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Anunna is a [http://en.wikipedia.org/wiki/High-performance_computing High Performance Computer] (HPC) infrastructure hosted by [http://www.wageningenur.nl/nl/activiteit/Opening-High-Performance-Computing-cluster-HPC.htm Wageningen University & Research Centre]. It is open for use for all WUR research groups as well as other organizations, including companies, that have collaborative projects with WUR. | |||
= Using Anunna = | |||
* [[Tariffs | Costs associated with resource usage]] | |||
== Gaining access to Anunna== | |||
== Gaining access to | |||
Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP]. | Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP]. | ||
* [[log_in_to_B4F_cluster | Logging into cluster using ssh | * [[log_in_to_B4F_cluster | Logging into cluster using ssh]] | ||
* [[Services | Alternative access methods, and extra features and services on | * [[file_transfer | File transfer options]] | ||
* [[Filesystems | | * [[Services | Alternative access methods, and extra features and services on Anunna]] | ||
* [[Filesystems | Data storage methods on Anunna]] | |||
== Access Policy == | == Access Policy == | ||
[[Access_Policy | Main Article: Access Policy]] | [[Access_Policy | Main Article: Access Policy]] | ||
Access needs to be granted actively (by creation of an account on the cluster by FB-IT). Use of resources is limited by the scheduler. Depending on availability of queues ('partitions') granted to a user, priority to the system's resources is regulated. Note that the use of | Access needs to be granted actively (by creation of an account on the cluster by FB-IT). Use of resources is limited by the scheduler. Depending on availability of queues ('partitions') granted to a user, priority to the system's resources is regulated. Note that the use of Anunna is not free of charge. List price of CPU time and storage, and possible discounts on that list price for your organisation, can be retrieved from Shared Research Facilities or FB-IT. | ||
= Events = | = Events = | ||
* [[Courses]] that have happened and are happening | * [[Courses]] that have happened and are happening | ||
* [[Downtime]] that will affect all users | * [[Downtime]] that will affect all users | ||
* [[Meetings]] that may affect the policies of | * [[Meetings]] that may affect the policies of Anunna | ||
= Other Software = | = Other Software = | ||
== Cluster Management Software and Scheduler == | == Cluster Management Software and Scheduler == | ||
Anunna uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler. | |||
* [[BCM_on_B4F_cluster | Monitor cluster status with BCM]] | * [[BCM_on_B4F_cluster | Monitor cluster status with BCM]] | ||
* [[ | * [[Using_Slurm | Submit jobs with Slurm]] | ||
* [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']] | * [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']] | ||
* [[SLURM_Compare | Rosetta Stone of Workload Managers]] | * [[SLURM_Compare | Rosetta Stone of Workload Managers]] | ||
| Line 37: | Line 39: | ||
* [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]] | * [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]] | ||
* [[Installing WRF and WPS]] | * [[Installing WRF and WPS]] | ||
* [[Running scripts on a fixed timeschedule (cron)]] | |||
== Installed software == | == Installed software == | ||
| Line 59: | Line 62: | ||
== Management == | == Management == | ||
[[ | Product Owner of Anunna is Alexander van Ittersum (Wageningen UR,FB-IT, C&PS). [[User: prins089 | Fons Prinsen (Wageningen UR, FB-IT, C&PS)]] is responsible for [[Maintenance_and_Management | Maintenance and Management]] of the cluster. | ||
* [[Roadmap | Ambitions regarding innovation, support and administration of Anunna ]] | |||
= Miscellaneous = | = Miscellaneous = | ||
* [[Mailinglist | Electronic mail discussion lists]] | * [[Mailinglist | Electronic mail discussion lists]] | ||
* [[History_of_the_Cluster | Historical information on the startup of | * [[History_of_the_Cluster | Historical information on the startup of Anunna]] | ||
* [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]] | * [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]] | ||
* [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]] | * [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]] | ||
| Line 71: | Line 74: | ||
* [[Manual GitLab | GitLab: Create projects and add scripts]] | * [[Manual GitLab | GitLab: Create projects and add scripts]] | ||
* [[Monitoring_executions | Monitoring job execution]] | * [[Monitoring_executions | Monitoring job execution]] | ||
* [[Shared_folders | Working with shared folders in the Lustre file system]] | |||
* [[Old_binaries | Running older binaries on the updated OS]] | |||
= See also = | = See also = | ||
| Line 84: | Line 89: | ||
|- valign="top" | |- valign="top" | ||
| width="30%" | | | width="30%" | | ||
* [ | * [https://www.wur.nl/en/Value-Creation-Cooperation/Facilities/Wageningen-Shared-Research-Facilities/Our-facilities/Show/High-Performance-Computing-Cluster-HPC-Anunna.htm SRF offers a HPC facilty] | ||
| width="30%" | | | width="30%" | | ||
* [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux] | * [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux] | ||
* [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages] | * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages] | ||
|} | |} | ||
Latest revision as of 16:17, 23 October 2023
Anunna is a High Performance Computer (HPC) infrastructure hosted by Wageningen University & Research Centre. It is open for use for all WUR research groups as well as other organizations, including companies, that have collaborative projects with WUR.
Using Anunna
Gaining access to Anunna
Access to the cluster and file transfer are traditionally done via SSH and SFTP.
- Logging into cluster using ssh
- File transfer options
- Alternative access methods, and extra features and services on Anunna
- Data storage methods on Anunna
Access Policy
Access needs to be granted actively (by creation of an account on the cluster by FB-IT). Use of resources is limited by the scheduler. Depending on availability of queues ('partitions') granted to a user, priority to the system's resources is regulated. Note that the use of Anunna is not free of charge. List price of CPU time and storage, and possible discounts on that list price for your organisation, can be retrieved from Shared Research Facilities or FB-IT.
Events
- Courses that have happened and are happening
- Downtime that will affect all users
- Meetings that may affect the policies of Anunna
Other Software
Cluster Management Software and Scheduler
Anunna uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.
- Monitor cluster status with BCM
- Submit jobs with Slurm
- Be aware of how much work the cluster is under right now with 'node_usage_graph'
- Rosetta Stone of Workload Managers
Installation of software by users
- Installing domain specific software: installation by users
- Setting local variables
- Installing R packages locally
- Setting up and using a virtual environment for Python3
- Setting up and using a virtual environment for Python3.4 or higher
- Installing WRF and WPS
- Running scripts on a fixed timeschedule (cron)
Installed software
Useful Notes
Being in control of Environment parameters
- Using environment modules
- Setting local variables
- Set a custom temporary directory location
- Installing R packages locally
- Setting up and using a virtual environment for Python3
Controlling costs
Management
Product Owner of Anunna is Alexander van Ittersum (Wageningen UR,FB-IT, C&PS). Fons Prinsen (Wageningen UR, FB-IT, C&PS) is responsible for Maintenance and Management of the cluster.
Miscellaneous
- Electronic mail discussion lists
- Historical information on the startup of Anunna
- Bioinformatics tips, tricks, and workflows
- Running parallel R code on SLURM
- Convert between MediaWiki format and other formats
- GitLab: Create projects and add scripts
- Monitoring job execution
- Working with shared folders in the Lustre file system
- Running older binaries on the updated OS
See also
- Maintenance and Management
- BCData
- Electronic mail discussion lists
- About ABGC
- High Performance Computing @ABGC
- Lustre Parallel File System layout