Main Page

2018-05-19T17:48:24Z

Eikel011: Added link to the new Parallel_R_code_on_SLURM page

The Agrogenomics cluster 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.

The Agrogenomics HPC was an initiative of the [http://www.breed4food.com/en/breed4food.htm Breed4Food] (B4F) consortium, consisting 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]. Currently, in addition to the original partners, the HPC (HPC-Ag) is used by other groups from Wageningen UR (Bioinformatics, Centre for Crop Systems Analysis, Environmental Sciences Group, and Plant Research International) and plant breeding industry (Rijk Zwaan).

== Events ==
* [[Courses]] that have happened and are happening
* [[Downtime]] that will affect all users
* [[Meetings]] that may affect the policies of the HPC

== Using the HPC-Ag ==
=== Gaining access to the HPC-Ag ===
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]]
* [[Services | Available features and services on the HPC]]
* [[Filesystems | Accessible storage methods on the HPC]]

== 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 the HPC-Ag 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 CAT-AGRO or FB-ICT.

=== Cluster Management Software and Scheduler ===
The HPC-Ag 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]]
* [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']]
* [[SLURM_Compare | Rosetta Stone of Workload Managers]]

=== Installation of software by users ===

* [[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 ]]
* [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]

=== Installed software ===

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

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

* [[Using_environment_modules | Using environment modules]]
* [[Setting local variables]]
* [[Setting_TMPDIR | Set a custom temporary directory location]]
* [[Installing_R_packages_locally | Installing R packages locally]]
* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]

=== Controlling costs ===

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

== Management ==
[[HPC_management | Main Article: HPC management]]

Project Leader of the HPC is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:lith010 | Jan van Lith (Wageningen UR,FB-IT, Infrastructure)]] and [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]].

== Miscellaneous ==
* [[Mailinglist | Electronic mail discussion lists]]
* [[History_of_the_Cluster | Historical information on the startup of the HPC]]
* [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]
* [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]
* [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]
* [[Manual GitLab | GitLab: Create projects and add scripts]]

== See also ==
* [[Maintenance_and_Management | Maintenance and Management]]
* [[BCData | BCData]]
* [[Mailinglist | Electronic mail discussion lists]]
* [[About_ABGC | About ABGC]]
* [[Computer_cluster | High Performance Computing @ABGC]]
* [[Lustre_PFS_layout | Lustre Parallel File System layout]]

== External links ==
{| width="90%"
|- valign="top"
| width="30%" |
* [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]
* [http://www.wageningenur.nl/en/Expertise-Services/Facilities/CATAgroFood-3/CATAgroFood-3/Our-facilities/Show/High-Performance-Computing-Cluster-HPC.htm CATAgroFood offers a HPC facilty]
* [http://www.cobb-vantress.com Cobb-Vantress homepage]

| width="30%" |
* [https://www.crv4all.nl CRV homepage]
* [http://www.hendrix-genetics.com Hendrix Genetics homepage]
* [http://www.topigs.com TOPIGS homepage]
| width="30%" |
* [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]
* [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]
|}

Parallel R code on SLURM

2018-05-19T17:41:37Z

Eikel011: Created the page Parallel R code on SLURM

== Using R code on SLURM for embarrassingly parallel calculations ==

The most well-known R packages that provide parallel functionality, e.g. doParallel or doSNOW, do not work properly on the HPC. Using these packages will be particularly problematic when you try to run (array) jobs over multiple nodes. However, the [https://cran.r-project.org/web/packages/rslurm/vignettes/rslurm.html rslurm package] allows you to do [https://en.wikipedia.org/wiki/Embarrassingly_parallel embarrassingly parallel] calculations on SLURM. The package automatically divides the computation over multiple nodes and writes the necessary submission scripts. It also includes functions to retrieve and combine the output from different nodes, as well as wrappers for common SLURM commands.

== External links ==
[https://cran.r-project.org/web/packages/rslurm/vignettes/rslurm.html Vignette for the rslurm package]

HPCwiki - User contributions [en]

Main Page

Parallel R code on SLURM