trackList.json

## Add BAM in coverage mode (SNPCoverage)
echo '{
"label" : "'${tissue}'_coverage",
"key" : "'${tissue}'_coverage",
"storeClass" : "JBrowse/Store/SeqFeature/BAM",
"urlTemplate" : "../track_symlinks/'${tissue}'",
"category" : "3. RNA-seq alignments",
"type" : "SNPCoverage"
}' | bin/add-track-json.pl data/trackList.json

done
</pre>

Make sure the BAM file can be read by a everybody if not use:
<pre>
chmod +r <BAM_file>
</pre>

Make sure that all directoryies in the full path of the BAMfile are executable:
<pre>
chmod +x <dir>
</pre>

===Variant tracks (VCF)===

To load a VCF file in JBrowse make sure the file is gzipped and indexed

<pre>
tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz

echo ' {
"label" : "Gallus_gallus_incl_consequences",
"key" : "Gallus_gallus_incl_consequences",
"storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",
"urlTemplate" : "../../ensembl_data/VCF/Gallus_gallus_incl_consequences.vcf.gz",
"category" : "2. Variants",
"type" : "HTMLVariants"
} ' | bin/add-track-json.pl data/trackList.json
</pre>

===Wiggle/BigWig tracks (WIG)===

You can load single BigWig-files by following command:
<pre>
bin/add-bw-track --label <label> --bw_url <url>
</pre>

===Evidence tracks===

Evidence tracks can be loaded in bed, gff and gbk format using

<pre>
bin/flatfile-to-json.pl
</pre>

Examples are given above.

ABGC modules

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Haars0011: Haars0011 moved page ABGC modules to ABGC/Modules: IA migration 1b: relocate ABGC modules → ABGC/Modules (group sub-page; leaving redirect) (via move-page on MediaWiki MCP Server)

#REDIRECT [[ABGC/Modules]]

ABGC/Modules

2026-06-19T12:04:24Z

Haars0011: Haars0011 moved page ABGC modules to ABGC/Modules: IA migration 1b: relocate ABGC modules → ABGC/Modules (group sub-page; leaving redirect) (via move-page on MediaWiki MCP Server)

All ABGC modules can be found in:

/cm/shared/apps/WUR/ABGC/modulefiles

== Modules available for ABGC ==

* [[asreml_3.0 | asreml/3.0fl-64]]
* [[asreml_4.0 | asreml/4.0kr]]
* [[asreml_4.1 | asreml/4.1.0]]
* [[Perl5.10_WUR_module | Perl/5.10.1_wur]]
* [[R3.0.2_WUR_module | R/3.0.2_wur]]

== Adding a custom module directory to your environment ==
To allow the <code>module</code> program to find the custom module directory, the location of that directory has to be added to <code>MODULEPATH</code> variable.

<pre>
export MODULEPATH=$MODULEPATH:/cm/shared/apps/WUR/ABGC/modulefiles
</pre>
This can be made permanent by adding this line of code to the <code>.bash_profile</code> file in the root of your home folder. To then load the modified <code>MODULEPATH</code> variable you have to load <code>.bash_profile</code> again:
<pre>
source .bash_profile
</pre>
This needs to be done only for terminals that are already open. Next time you login, <code>.bash_profile</code> will be loaded automatically.

You can check if the modules are found.
<pre>
module avail
</pre>
This should give output that includes something similar to this:

----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles -----------------------------------
bwa/0.5.9 bwa/0.7.5a

== See also ==
* [[Globally_installed_software | Globally installed software]]
* [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]
* [[Setting local variables]]
* [[Installing_R_packages_locally | Installing R packages locally]]
* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]

== External links ==

Ssh without password

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Haars0011:

Secure shell (ssh) protocols can be configure to work without entering your password every time. This is particularly helpful for machines that are used often.
Although we mention that you can use SSH keys without passwords, that is something you should really '''not''' do, if someone gets a hold of your keys (without password), they can access our servers as if they are you, and thus incur costs/manage or delete data in your name.

== Configuring ssh without password from a POSIX-compliant terminal ==

=== Step 1: create a public key and copy to remote computer ===
* Log into WSL, a local Linux or MacOSX computer
* Type the following to generate the ssh key:
<pre>
ssh-keygen -t ed25519 -a 200 -C $USER@$(hostname)
</pre>
* Accept the default key location by pressing <code>Enter</code>.
* Please use a '''different''' password/passphrase for your SSH key than your WUR password.
* Secure permission of your authentication keys by closing permission to your home directory, .ssh directory, and authentication files
<pre>
chmod go-wx $HOME
chmod 700 $HOME/.ssh
chmod 600 $HOME/.ssh/*
</pre>
* Type the following to copy the key to the remote server (this will prompt for a password).
<pre>
ssh-copy-id remote_username@remote_host
</pre>

== Configuring ssh without password for Anunna ==

* Create a public key as in Step 1 of the previous section and copy it to Anunna. Note that a public/private key pair needs to be made only once per machine.
* Similar to step 2 of the previous section, add the public key to the <code>$HOME/.ssh/authorized_keys2</code> file. There is already a <code>$HOME/.ssh/authorized_keys</code> present. You may append the key to this file as an alternative, but take care not to remove content that is already there. The cluster is configured so that passwordless communication will all other nodes is default.

== Configuring ssh without password using PuTTY ==
Use '''pageant''': http://the.earth.li/~sgtatham/putty/0.58/htmldoc/Chapter9.html to generate local keys. You'll want have a copy of the pubkey in plaintext available.

Make sure to paste that plaintext string into ~/.ssh/authorized_keys in one single line. Chmod the file 600 (so it shows -rw------- in ls -l) and the directory .ssh to 700 (drwx------).

Now PuTTY will login passwordlessly whenever '''pageant''' is running.

Finally, get '''pageant''' to load on startup: http://blog.shvetsov.com/2010/03/making-pageant-automatically-load-keys.html
== Configuring ssh without password using MobaXterm ==

Have a look here: https://docs.gcc.rug.nl/hyperchicken/generate-key-pair-mobaxterm/

== Configuring ssh without password using WinSCP ==
WinSCP has provided a detailed instruction in https://winscp.net/eng/docs/public_key, and https://winscp.net/eng/docs/ui_login_authentication

== Configuring ssh without password on a Mac ==
* Create a public key as in Step 1 of the first section and copy it to Anunna.
* Add the passphrase that you entered above to the keychain on your mac:
ssh-add -K /path/to/private/key/file

== Selecting which settings to use ==

To have your SSH client to use certain settings, one can use a config file, at ~/.ssh/config

For example :
<pre>

Host *.wurnet.nl *.wur.nl
User haars001
Compression no
RequestTTY force

Host *
Compression yes
Protocol 2
ServerAliveInterval 120
ServerAliveCountMax 50
TCPKeepAlive no
ConnectTimeout 60
IdentityFile ~/.ssh/id_ed25519
AddKeysToAgent yes

</pre>

As the config file is used top to bottom, the connection wur(net).nl servers will be using no compression, but the rest of the servers you might access will.
More options and settings can be found by using `man ssh_config`

== See also ==
* [[log_in_to_Anunna |Logging into cluster using ssh and file transfer]]
* [[Using a hardware key for better security]]

== External Links ==

Network & Security

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Haars0011:

This page describes how Anunna is connected and how access to it is secured.

== Network ==

Internally, the compute nodes and the [[Filesystems | Lustre filesystem]] are linked by a high-speed, low-latency interconnect, which is what lets the parallel filesystem and multi-node jobs perform well. 

From outside, the cluster services are reached through two loadbalancers. SSH to <code>login.anunna.wur.nl</code>, other services to their respective URLs . Access to some services may be restricted to certain IP ranges, and are thus are only reachable over the WUR VPN or from within WURNET. See [[Log in to Anunna]] for how to connect.

== Authentication ==

You log in with your WUR or outside group account. For stronger protection you can add multi-factor authentication to your SSH access using a hardware security key — see [[Using a hardware key for better security]]. You can also configure key-based login so you are not prompted for a password each time; see [[Ssh without password]].

== Data security ==



For how file and folder permissions work on the cluster, see [[Shared folders]]. For storing confidential data, contact the HPC team via [[Support]].

== See also ==

* [[Cluster Architecture Overview]]
* [[Log in to Anunna]]
* [[Using a hardware key for better security]]
* [[Filesystems]]

Support

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Haars0011: IA migration §1c: replace Support redirect with the §10 section landing hub (via update-page on MediaWiki MCP Server)

How to get help with Anunna, report problems, and keep up with the cluster's status.

== In this section ==

* [[How to Get Help]] — who to contact and how
* [[Support Ticket System]] — the WUR support portal
* [[Reporting Incidents]] — writing a good problem report
* [[Known Issues]] — current problems and workarounds
* [[User's group]] — the Anunna user community
* [[Maintenance Schedule]] — planned downtimes
* [[System Status Page]] — whether the cluster is up

For PIs

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Haars0011: IA migration §1c: create For PIs section landing hub (via create-page on MediaWiki MCP Server)

Training

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Haars0011: IA migration §1c: create Training section landing hub (via create-page on MediaWiki MCP Server)

Courses, tutorials, and reference material for learning to use Anunna.

== In this section ==

* [[Training Materials]] — course slides and self-study resources
* [[Tutorials]] — hands-on tutorials
* [[Workshops]] — instructor-led courses and their dates
* [[Glossary of Terms]] — common HPC and Anunna terms explained

Workflows

2026-06-19T07:56:07Z

Haars0011: IA migration §1c: create Workflows section landing hub (via create-page on MediaWiki MCP Server)

Guidelines and tools for building reproducible, efficient research workflows on Anunna.

== In this section ==

* [[Workflow Migration from Laptop to HPC]] — moving your work to the cluster
* [[Reproducibility Guidelines]] — keeping your work reproducible
* [[Workflow Engines (Snakemake, Nextflow)]] — managing multi-step pipelines
* [[Debugging Jobs]] — working out why a job failed
* [[Checkpointing]] — saving and restarting long jobs
* [[Scheduled tasks (cron)]] — running recurring tasks with scrontab

=== Performance optimization ===

* [[Performance Optimization/Multiple CPUs]] — using several cores in one job
* [[Performance Optimization/Multiple nodes (MPI)]] — scaling across nodes with MPI
* [[Performance Optimization/Multiple nodes (arrayjobs)]] — scaling with job arrays

Storage

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Haars0011: IA migration §1c: create Storage section landing hub (via create-page on MediaWiki MCP Server)

Software

2026-06-19T07:55:56Z

Haars0011: IA migration §1c: create Software section landing hub (via create-page on MediaWiki MCP Server)

The software available on Anunna and how to use, install, and manage it.

== In this section ==

* [[Software Overview]] — the software landscape
* [[Environment Modules]] — loading software with modules and buckets
* [[Installing Personal Software]] — installing into your own space
* [[Python]] — Python (modules, Miniforge, virtual environments)
* [[R]] — R and R libraries
* [[Apptainer]] — containers
* [[Licensed Software]] — software that needs a licence

Scheduling

2026-06-19T07:55:55Z

Haars0011: IA migration §1c: create Scheduling section landing hub (via create-page on MediaWiki MCP Server)

Anunna uses the SLURM scheduler to share compute resources fairly. This section covers how to submit, monitor, and manage jobs.

== In this section ==

* [[Scheduler Overview (Slurm)]] — how scheduling works
* [[Partitions / Queues]] — the available partitions
* [[Choosing a node (constraints)]] — targeting particular hardware
* [[Batch Jobs]] — submitting a batch script
* [[Interactive Jobs]] — an interactive shell on a compute node
* [[Array Jobs]] — running many similar jobs at once
* [[Monitoring Jobs]] — checking on your jobs
* [[Cancelling Jobs]] — stopping a job
* [[Reservations]] — reserving nodes
* [[Fair Use Policy]] — using shared resources considerately

System Access

2026-06-19T07:55:51Z

Haars0011: IA migration §1c: create System Access section landing hub (via create-page on MediaWiki MCP Server)

How to reach and use the different parts of the cluster: the nodes you connect to, the filesystems, and how to move data in and out.

== In this section ==

* [[Login Nodes]] — the entry point you connect to
* [[Compute Nodes]] — where your jobs run, and how to reach them
* [[Storage Systems Overview|File systems]] — the storage tiers
* [[Quotas]] — storage limits and how to check them
* [[Data Transfer Methods]] — moving data to and from Anunna

== See also ==
* [[SSH Access]]
* [[Storage Systems Overview]]

Get Started

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Haars0011: IA migration §1c: create Get Started section landing hub (via create-page on MediaWiki MCP Server)

New to Anunna? Start here. This section covers who can use the cluster, how to get an account, and how to log in.

== In this section ==

* [[Who Can Access?]] — eligibility
* [[Account Application Process]] — how to request an account
* [[User Responsibilities]] — what is expected of you as a user
* [[SSH Access]] — logging in over SSH
* [[Apps Portal]] — using Anunna through your web browser

== See also ==
* [[Workflow Migration from Laptop to HPC]] — moving your work to the cluster

About

2026-06-19T07:55:46Z

Haars0011: IA migration §1c: create About section landing hub (via create-page on MediaWiki MCP Server)

Wiki TODO

2026-06-19T07:35:24Z

Haars0011: Add Project Creation + Storage Requests tasks (via update-page on MediaWiki MCP Server)

This page lists Anunna documentation that has been published but still needs current or authoritative information filled in. The pages below are usable as they stand, but each contains placeholders — marked in the page source with <code></code> comments — where someone with current operational knowledge needs to add or confirm details.

To pick up a task: open the page, find the <code>TODO</code> comment(s) in its source, add the information, and remove the item from this list.

== Hardware and network ==

* '''[[Cluster Architecture Overview]]''' — confirm the current interconnect (Omnipath and/or InfiniBand) and topology; add a current architecture diagram (the old schematics were out of date and were removed).
* '''[[Compute Hardware Overview]]''' — fill in the per-node specifications: number of CPU nodes, cores and memory per node, CPU model(s), and whether there are high-memory "fat" nodes; number of NVIDIA GPU nodes, GPUs per node, and host CPU/memory; AMD GPU model and node details.
* '''[[Network & Security]]''' — confirm the interconnect (as above) and document the data-security posture: how data is protected at rest and in transit, access control, handling of confidential or personal data, and backup/retention.
* '''[[Performance Optimization/Multiple nodes (MPI)]]''' — confirm the recommended MPI library and module names, any required <code>srun --mpi=...</code> plugin flag, and whether specific interconnect/fabric tuning is needed. The old mvapich2 + InfiniBand (ib0) example was Breed4Food-era and was removed.

== Storage ==

* '''[[Quotas]]''' — document the Lustre quota model (per-user or per-group, and the default sizes for /lustre/backup, /lustre/nobackup, /lustre/scratch), the command(s) users run to check their current usage, and how to request more space. Only the home-directory quota (200 GB) is currently documented.
* '''[[Archival Storage]]''' — clarify how the manual iRODS/itape workflow relates to Tapeworm, now that Tapeworm manages archival from /archive to tape automatically: is itape still the recommended way to push data to tape, or is iRODS now used mainly for retrieving archived datasets?

== Software and workflows ==

* '''[[Workflow Engines (Snakemake, Nextflow)]]''' — confirm the recommended way to run Snakemake on Anunna (the documented profile is the older Snakemake <8 style; Snakemake 8+ uses the <code>--executor slurm</code> plugin), and write the Nextflow section (loading/installing Nextflow, the SLURM executor configuration, and a minimal example).
* '''[[Conda for teaching]]''' — modernise for current Anunna: the page still describes the old Bright <code>/cm/shared</code> paths and tcl modulefiles. Replace with a Miniforge environment on Lustre and the current course-kernel route (kernel registered at notebook.anunna.wur.nl; see [[Steps for courses]]).

== Support and operations ==

* '''[[Maintenance Schedule]]''' — confirm where planned-maintenance dates are announced (Apps Portal message of the day, mailing list, Teams) and add the next scheduled downtime, or a link to a live maintenance schedule. Only the general cadence (roughly April/May and October) is documented.
* '''[[System Status Page]]''' — add the Anunna status / health dashboard URL, or confirm whether such a dashboard exists.
* '''[[Reporting Usage]]''' — document the reports.anunna.wur.nl usage and cost dashboard: what reports it offers, who can see what (your own usage versus your group's), and how to read them.
* '''[[Managing Group Members]]''' — confirm how a PI adds or removes members from their Anunna group (self-service, via the AD group owner, or via the administrators) and document the steps.
* '''[[Project Creation]]''' — document the project / billing-account creation process: how a PI requests one, how a commitment is agreed, and who can be added.
* '''[[Storage Requests]]''' — confirm whether storage requests use a dedicated form or the general HPC (Anunna) support service, and any approval or group-owner requirements.

== Policy and governance ==

* '''[[Mission and Governance]]''' — confirm and document the current governance bodies (for example a steering group and user group) and their membership. The previous roster was from the Breed4Food era and was removed.
* '''[[Roadmap]]''' — add the current roadmap, or link the latest roadmap document. The 2019–2020 version was removed.
* '''[[Sustainability]]''' — add the sustainability / green-HPC policy and any concrete measures: energy sourcing, cooling, hardware lifecycle, and institutional targets.
* '''[[Policies and Terms of Use]]''' — supply the formal terms of use / acceptable-use policy (data ownership and responsibilities, security obligations, consequences of misuse) and confirm the current account-request route and per-group access contacts. The previous access-contact list was from the Breed4Food era and was removed.
* '''[[Account Application Process]]''' — confirm whether WUR users request an Anunna account through the general "HPC (Anunna)" support service or a dedicated account-request form, and what details are needed (group/affiliation, sponsor, intended use).
* '''[[User's group]]''' — document any formal user representation: regular user meetings, how users feed back into decisions, and how that relates to the governance bodies. Currently only the Anunna Users Teams community is documented.

== Nice to have ==

* '''[[FAQ]]''' — extend with the questions the HPC team is asked most often (for example quota limits, GPU access, course accounts, data transfer).

== See also ==

* [[Support]]

Project Creation

2026-06-19T07:34:41Z

Haars0011: IA migration §11: new Project Creation (skeleton with TODO) (via create-page on MediaWiki MCP Server)

A project on Anunna is a billing account that your jobs and storage are charged to, usually tied to a group with a commitment. As a PI, you set up a project so that your team's usage is tracked and billed correctly.

== Setting up a project ==

To set up a new project or billing account, contact the HPC team through [[How to Get Help]].



Once a project exists, you can track its usage and costs (see [[Reporting Usage]]), add members (see [[Managing Group Members]]), and request storage for it (see [[Storage Requests]]).

== See also ==
* [[Account Application Process]]
* [[Managing Group Members]]
* [[Reporting Usage]]
* [[Storage Requests]]

Storage Requests

2026-06-19T07:34:38Z

Haars0011: IA migration §11: new Storage Requests (via create-page on MediaWiki MCP Server)

If you need more storage than your current [[Quotas|quota]] allows — a larger Lustre allocation, more home space, or archive space — you can request it from the HPC team.

== Requesting more storage ==

Submit a request through [[How to Get Help]] (the WUR support portal, '''HPC (Anunna)''' service). It helps to include:

* which filesystem you need more of — home, [[Compute Storage|Lustre]] (backup / nobackup / scratch), or [[Archival Storage|/archive]];
* how much space you need, and for how long;
* the group or project it is for.

Storage is charged per TB — see [[Tariffs]] — so request what you need. If your group has a commitment, additional storage is deducted from it.



== See also ==
* [[Quotas]]
* [[Storage Systems Overview]]
* [[How to Get Help]]
* [[Tariffs]]

Dos and Don'ts

2026-06-19T07:34:33Z

Haars0011: IA migration §11: new Dos and Don'ts checklist (via create-page on MediaWiki MCP Server)

A quick checklist of good and bad practices on Anunna. For the detail behind each point, follow the links.

== Do ==

* '''Do''' run computation as jobs through the scheduler, and request only the resources you need — see [[Scheduler Overview (Slurm)]] and the [[Fair Use Policy]].
* '''Do''' keep active data on [[Compute Storage|Lustre]], and know what is backed up — see [[Backup Policy]].
* '''Do''' keep your own copies of anything you cannot afford to lose, and archive data you are finished with — see [[Archival Storage]].
* '''Do''' pin software versions and keep your work reproducible — see [[Reproducibility Guidelines]].
* '''Do''' watch your spending — see [[Reporting Usage]] and [[Tariffs]].

== Don't ==

* '''Don't''' run heavy work, or heavy I/O such as logging, on the [[Login Nodes|login nodes]] or against your [[Home Directory|home directory]].
* '''Don't''' run jobs outside the scheduler.
* '''Don't''' over-request resources "to be safe" — it wastes your budget and makes your jobs wait longer in the queue.
* '''Don't''' leave large files on [[Compute Storage|/lustre/scratch]] — it may be purged, and it costs money.
* '''Don't''' share your account or credentials — see [[User Responsibilities]].

== See also ==
* [[User Responsibilities]]
* [[Fair Use Policy]]
* [[Reproducibility Guidelines]]