https://wiki.anunna.wur.nl/api.php?action=feedcontributions&feedformat=atom&user=Vaend001 2026-04-18T13:52:15Z User contributions MediaWiki 1.43.1 https://wiki.anunna.wur.nl/index.php?title=Main_Page&diff=2057 2019-10-11T11:48:50Z

<p>Vaend001: </p> <hr /> <div>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 &amp; 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. <br /> <br /> = Using Anunna =<br /> * [[Tariffs | Costs associated with resource usage]]<br /> <br /> == Gaining access to Anunna==<br /> Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP].<br /> * [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]<br /> * [[Services | Alternative access methods, and extra features and services on Anunna]]<br /> * [[Filesystems | Accessible storage methods on Anunna]]<br /> <br /> == Access Policy ==<br /> [[Access_Policy | Main Article: Access Policy]]<br /> <br /> 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 CAT-AGRO or FB-ICT.<br /> <br /> = Events =<br /> * [[Courses]] that have happened and are happening<br /> * [[Downtime]] that will affect all users<br /> * [[Meetings]] that may affect the policies of Anunna<br /> <br /> = Other Software =<br /> <br /> == Cluster Management Software and Scheduler ==<br /> Anunna uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.<br /> * [[BCM_on_B4F_cluster | Monitor cluster status with BCM]]<br /> * [[Using_Slurm | Submit jobs with Slurm]]<br /> * [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']]<br /> * [[SLURM_Compare | Rosetta Stone of Workload Managers]]<br /> <br /> == Installation of software by users ==<br /> <br /> * [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]<br /> * [[Setting local variables]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> * [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]<br /> * [[Installing WRF and WPS]]<br /> <br /> == Installed software ==<br /> <br /> * [[Globally_installed_software | Globally installed software]]<br /> * [[ABGC_modules | ABGC specific modules]]<br /> <br /> = Useful Notes = <br /> <br /> == Being in control of Environment parameters ==<br /> <br /> * [[Using_environment_modules | Using environment modules]]<br /> * [[Setting local variables]]<br /> * [[Setting_TMPDIR | Set a custom temporary directory location]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> <br /> == Controlling costs ==<br /> <br /> * [[SACCT | using SACCT to see your costs]]<br /> * [[get_my_bill | using the &quot;get_my_bill&quot; script to estimate costs]]<br /> <br /> == Management ==<br /> Project Leader of Anunna is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] and [[User:bexke002 | Stefan Bexkens (Wageningen UR,FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]] of the cluster.<br /> <br /> * [[Roadmap | Ambitions regarding innovation, support and administration of Anunna ]]<br /> <br /> = Miscellaneous =<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[History_of_the_Cluster | Historical information on the startup of Anunna]]<br /> * [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]<br /> * [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]<br /> * [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]<br /> * [[Manual GitLab | GitLab: Create projects and add scripts]]<br /> * [[Monitoring_executions | Monitoring job execution]]<br /> * [[Shared_folders | Working with shared folders in the Lustre file system]]<br /> <br /> = See also =<br /> * [[Maintenance_and_Management | Maintenance and Management]]<br /> * [[BCData | BCData]]<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[About_ABGC | About ABGC]]<br /> * [[Computer_cluster | High Performance Computing @ABGC]]<br /> * [[Lustre_PFS_layout | Lustre Parallel File System layout]]<br /> <br /> = External links =<br /> {| width=&quot;90%&quot;<br /> |- valign=&quot;top&quot;<br /> | width=&quot;30%&quot; |<br /> * [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]<br /> * [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]<br /> * [http://www.cobb-vantress.com Cobb-Vantress homepage]<br /> <br /> | width=&quot;30%&quot; |<br /> * [https://www.crv4all.nl CRV homepage]<br /> * [http://www.hendrix-genetics.com Hendrix Genetics homepage]<br /> * [http://www.topigs.com TOPIGS homepage]<br /> | width=&quot;30%&quot; |<br /> * [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]<br /> * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]<br /> |}</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Main_Page&diff=2034 2019-07-08T06:08:21Z

<p>Vaend001: </p> <hr /> <div>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 &amp; 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. <br /> <br /> = Using Anunna =<br /> * [[Tariffs | Costs associated with resource usage]]<br /> <br /> == Gaining access to Anunna==<br /> Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP].<br /> * [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]<br /> * [[Services | Alternative access methods, and extra features and services on Anunna]]<br /> * [[Filesystems | Accessible storage methods on Anunna]]<br /> <br /> == Access Policy ==<br /> [[Access_Policy | Main Article: Access Policy]]<br /> <br /> 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 CAT-AGRO or FB-ICT.<br /> <br /> = Events =<br /> * [[Courses]] that have happened and are happening<br /> * [[Downtime]] that will affect all users<br /> * [[Meetings]] that may affect the policies of Anunna<br /> <br /> = Other Software =<br /> <br /> == Cluster Management Software and Scheduler ==<br /> Anunna uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.<br /> * [[BCM_on_B4F_cluster | Monitor cluster status with BCM]]<br /> * [[Using_Slurm | Submit jobs with Slurm]]<br /> * [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']]<br /> * [[SLURM_Compare | Rosetta Stone of Workload Managers]]<br /> <br /> == Installation of software by users ==<br /> <br /> * [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]<br /> * [[Setting local variables]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> * [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]<br /> * [[Installing WRF and WPS]]<br /> <br /> == Installed software ==<br /> <br /> * [[Globally_installed_software | Globally installed software]]<br /> * [[ABGC_modules | ABGC specific modules]]<br /> <br /> = Useful Notes = <br /> <br /> == Being in control of Environment parameters ==<br /> <br /> * [[Using_environment_modules | Using environment modules]]<br /> * [[Setting local variables]]<br /> * [[Setting_TMPDIR | Set a custom temporary directory location]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> <br /> == Controlling costs ==<br /> <br /> * [[SACCT | using SACCT to see your costs]]<br /> * [[get_my_bill | using the &quot;get_my_bill&quot; script to estimate costs]]<br /> <br /> == Management ==<br /> Project Leader of Anunna is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] and [[User:vaend001 | Catharina Vaendel (Wageningen UR,FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]] of the cluster.<br /> <br /> * [[Roadmap | Ambitions regarding innovation, support and administration of Anunna ]]<br /> <br /> = Miscellaneous =<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[History_of_the_Cluster | Historical information on the startup of Anunna]]<br /> * [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]<br /> * [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]<br /> * [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]<br /> * [[Manual GitLab | GitLab: Create projects and add scripts]]<br /> * [[Monitoring_executions | Monitoring job execution]]<br /> * [[Shared_folders | Working with shared folders in the Lustre file system]]<br /> <br /> = See also =<br /> * [[Maintenance_and_Management | Maintenance and Management]]<br /> * [[BCData | BCData]]<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[About_ABGC | About ABGC]]<br /> * [[Computer_cluster | High Performance Computing @ABGC]]<br /> * [[Lustre_PFS_layout | Lustre Parallel File System layout]]<br /> <br /> = External links =<br /> {| width=&quot;90%&quot;<br /> |- valign=&quot;top&quot;<br /> | width=&quot;30%&quot; |<br /> * [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]<br /> * [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]<br /> * [http://www.cobb-vantress.com Cobb-Vantress homepage]<br /> <br /> | width=&quot;30%&quot; |<br /> * [https://www.crv4all.nl CRV homepage]<br /> * [http://www.hendrix-genetics.com Hendrix Genetics homepage]<br /> * [http://www.topigs.com TOPIGS homepage]<br /> | width=&quot;30%&quot; |<br /> * [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]<br /> * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]<br /> |}</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Main_Page&diff=2012 2019-04-29T11:43:13Z

<p>Vaend001: /* Using Anunna */</p> <hr /> <div>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 &amp; 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. <br /> <br /> = Using Anunna =<br /> * [[Tariffs | Costs associated with resource usage]]<br /> <br /> == Gaining access to Anunna==<br /> Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP].<br /> * [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]<br /> * [[Services | Alternative access methods, and extra features and services on Anunna]]<br /> * [[Filesystems | Accessible storage methods on Anunna]]<br /> <br /> == Access Policy ==<br /> [[Access_Policy | Main Article: Access Policy]]<br /> <br /> 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 CAT-AGRO or FB-ICT.<br /> <br /> = Events =<br /> * [[Courses]] that have happened and are happening<br /> * [[Downtime]] that will affect all users<br /> * [[Meetings]] that may affect the policies of Anunna<br /> <br /> = Other Software =<br /> <br /> == Cluster Management Software and Scheduler ==<br /> Anunna uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.<br /> * [[BCM_on_B4F_cluster | Monitor cluster status with BCM]]<br /> * [[Using_Slurm | Submit jobs with Slurm]]<br /> * [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']]<br /> * [[SLURM_Compare | Rosetta Stone of Workload Managers]]<br /> <br /> == Installation of software by users ==<br /> <br /> * [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]<br /> * [[Setting local variables]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> * [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]<br /> * [[Installing WRF and WPS]]<br /> <br /> == Installed software ==<br /> <br /> * [[Globally_installed_software | Globally installed software]]<br /> * [[ABGC_modules | ABGC specific modules]]<br /> <br /> = Useful Notes = <br /> <br /> == Being in control of Environment parameters ==<br /> <br /> * [[Using_environment_modules | Using environment modules]]<br /> * [[Setting local variables]]<br /> * [[Setting_TMPDIR | Set a custom temporary directory location]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> <br /> == Controlling costs ==<br /> <br /> * [[SACCT | using SACCT to see your costs]]<br /> * [[get_my_bill | using the &quot;get_my_bill&quot; script to estimate costs]]<br /> <br /> == Management ==<br /> Project Leader of Anunna is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:lith010 | Jan van Lith (Wageningen UR,FB-IT, Infrastructure)]], [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] and [[User:vaend001 | Catharina Vaendel(Wageningen UR,FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]].<br /> <br /> * [[Roadmap | Ambitions regarding innovation, support and administration of Anunna ]]<br /> <br /> = Miscellaneous =<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[History_of_the_Cluster | Historical information on the startup of Anunna]]<br /> * [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]<br /> * [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]<br /> * [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]<br /> * [[Manual GitLab | GitLab: Create projects and add scripts]]<br /> * [[Monitoring_executions | Monitoring job execution]]<br /> * [[Shared_folders | Working with shared folders in the Lustre file system]]<br /> <br /> = See also =<br /> * [[Maintenance_and_Management | Maintenance and Management]]<br /> * [[BCData | BCData]]<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[About_ABGC | About ABGC]]<br /> * [[Computer_cluster | High Performance Computing @ABGC]]<br /> * [[Lustre_PFS_layout | Lustre Parallel File System layout]]<br /> <br /> = External links =<br /> {| width=&quot;90%&quot;<br /> |- valign=&quot;top&quot;<br /> | width=&quot;30%&quot; |<br /> * [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]<br /> * [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]<br /> * [http://www.cobb-vantress.com Cobb-Vantress homepage]<br /> <br /> | width=&quot;30%&quot; |<br /> * [https://www.crv4all.nl CRV homepage]<br /> * [http://www.hendrix-genetics.com Hendrix Genetics homepage]<br /> * [http://www.topigs.com TOPIGS homepage]<br /> | width=&quot;30%&quot; |<br /> * [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]<br /> * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]<br /> |}</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Main_Page&diff=2011 2019-04-29T11:42:57Z

<p>Vaend001: /* Gaining access to Anunna */</p> <hr /> <div>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 &amp; 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. <br /> <br /> = Using Anunna =<br /> == Gaining access to Anunna==<br /> Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP].<br /> * [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]<br /> * [[Services | Alternative access methods, and extra features and services on Anunna]]<br /> * [[Filesystems | Accessible storage methods on Anunna]]<br /> <br /> == Access Policy ==<br /> [[Access_Policy | Main Article: Access Policy]]<br /> <br /> 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 CAT-AGRO or FB-ICT.<br /> <br /> = Events =<br /> * [[Courses]] that have happened and are happening<br /> * [[Downtime]] that will affect all users<br /> * [[Meetings]] that may affect the policies of Anunna<br /> <br /> = Other Software =<br /> <br /> == Cluster Management Software and Scheduler ==<br /> Anunna uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.<br /> * [[BCM_on_B4F_cluster | Monitor cluster status with BCM]]<br /> * [[Using_Slurm | Submit jobs with Slurm]]<br /> * [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']]<br /> * [[SLURM_Compare | Rosetta Stone of Workload Managers]]<br /> <br /> == Installation of software by users ==<br /> <br /> * [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]<br /> * [[Setting local variables]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> * [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]<br /> * [[Installing WRF and WPS]]<br /> <br /> == Installed software ==<br /> <br /> * [[Globally_installed_software | Globally installed software]]<br /> * [[ABGC_modules | ABGC specific modules]]<br /> <br /> = Useful Notes = <br /> <br /> == Being in control of Environment parameters ==<br /> <br /> * [[Using_environment_modules | Using environment modules]]<br /> * [[Setting local variables]]<br /> * [[Setting_TMPDIR | Set a custom temporary directory location]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> <br /> == Controlling costs ==<br /> <br /> * [[SACCT | using SACCT to see your costs]]<br /> * [[get_my_bill | using the &quot;get_my_bill&quot; script to estimate costs]]<br /> <br /> == Management ==<br /> Project Leader of Anunna is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:lith010 | Jan van Lith (Wageningen UR,FB-IT, Infrastructure)]], [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] and [[User:vaend001 | Catharina Vaendel(Wageningen UR,FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]].<br /> <br /> * [[Roadmap | Ambitions regarding innovation, support and administration of Anunna ]]<br /> <br /> = Miscellaneous =<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[History_of_the_Cluster | Historical information on the startup of Anunna]]<br /> * [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]<br /> * [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]<br /> * [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]<br /> * [[Manual GitLab | GitLab: Create projects and add scripts]]<br /> * [[Monitoring_executions | Monitoring job execution]]<br /> * [[Shared_folders | Working with shared folders in the Lustre file system]]<br /> <br /> = See also =<br /> * [[Maintenance_and_Management | Maintenance and Management]]<br /> * [[BCData | BCData]]<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[About_ABGC | About ABGC]]<br /> * [[Computer_cluster | High Performance Computing @ABGC]]<br /> * [[Lustre_PFS_layout | Lustre Parallel File System layout]]<br /> <br /> = External links =<br /> {| width=&quot;90%&quot;<br /> |- valign=&quot;top&quot;<br /> | width=&quot;30%&quot; |<br /> * [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]<br /> * [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]<br /> * [http://www.cobb-vantress.com Cobb-Vantress homepage]<br /> <br /> | width=&quot;30%&quot; |<br /> * [https://www.crv4all.nl CRV homepage]<br /> * [http://www.hendrix-genetics.com Hendrix Genetics homepage]<br /> * [http://www.topigs.com TOPIGS homepage]<br /> | width=&quot;30%&quot; |<br /> * [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]<br /> * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]<br /> |}</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=User:Vaend001&diff=2010 2019-04-29T11:13:30Z

<p>Vaend001: </p> <hr /> <div> [https://www.vcard.wur.nl/Views/Profile/View.aspx?id=79032 Catharina Vaendel's VCard]<br /> <br /> Linux System Admin<br /> - HPC Anunna <br /> - Managed Servers</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=2009 2019-04-26T13:02:37Z

<p>Vaend001: </p> <hr /> <div>== Upcoming: HPC Basic Course - 2019-06-28==<br /> <br /> A course for beginners will be organised on the 28th of June, aiming to help absolute beginners to begin to use the main job scheduler, SLURM. You can register [https://oneschool.wur.nl/Lists/Cursus/DispForm.aspx?ID=100 here].<br /> <br /> == Upcoming Linux Basic Course - 2019-06-13 ==<br /> <br /> A course for beginners will be organised on the 13th of June, to help beginner Linux users gain some skills in using Linux. You can register for this course [https://www.wur.nl/en/activity/Linux-basic-course-on-13-June-2019.htm here]<br /> <br /> == Upcoming: HPC Advanced Course - 2019-05-28 ==<br /> <br /> A course for experienced users will be organised on the 28th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> You can register [http://https://www.wur.nl/nl/activiteit/High-Performance-Computing-Cluster-advanced-course-on-28-May-2019.htm here]<br /> <br /> == Upcoming: HPC Basic Course - 2019-05-07 - FULL==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Linux Basic Course - 2019-04-16 ==<br /> <br /> A course for beginners was organised on the 16th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=2008 2019-04-26T13:02:14Z

<p>Vaend001: </p> <hr /> <div>== Upcoming: HPC Basic Course - 2019-06-28==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM. You can register [https://oneschool.wur.nl/Lists/Cursus/DispForm.aspx?ID=100 here].<br /> <br /> == Upcoming Linux Basic Course - 2019-06-13 ==<br /> <br /> A course for beginners will be organised on the 13th of June, to help beginner Linux users gain some skills in using Linux. You can register for this course [https://www.wur.nl/en/activity/Linux-basic-course-on-13-June-2019.htm here]<br /> <br /> == Upcoming: HPC Advanced Course - 2019-05-28 ==<br /> <br /> A course for experienced users will be organised on the 28th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> You can register [http://https://www.wur.nl/nl/activiteit/High-Performance-Computing-Cluster-advanced-course-on-28-May-2019.htm here]<br /> <br /> == Upcoming: HPC Basic Course - 2019-05-07 - FULL==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Linux Basic Course - 2019-04-16 ==<br /> <br /> A course for beginners was organised on the 16th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=2007 2019-04-26T12:28:03Z

<p>Vaend001: </p> <hr /> <div>== Upcoming Linux Basic Course - 2019-06-13 ==<br /> <br /> A course for beginners will be organised on the 13th of June, to help beginner Linux users gain some skills in using Linux. You can register for this course [https://www.wur.nl/en/activity/Linux-basic-course-on-13-June-2019.htm here]<br /> <br /> == Upcoming: HPC Advanced Course - 2019-05-28 ==<br /> <br /> A course for experienced users will be organised on the 28th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> You can register [http://https://www.wur.nl/nl/activiteit/High-Performance-Computing-Cluster-advanced-course-on-28-May-2019.htm here]<br /> <br /> == Upcoming: HPC Basic Course - 2019-05-07 - FULL==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Linux Basic Course - 2019-04-16 ==<br /> <br /> A course for beginners was organised on the 16th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Roadmap&diff=1959 2019-03-08T15:36:17Z

<p>Vaend001: </p> <hr /> <div><br /> == Roadmap march 2019 - march 2020==<br /> <br /> We hereby present our ambitions for Anunna's innovation, administration and support for 2019. We strive to update this roadmap every quarter. &lt;br /&gt;<br /> Although we commit ourselves to the contents of the roadmap, we do not guarantee to achieve these items, since priority and/or contents may change over time. <br /> <br /> [[File:Anunna_ambition_roadmap_2019.pdf|1200px]]<br /> <br /> ----</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Roadmap&diff=1958 2019-03-08T15:10:02Z

<p>Vaend001: Created page with &quot; == Roadmap march 2019 - march 2020== We hereby present our ambitions for Anunna&#039;s innovation, administration and support for 2019. We strive to update this roadmap every qua...&quot;</p> <hr /> <div><br /> == Roadmap march 2019 - march 2020==<br /> <br /> We hereby present our ambitions for Anunna's innovation, administration and support for 2019. We strive to update this roadmap every quarter. &lt;br /&gt;<br /> Although we commit ourselves to the contents of the roadmap, we do not guarantee to achieve these items, since priority and/or contents may change over time. <br /> <br /> [[File:Anunna_ambition_roadmap_2019.pdf]]<br /> <br /> ----</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=File:Anunna_ambition_roadmap_2019.pdf&diff=1957 2019-03-08T14:44:12Z

<p>Vaend001: Vaend001 uploaded a new version of File:Anunna ambition roadmap 2019.pdf</p> <hr /> <div></div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=File:Anunna_ambition_roadmap_2019.pdf&diff=1956 2019-03-08T14:38:05Z

<p>Vaend001: </p> <hr /> <div></div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Main_Page&diff=1955 2019-03-08T14:34:38Z

<p>Vaend001: </p> <hr /> <div>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 &amp; 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. <br /> <br /> = Using Anunna =<br /> == Gaining access to Anunna==<br /> Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP].<br /> * [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]<br /> * [[Services | Alternative access methods, and extra features and services on Anunna]]<br /> * [[Filesystems | Accessible storage methods on Anunna]]<br /> <br /> == Access Policy ==<br /> [[Access_Policy | Main Article: Access Policy]]<br /> <br /> 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 CAT-AGRO or FB-ICT.<br /> <br /> = Events =<br /> * [[Courses]] that have happened and are happening<br /> * [[Downtime]] that will affect all users<br /> * [[Meetings]] that may affect the policies of Anunna<br /> <br /> = Other Software =<br /> <br /> == Cluster Management Software and Scheduler ==<br /> Anunna uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.<br /> * [[BCM_on_B4F_cluster | Monitor cluster status with BCM]]<br /> * [[SLURM_on_B4F_cluster | Submit jobs with Slurm]]<br /> * [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']]<br /> * [[SLURM_Compare | Rosetta Stone of Workload Managers]]<br /> <br /> == Installation of software by users ==<br /> <br /> * [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]<br /> * [[Setting local variables]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> * [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]<br /> * [[Installing WRF and WPS]]<br /> <br /> == Installed software ==<br /> <br /> * [[Globally_installed_software | Globally installed software]]<br /> * [[ABGC_modules | ABGC specific modules]]<br /> <br /> = Useful Notes = <br /> <br /> == Being in control of Environment parameters ==<br /> <br /> * [[Using_environment_modules | Using environment modules]]<br /> * [[Setting local variables]]<br /> * [[Setting_TMPDIR | Set a custom temporary directory location]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> <br /> == Controlling costs ==<br /> <br /> * [[SACCT | using SACCT to see your costs]]<br /> * [[get_my_bill | using the &quot;get_my_bill&quot; script to estimate costs]]<br /> <br /> == Management ==<br /> Project Leader of Anunna is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:lith010 | Jan van Lith (Wageningen UR,FB-IT, Infrastructure)]], [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] and [[User:vaend001 | Catharina Vaendel(Wageningen UR,FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]].<br /> <br /> * [[Roadmap | Ambitions regarding innovation, support and administration of Anunna ]]<br /> <br /> = Miscellaneous =<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[History_of_the_Cluster | Historical information on the startup of Anunna]]<br /> * [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]<br /> * [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]<br /> * [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]<br /> * [[Manual GitLab | GitLab: Create projects and add scripts]]<br /> * [[Monitoring_executions | Monitoring job execution]]<br /> * [[Shared_folders | Working with shared folders in the Lustre file system]]<br /> <br /> = See also =<br /> * [[Maintenance_and_Management | Maintenance and Management]]<br /> * [[BCData | BCData]]<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[About_ABGC | About ABGC]]<br /> * [[Computer_cluster | High Performance Computing @ABGC]]<br /> * [[Lustre_PFS_layout | Lustre Parallel File System layout]]<br /> <br /> = External links =<br /> {| width=&quot;90%&quot;<br /> |- valign=&quot;top&quot;<br /> | width=&quot;30%&quot; |<br /> * [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]<br /> * [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]<br /> * [http://www.cobb-vantress.com Cobb-Vantress homepage]<br /> <br /> | width=&quot;30%&quot; |<br /> * [https://www.crv4all.nl CRV homepage]<br /> * [http://www.hendrix-genetics.com Hendrix Genetics homepage]<br /> * [http://www.topigs.com TOPIGS homepage]<br /> | width=&quot;30%&quot; |<br /> * [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]<br /> * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]<br /> |}</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Environment_Modules&diff=1954 2019-03-08T14:17:24Z

<p>Vaend001: </p> <hr /> <div>== Preface ==<br /> Environment modules [http://modules.sourceforge.net] are a smart way to provide interchangeable blocks of executables and reproducible environments for use in an HPC. It's also the only way to provide simultaneous versions of the same software without collisions, as each module is housed entirely in its own subfolder structure.<br /> <br /> == Using modules ==<br /> The module executable is automatically provided to you upon login. Most users have some modules automatically loaded as well; to see these, use<br /> <br /> &lt;nowiki&gt;module list&lt;/nowiki&gt;<br /> <br /> You should be able to see which modules are loaded.<br /> <br /> One of the most important modules to load is 'shared' - this is Anunna specific, as it will extend the MODULEPATH environment variable to use modules present in /cm/shared as well as /cm/local/ . Without this, many modules will not be available to you.<br /> <br /> == Loading modules ==<br /> Availability of (different versions of) software can be checked by the following command:<br /> &lt;nowiki&gt;module avail&lt;/nowiki&gt;<br /> <br /> For example, you should be able to find the basic module slurm. This provides the path to the sbatch, srun, etc. executables for job submission. To load this, simply:<br /> &lt;nowiki&gt;module load slurm&lt;/nowiki&gt;<br /> <br /> And you will see that it will automatically load the latest version - no need to write out any further.<br /> <br /> Many of the hand-installed programs have a path such as:<br /> &lt;nowiki&gt;hdf5/gcc/64/1.8.14&lt;/nowiki&gt;<br /> Which translates into:<br /> &lt;nowiki&gt;SOFTWARE/COMPILER/BITS/VERSION&lt;/nowiki&gt;<br /> <br /> You can elect to load this to various levels:<br /> <br /> &lt;nowiki&gt;module load hdf5 # loads the latest version, not caring for compiler<br /> module load hdf5/gcc # loads the latest gcc-compiled version, not caring for 32/64 bits (default 64)<br /> module load hdf5/gcc/64 # loads the latest 64-bit gcc-compiled version<br /> module load hdf5/gcc/64/1.8.14 # loads this specific version of hdf5&lt;/nowiki&gt;<br /> <br /> This allows your job scripts to either automatically be upgraded when the latest executables are installed, or elect to use only one specific version of a piece of code.<br /> <br /> == Switching modules ==<br /> <br /> If you want to remove a module, simply<br /> &lt;nowiki&gt;module unload module/1&lt;/nowiki&gt;<br /> This will remove the executable path from your environment. It'll also follow the same logic as above, i.e. you can unload all loaded slurm modules independent of version by just unloading the base module name. You can then load up a new one. You can do this in one command, with:<br /> &lt;nowiki&gt;module switch module/1 module/2&lt;/nowiki&gt;<br /> <br /> Some modules will not allow themselves to be loaded when another one is loaded, for instance, for sanity reasons it's not possible to load two java modules at the same time. Trying to do this will give:<br /> <br /> &lt;nowiki&gt;Module 'module/2' conflicts with the currently loaded module(s) 'module/1'&lt;/nowiki&gt;<br /> If you're seeing this, you must unload or switch your modules rather than overloading them:<br /> &lt;nowiki&gt;module switch module/2&lt;/nowiki&gt;<br /> This works if both modules have the same base path.<br /> <br /> <br /> == External links ==<br /> * http://modules.sourceforge.net<br /> * http://www.admin-magazine.com/HPC/Articles/Environment-Modules</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=User:Vaend001&diff=1953 2019-02-19T19:24:07Z

<p>Vaend001: Created page with &quot; [https://www.vcard.wur.nl/Views/Profile/View.aspx?id=79032 Catharina Vaendel&#039;s VCard] System Administrator for Anunna.&quot;</p> <hr /> <div> [https://www.vcard.wur.nl/Views/Profile/View.aspx?id=79032 Catharina Vaendel's VCard]<br /> <br /> System Administrator for Anunna.</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=User:Dawes001&diff=1952 2019-02-19T19:12:58Z

<p>Vaend001: </p> <hr /> <div> [https://www.vcard.wur.nl/Views/Profile/View.aspx?id=34115 Gwen Dawes' VCard]<br /> <br /> System Administrator for Anunna.</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Shared_folders&diff=1951 2019-02-19T19:09:32Z

<p>Vaend001: </p> <hr /> <div><br /> == Working with shared folders in the Lustre file system ==<br /> <br /> If you work in a group or team and use large volumes of data, it is useful to work within a shared space. User can thus share inputs to their models and make their outputs also easily available. This article explains how to do so within the Lustre file system, that presently supports Anunna.<br /> <br /> There are two main methods available to you: Access Control List (ACL) access (that you can administer yourself) or group access (that is centrally administered).<br /> <br /> == ACL shared directories ==<br /> You may create a folder that can be accessed by yourself and someone else in the following manner:<br /> <br /> &lt;source lang='bash'&gt;<br /> cd /lustre/shared<br /> mkdir shared_folder<br /> chmod 700 shared_folder<br /> setfacl -R -m u:my_id:rwx shared_folder<br /> setfacl -R -d -m u:my_id:rwx shared_folder<br /> &lt;/source&gt;<br /> <br /> Then, for each person who you want to have access to this:<br /> &lt;source lang='bash'&gt;<br /> setfacl -R -m u:my_friend:rwx shared_folder<br /> setfacl -R -d -m u:my_friend:rwx shared_folder<br /> &lt;/source&gt;<br /> <br /> Adding users later can be done using the same method, but it's messy. You may have trouble updating ACLs on files you don't own, though, and you cannot chown files to yourself. Each user with files will need to update their ACLs appropriately, or you can contact your sysadmin to assist.<br /> <br /> <br /> == Group shared directories ==<br /> <br /> Users access Anunna cluster with their WUR-wide account. This means that all the membership information is also available on Anunna. To check of which groups is your user a member of, use the following command:<br /> <br /> &lt;code&gt;groups &lt;username&gt;&lt;/code&gt;<br /> <br /> This can result in a rather long list, reflecting permissions in the overall WUR systems. Within these groups you must then identify the one that is closer to match the team or group with which you wish to collaborate.<br /> <br /> For instance, if I wish to work together with colleagues at ISRIC, I can search within my groups an appropriate match:<br /> <br /> &lt;code&gt;groups duque004 | grep isric&lt;/code&gt;<br /> <br /> In my case the group des-isric-users looked appropriate. Then next step is to confirm if the other users in my team are also members of the group.<br /> <br /> === Creating a shared folder with correct permissions ===<br /> <br /> The Lustre file system is accessible in the &lt;code&gt;/lustre&lt;/code&gt; folder and then divided into the &lt;code&gt;/backup&lt;/code&gt; and &lt;code&gt;/nobackup&lt;/code&gt; sections (corresponding to the different usage plans). Inside each of these folders there is a sub-folder named &lt;code&gt;SHARED&lt;/code&gt; in which users are to create their own assets.<br /> <br /> You start by creating a folder in this space; it is probably better if it matches the name of your group or team, e.g.:<br /> <br /> &lt;code&gt;mkdir /lustre/nobackup/SHARED/myTeamWorkspace&lt;/code&gt; <br /> <br /> Or in alternative:<br /> <br /> &lt;code&gt;cd /lustre/nobackup/SHARED<br /> <br /> mkdir myTeamWorkspace&lt;/code&gt; <br /> <br /> === Setting permissions ===<br /> <br /> Three basic steps are involved in stepping permissions correctly:<br /> <br /> 1. Pass the ownership of the group to the team. In the example below it is applied recursively to all sub-folder and files that may exist:<br /> <br /> &lt;code&gt;chgrp -R my-team-group myTeamWorkspace&lt;/code&gt;<br /> <br /> 2. Concede read/write permissions to the group. This allows other members of the group to read and write in the shared folder. If you wish other team members to only read from the folder then remove the &lt;code&gt;w&lt;/code&gt; character from the &lt;code&gt;+rw&lt;/code&gt; bit:<br /> <br /> &lt;code&gt;chmod -R g+rw myTeamWorkspace&lt;/code&gt;<br /> <br /> 3. Set default ownership within the group. This guarantees that any new files or folders created within the shared folder are owned by default owned by your team group:<br /> <br /> &lt;code&gt;chmod -R g+s myTeamWorkspace&lt;/code&gt;<br /> <br /> In case the contents of the shared are sensitive or private, and should be accessed by your team, you can block access from any other users with the following command:<br /> <br /> &lt;code&gt;chmod -R o-rw myTeamWorkspace&lt;/code&gt;<br /> <br /> == Further reading ==<br /> <br /> [https://www.digitalocean.com/community/tutorials/an-introduction-to-linux-permissions An Introduction to Linux Permissions]<br /> <br /> [https://www.linode.com/docs/tools-reference/linux-users-and-groups/ Linux Users and Groups]<br /> <br /> [https://www.digitalocean.com/community/tutorials/linux-permissions-basics-and-how-to-use-umask-on-a-vps#types-of-permissions Linux Permissions Basics and How to Use Umask on a VPS]<br /> <br /> [http://www.yolinux.com/TUTORIALS/LinuxTutorialManagingGroups.html Linux Tutorial - Managing Group Access on Linux and UNIX]</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Parallel_R_code_on_SLURM&diff=1950 2019-02-19T19:07:30Z

<p>Vaend001: </p> <hr /> <div><br /> == Using R code on SLURM for embarrassingly parallel calculations ==<br /> <br /> The most well-known R packages that provide parallel functionality, e.g. doParallel or doSNOW, do not work properly on Anunna. 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.<br /> <br /> === Example code ===<br /> &lt;code lang='R'&gt;library(rslurm)<br /> sjob &lt;- slurm_apply(test_func, pars, jobname = 'test_apply',<br /> nodes = 2, cpus_per_node = 2, submit = FALSE)&lt;/code&gt;<br /> <br /> Please be aware that new Slurm jobs will have a few seconds of lead time before executing, so try to make sure that your new tasks are appropriately long-living (~60s is a good minimum). Otherwise most of your 'compute' time will be waiting for jobs to start and stop.<br /> <br /> == External links ==<br /> [https://cran.r-project.org/web/packages/rslurm/vignettes/rslurm.html Vignette for the rslurm package]</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=History_of_the_Cluster&diff=1949 2019-02-19T19:05:45Z

<p>Vaend001: </p> <hr /> <div><br /> == Rationale and Requirements for a new cluster ==<br /> [[File:Breed4food-logo.jpg|thumb|right|200px|The Breed4Food logo]]<br /> 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.<br /> {{-}}<br /> <br /> == Process of acquisition and financing ==<br /> <br /> [[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.]]<br /> 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.<br /> {{-}}<br /> <br /> == Architecture of the cluster ==<br /> [[Architecture_of_the_HPC | Main Article: Architecture of the Agrogenomics HPC]]<br /> [[File:Cluster_scheme.png|thumb|right|600px|Schematic overview of the cluster.]]<br /> 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.<br /> {{-}}</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Mailinglist&diff=1948 2019-02-19T19:03:55Z

<p>Vaend001: </p> <hr /> <div>== Available mailling lists ==<br /> In order to improve collaboration between Anunna users and to provide an easy to use platform in order to exchange ideas, Anunna has a public mailing list service available.<br /> <br /> More info about the software itself, mailman, can be found on this [http://www.list.org/ website].<br /> <br /> All users are automatically added to the mailing list on registration, but if you're not, then subscribe to the [https://master1.anunna.wur.nl/mailman/listinfo/ Annuna's] mailing list. Via the website you will be able to start the subscription process.<br /> <br /> Information about which lists are hosted on Anunna, is available [https://master1.anunna.wur.nl/mailman/listinfo here].</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Mailinglist&diff=1947 2019-02-19T19:00:56Z

<p>Vaend001: </p> <hr /> <div>== Available mailling lists ==<br /> In order to improve collaboration between Anunna users and to provide an easy to use platform in order to exchange ideas, Anunna has a public mailing list service available.<br /> <br /> More info about the software itself, mailman, can be found on this [http://www.list.org/ website].<br /> <br /> All users are automatically added to the mailing list on registration, but if you're not, then subscribe to the [https://master1.anunna.wur.nl/mailman/listinfo/hpcag hpcag] list. Via the website you will be able to start the subscription process.<br /> <br /> Information about which lists are hosted on anunna, is available [https://master1.anunna.wur.nl/mailman/listinfo here].</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=SACCT&diff=1946 2019-02-19T18:58:25Z

<p>Vaend001: </p> <hr /> <div>The command [http://slurm.schedmd.com/sacct.html sacct] is ment to show your costs from Anunna.<br /> <br /> For instance at the login screen the command: sacct -a gives the following result:<br /> <br /> '''[test001@nfs01 ~]$ sacct -a'''<br /> <br /> [[File:sacct capture.jpg]]<br /> <br /> It is a standard view to see all the users jobs of that day.<br /> Better is to modify this command with special parameters to see what you are using from Anunna.<br /> <br /> '''[test001@nfs01 ~]$ sacct -X --format=comment%15,User,Partition%20,JobID,JobName,ncpus,nnodes,NodeList,Start,alloccpus,cputime%12,cputimeraw,state -S 03.01.14 -E 04.01.14 &gt;report20140304.txt'''<br /> <br /> The txt-file can be uploaded in Excel. This gives you the next overview. <br /> Cputimeraw is the time of cpu-usage in seconds. The parameters &quot;-S 03.01.14 -E 04.01.14&quot; give you the start date and the end date of period you want to present.<br /> <br /> [[File:sacct uitgebreid.jpg]]</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Using_environment_modules&diff=1945 2019-02-19T18:56:50Z

<p>Vaend001: </p> <hr /> <div>=== Environment Modules ===<br /> [http://modules.sourceforge.net/ Environment modules] are a simple way to allow multiple potentially clashing programs to coexist on a large shared machine such as an HPC. It allows a user to specify exactly which programs are loaded, and even which version of each program, whilst simultaneously allowing the administrator the ability to automatically configure the appropriate environment variables for the system itself.<br /> <br /> == Viewing Modules ==<br /> Upon logging in to Anunna, you should find that when you do:<br /> module list<br /> <br /> You will see something like this:<br /> &lt;source lang='bash'&gt;<br /> -bash-4.1$ module list<br /> Currently Loaded Modulefiles:<br /> 1) shared 2) slurm/2.5.7<br /> &lt;/source&gt;<br /> <br /> This is a list of all loaded modules in your shell session. To get a list of all available modules, simply<br /> module available<br /> <br /> And this will show you the (very exhaustive) list of modules on Anunna:<br /> <br /> &lt;source lang='bash'&gt;<br /> -bash-4.1$ module avail<br /> <br /> ---------------------------- /cm/shared/modulefiles ----------------------------<br /> acml/gcc/64/5.3.1 netcdf/gcc/64/4.1.3<br /> acml/gcc/fma4/5.3.1 netcdf/gcc/64/4.3.0<br /> acml/gcc/mp/64/5.3.1 netcdf/gcc/64/4.3.2<br /> acml/gcc/mp/fma4/5.3.1 netcdf/gcc/64/4.3.3<br /> acml/gcc-int64/64/5.3.1 netcdf/gcc/64/4.3.3.1<br /> acml/gcc-int64/fma4/5.3.1 netcdf/intel/64/4.1.3<br /> ...<br /> &lt;/source&gt;<br /> <br /> Let's look at each of these module names. Each module is named for the application it provides, plus a subfolder of which compiler it was compiled with (if compiled), the number of address bits or options (if compiled), and the version.<br /> <br /> If you want to see a list for a specific module, you can<br /> module avail netcdf<br /> <br /> And the complete list of versions will be shown.<br /> <br /> == Loading Modules ==<br /> To load a module, simply<br /> module load foo<br /> <br /> And the most recent version of module foo will automatically be loaded. If foo is compiled, it will automatically select the gcc version. If you want to specify a certain version, then<br /> module load foo/gcc/64/1.0.0<br /> <br /> Will load foo version 1, compiled with gcc. Be advised that this may not always work, as some modules are not compatible with each other, but a message will be shown if this is the case. Additionally, some modules will automatically load other modules with them for them to operate.<br /> <br /> == Unloading Modules ==<br /> If you want to remove a module that you've loaded, then<br /> module unload foo<br /> <br /> Will remove all module foo's loaded.<br /> <br /> <br /> == Example ==<br /> Consider this simple python3 script that should calculate Pi to 1 million digits:<br /> &lt;source lang='python'&gt;<br /> from decimal import *<br /> D=Decimal<br /> getcontext().prec=10000000<br /> p=sum(D(1)/16**k*(D(4)/(8*k+1)-D(2)/(8*k+4)-D(1)/(8*k+5)-D(1)/(8*k+6))for k in range(411))<br /> print(str(p)[:10000002])<br /> &lt;/source&gt; <br /> <br /> This script will not run at all in the default 2.4 version of Python on the cluster. In order for this script to run you must use Python3. To do this, first list all versions of Python:<br /> &lt;source lang='bash'&gt;<br /> -bash-4.1$ module avail python<br /> <br /> ---------------------------- /cm/shared/modulefiles ----------------------------<br /> python/2.7.6 python/3.3.3 python/3.4.2<br /> &lt;/source&gt;<br /> <br /> Then you can load the specific version you need:<br /> module load python/3.3.3<br /> <br /> Now you have access to the executable python3.<br /> <br /> == See also ==<br /> * [[B4F_cluster | B4F Cluster]]<br /> * [[Lx6_and_Lx7_compute_nodes | Lx6 and Lx7 compute nodes]]<br /> * [[Environment_Modules | Environment Modules]]<br /> * [[Control_R_environment_using_modules | Control R environment using modules]]<br /> * [[Create_shortcut_log-in_command | Create a shortcut for the ssh log-in command]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> <br /> == External links ==<br /> * http://modules.sourceforge.net<br /> * http://www.admin-magazine.com/HPC/Articles/Environment-Modules</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=BCM_on_Anunna&diff=1944 2019-02-19T18:52:15Z

<p>Vaend001: </p> <hr /> <div>Computing clusters are usually managed by [http://en.wikipedia.org/wiki/Cluster_manager cluster managing software]. Anunna uses the cluster management sofware from [http://www.brightcomputing.com Bright ]. BCM is currently is a popular choice for compute clusters of any size, including some very large ones. Bright is a spin-off from [http://www.clustervision.com ClusterVision], the company that aided in implementing the cluster. Furthermore, ClusterVision and [http://www.clustervision.com/eNews/Nov2012/Headlines/Dell Dell] have engaged in a strategic alliance, and BCM is currently very often the [http://www.brightcomputing.com/News-Bright-Computing-Collaborates-with-Dell-for-Genomic-Analysis.php default cluster manager software in Dell-based clusters].<br /> <br /> ''' IMPORTANT - DO NOT TAKE THESE GRAPHS SERIOUSLY - THEY ARE NOT BASED ON RESERVED RESOURCES BUT USED RESOURCES, SO ARE USELESS FOR TELLING IF ANUNNA IS EMPTY! '''<br /> <br /> == Logging into Bright Cluster Manager Portal ==<br /> <br /> Logging into the BCM Portal can be done through a web browser. The address for the portal is:<br /> https://portal.anunna.wur.nl/userportal<br /> <br /> [[File:BCM_loggin.png|thumb|left|500px]]<br /> {{-}}<br /> <br /> == Using the Bright Cluster Manager Portal ==<br /> Through the portal various parameters and statistics can be found. This includes the architecture of the cluster, including available nodes, queues (partitions) etc, as well as the availability and current use of resources.<br /> [[File:BCM.png|thumb|left|600px]]<br /> {{-}}<br /> <br /> == Further reading is provided through the BCM Portal ==<br /> The portal offers various links that can be of interest to users of Anunna.<br /> [[File:BCM_docs.png|thumb|left|600px]]<br /> {{-}}<br /> <br /> == external links ==<br /> * [http://www.brightcomputing.com Official website of Bright Computing ]</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Main_Page&diff=1943 2019-02-19T18:14:49Z

<p>Vaend001: </p> <hr /> <div>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 &amp; 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. <br /> <br /> = Using Anunna =<br /> == Gaining access to Anunna==<br /> Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP].<br /> * [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]<br /> * [[Services | Alternative access methods, and extra features and services on Anunna]]<br /> * [[Filesystems | Accessible storage methods on Anunna]]<br /> <br /> == Access Policy ==<br /> [[Access_Policy | Main Article: Access Policy]]<br /> <br /> 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 CAT-AGRO or FB-ICT.<br /> <br /> = Events =<br /> * [[Courses]] that have happened and are happening<br /> * [[Downtime]] that will affect all users<br /> * [[Meetings]] that may affect the policies of Anunna<br /> <br /> = Other Software =<br /> <br /> == Cluster Management Software and Scheduler ==<br /> Anunna uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.<br /> * [[BCM_on_B4F_cluster | Monitor cluster status with BCM]]<br /> * [[SLURM_on_B4F_cluster | Submit jobs with Slurm]]<br /> * [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']]<br /> * [[SLURM_Compare | Rosetta Stone of Workload Managers]]<br /> <br /> == Installation of software by users ==<br /> <br /> * [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]<br /> * [[Setting local variables]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> * [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]<br /> * [[Installing WRF and WPS]]<br /> <br /> == Installed software ==<br /> <br /> * [[Globally_installed_software | Globally installed software]]<br /> * [[ABGC_modules | ABGC specific modules]]<br /> <br /> = Useful Notes = <br /> <br /> == Being in control of Environment parameters ==<br /> <br /> * [[Using_environment_modules | Using environment modules]]<br /> * [[Setting local variables]]<br /> * [[Setting_TMPDIR | Set a custom temporary directory location]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> <br /> == Controlling costs ==<br /> <br /> * [[SACCT | using SACCT to see your costs]]<br /> * [[get_my_bill | using the &quot;get_my_bill&quot; script to estimate costs]]<br /> <br /> == Management ==<br /> Project Leader of Anunna is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:lith010 | Jan van Lith (Wageningen UR,FB-IT, Infrastructure)]], [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] and [[User:vaend001 | Catharina Vaendel(Wageningen UR,FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]].<br /> <br /> = Miscellaneous =<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[History_of_the_Cluster | Historical information on the startup of Anunna]]<br /> * [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]<br /> * [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]<br /> * [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]<br /> * [[Manual GitLab | GitLab: Create projects and add scripts]]<br /> * [[Monitoring_executions | Monitoring job execution]]<br /> * [[Shared_folders | Working with shared folders in the Lustre file system]]<br /> <br /> = See also =<br /> * [[Maintenance_and_Management | Maintenance and Management]]<br /> * [[BCData | BCData]]<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[About_ABGC | About ABGC]]<br /> * [[Computer_cluster | High Performance Computing @ABGC]]<br /> * [[Lustre_PFS_layout | Lustre Parallel File System layout]]<br /> <br /> = External links =<br /> {| width=&quot;90%&quot;<br /> |- valign=&quot;top&quot;<br /> | width=&quot;30%&quot; |<br /> * [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]<br /> * [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]<br /> * [http://www.cobb-vantress.com Cobb-Vantress homepage]<br /> <br /> | width=&quot;30%&quot; |<br /> * [https://www.crv4all.nl CRV homepage]<br /> * [http://www.hendrix-genetics.com Hendrix Genetics homepage]<br /> * [http://www.topigs.com TOPIGS homepage]<br /> | width=&quot;30%&quot; |<br /> * [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]<br /> * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]<br /> |}</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Main_Page&diff=1942 2019-02-19T18:13:57Z

<p>Vaend001: </p> <hr /> <div>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 &amp; 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. <br /> <br /> = Using Anunna =<br /> == Gaining access to Anunna==<br /> Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP].<br /> * [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]<br /> * [[Services | Alternative access methods, and extra features and services on Anunna]]<br /> * [[Filesystems | Accessible storage methods on Anunna]]<br /> <br /> == Access Policy ==<br /> [[Access_Policy | Main Article: Access Policy]]<br /> <br /> 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 CAT-AGRO or FB-ICT.<br /> <br /> = Events =<br /> * [[Courses]] that have happened and are happening<br /> * [[Downtime]] that will affect all users<br /> * [[Meetings]] that may affect the policies of Anunna<br /> <br /> = Other Software =<br /> <br /> == Cluster Management Software and Scheduler ==<br /> Anunna uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.<br /> * [[BCM_on_B4F_cluster | Monitor cluster status with BCM]]<br /> * [[SLURM_on_B4F_cluster | Submit jobs with Slurm]]<br /> * [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']]<br /> * [[SLURM_Compare | Rosetta Stone of Workload Managers]]<br /> <br /> == Installation of software by users ==<br /> <br /> * [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]<br /> * [[Setting local variables]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> * [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]<br /> * [[Installing WRF and WPS]]<br /> <br /> == Installed software ==<br /> <br /> * [[Globally_installed_software | Globally installed software]]<br /> * [[ABGC_modules | ABGC specific modules]]<br /> <br /> = Useful Notes = <br /> <br /> == Being in control of Environment parameters ==<br /> <br /> * [[Using_environment_modules | Using environment modules]]<br /> * [[Setting local variables]]<br /> * [[Setting_TMPDIR | Set a custom temporary directory location]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> <br /> == Controlling costs ==<br /> <br /> * [[SACCT | using SACCT to see your costs]]<br /> * [[get_my_bill | using the &quot;get_my_bill&quot; script to estimate costs]]<br /> <br /> == Management ==<br /> [[Anunna | Main Article: Anunna management]]<br /> <br /> Project Leader of Anunna is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:lith010 | Jan van Lith (Wageningen UR,FB-IT, Infrastructure)]], [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] and [[User:vaend001 | Catharina Vaendel(Wageningen UR,FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]].<br /> <br /> = Miscellaneous =<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[History_of_the_Cluster | Historical information on the startup of Anunna]]<br /> * [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]<br /> * [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]<br /> * [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]<br /> * [[Manual GitLab | GitLab: Create projects and add scripts]]<br /> * [[Monitoring_executions | Monitoring job execution]]<br /> * [[Shared_folders | Working with shared folders in the Lustre file system]]<br /> <br /> = See also =<br /> * [[Maintenance_and_Management | Maintenance and Management]]<br /> * [[BCData | BCData]]<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[About_ABGC | About ABGC]]<br /> * [[Computer_cluster | High Performance Computing @ABGC]]<br /> * [[Lustre_PFS_layout | Lustre Parallel File System layout]]<br /> <br /> = External links =<br /> {| width=&quot;90%&quot;<br /> |- valign=&quot;top&quot;<br /> | width=&quot;30%&quot; |<br /> * [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]<br /> * [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]<br /> * [http://www.cobb-vantress.com Cobb-Vantress homepage]<br /> <br /> | width=&quot;30%&quot; |<br /> * [https://www.crv4all.nl CRV homepage]<br /> * [http://www.hendrix-genetics.com Hendrix Genetics homepage]<br /> * [http://www.topigs.com TOPIGS homepage]<br /> | width=&quot;30%&quot; |<br /> * [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]<br /> * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]<br /> |}</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Main_Page&diff=1941 2019-02-19T18:13:44Z

<p>Vaend001: </p> <hr /> <div>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 &amp; 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. <br /> <br /> = Using Anunna =<br /> == Gaining access to Anunna==<br /> Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP].<br /> * [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]<br /> * [[Services | Alternative access methods, and extra features and services on Anunna]]<br /> * [[Filesystems | Accessible storage methods on Anunna]]<br /> <br /> == Access Policy ==<br /> [[Access_Policy | Main Article: Access Policy]]<br /> <br /> 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 CAT-AGRO or FB-ICT.<br /> <br /> = Events =<br /> * [[Courses]] that have happened and are happening<br /> * [[Downtime]] that will affect all users<br /> * [[Meetings]] that may affect the policies of Anunna<br /> <br /> = Other Software =<br /> <br /> == Cluster Management Software and Scheduler ==<br /> Anunna uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.<br /> * [[BCM_on_B$F_cluster | Monitor cluster status with BCM]]<br /> * [[SLURM_on_B4F_cluster | Submit jobs with Slurm]]<br /> * [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']]<br /> * [[SLURM_Compare | Rosetta Stone of Workload Managers]]<br /> <br /> == Installation of software by users ==<br /> <br /> * [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]<br /> * [[Setting local variables]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> * [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]<br /> * [[Installing WRF and WPS]]<br /> <br /> == Installed software ==<br /> <br /> * [[Globally_installed_software | Globally installed software]]<br /> * [[ABGC_modules | ABGC specific modules]]<br /> <br /> = Useful Notes = <br /> <br /> == Being in control of Environment parameters ==<br /> <br /> * [[Using_environment_modules | Using environment modules]]<br /> * [[Setting local variables]]<br /> * [[Setting_TMPDIR | Set a custom temporary directory location]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> <br /> == Controlling costs ==<br /> <br /> * [[SACCT | using SACCT to see your costs]]<br /> * [[get_my_bill | using the &quot;get_my_bill&quot; script to estimate costs]]<br /> <br /> == Management ==<br /> [[Anunna | Main Article: Anunna management]]<br /> <br /> Project Leader of Anunna is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:lith010 | Jan van Lith (Wageningen UR,FB-IT, Infrastructure)]], [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] and [[User:vaend001 | Catharina Vaendel(Wageningen UR,FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]].<br /> <br /> = Miscellaneous =<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[History_of_the_Cluster | Historical information on the startup of Anunna]]<br /> * [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]<br /> * [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]<br /> * [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]<br /> * [[Manual GitLab | GitLab: Create projects and add scripts]]<br /> * [[Monitoring_executions | Monitoring job execution]]<br /> * [[Shared_folders | Working with shared folders in the Lustre file system]]<br /> <br /> = See also =<br /> * [[Maintenance_and_Management | Maintenance and Management]]<br /> * [[BCData | BCData]]<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[About_ABGC | About ABGC]]<br /> * [[Computer_cluster | High Performance Computing @ABGC]]<br /> * [[Lustre_PFS_layout | Lustre Parallel File System layout]]<br /> <br /> = External links =<br /> {| width=&quot;90%&quot;<br /> |- valign=&quot;top&quot;<br /> | width=&quot;30%&quot; |<br /> * [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]<br /> * [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]<br /> * [http://www.cobb-vantress.com Cobb-Vantress homepage]<br /> <br /> | width=&quot;30%&quot; |<br /> * [https://www.crv4all.nl CRV homepage]<br /> * [http://www.hendrix-genetics.com Hendrix Genetics homepage]<br /> * [http://www.topigs.com TOPIGS homepage]<br /> | width=&quot;30%&quot; |<br /> * [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]<br /> * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]<br /> |}</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Main_Page&diff=1940 2019-02-19T18:12:52Z

<p>Vaend001: </p> <hr /> <div>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 &amp; 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. <br /> <br /> = Using Anunna =<br /> == Gaining access to Anunna==<br /> Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP].<br /> * [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]<br /> * [[Services | Alternative access methods, and extra features and services on Anunna]]<br /> * [[Filesystems | Accessible storage methods on Anunna]]<br /> <br /> == Access Policy ==<br /> [[Access_Policy | Main Article: Access Policy]]<br /> <br /> 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 CAT-AGRO or FB-ICT.<br /> <br /> = Events =<br /> * [[Courses]] that have happened and are happening<br /> * [[Downtime]] that will affect all users<br /> * [[Meetings]] that may affect the policies of Anunna<br /> <br /> = Other Software =<br /> <br /> == Cluster Management Software and Scheduler ==<br /> Anunna uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.<br /> * [[BCM_on_Anunna | Monitor cluster status with BCM]]<br /> * [[SLURM_on_B4F_cluster | Submit jobs with Slurm]]<br /> * [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']]<br /> * [[SLURM_Compare | Rosetta Stone of Workload Managers]]<br /> <br /> == Installation of software by users ==<br /> <br /> * [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]<br /> * [[Setting local variables]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> * [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]<br /> * [[Installing WRF and WPS]]<br /> <br /> == Installed software ==<br /> <br /> * [[Globally_installed_software | Globally installed software]]<br /> * [[ABGC_modules | ABGC specific modules]]<br /> <br /> = Useful Notes = <br /> <br /> == Being in control of Environment parameters ==<br /> <br /> * [[Using_environment_modules | Using environment modules]]<br /> * [[Setting local variables]]<br /> * [[Setting_TMPDIR | Set a custom temporary directory location]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> <br /> == Controlling costs ==<br /> <br /> * [[SACCT | using SACCT to see your costs]]<br /> * [[get_my_bill | using the &quot;get_my_bill&quot; script to estimate costs]]<br /> <br /> == Management ==<br /> [[Anunna | Main Article: Anunna management]]<br /> <br /> Project Leader of Anunna is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:lith010 | Jan van Lith (Wageningen UR,FB-IT, Infrastructure)]], [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] and [[User:vaend001 | Catharina Vaendel(Wageningen UR,FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]].<br /> <br /> = Miscellaneous =<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[History_of_the_Cluster | Historical information on the startup of Anunna]]<br /> * [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]<br /> * [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]<br /> * [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]<br /> * [[Manual GitLab | GitLab: Create projects and add scripts]]<br /> * [[Monitoring_executions | Monitoring job execution]]<br /> * [[Shared_folders | Working with shared folders in the Lustre file system]]<br /> <br /> = See also =<br /> * [[Maintenance_and_Management | Maintenance and Management]]<br /> * [[BCData | BCData]]<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[About_ABGC | About ABGC]]<br /> * [[Computer_cluster | High Performance Computing @ABGC]]<br /> * [[Lustre_PFS_layout | Lustre Parallel File System layout]]<br /> <br /> = External links =<br /> {| width=&quot;90%&quot;<br /> |- valign=&quot;top&quot;<br /> | width=&quot;30%&quot; |<br /> * [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]<br /> * [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]<br /> * [http://www.cobb-vantress.com Cobb-Vantress homepage]<br /> <br /> | width=&quot;30%&quot; |<br /> * [https://www.crv4all.nl CRV homepage]<br /> * [http://www.hendrix-genetics.com Hendrix Genetics homepage]<br /> * [http://www.topigs.com TOPIGS homepage]<br /> | width=&quot;30%&quot; |<br /> * [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]<br /> * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]<br /> |}</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=BCM_on_Anunna&diff=1939 2019-02-19T18:11:39Z

<p>Vaend001: </p> <hr /> <div>Computing clusters are usually managed by [http://en.wikipedia.org/wiki/Cluster_manager cluster managing software]. Anunna uses the cluster management sofware from [http://www.brightcomputing.com Bright ]. BCM is currently is a popular choice for compute clusters of any size, including some very large ones. Bright is a spin-off from [http://www.clustervision.com ClusterVision], the company that aided in implementing the cluster. Furthermore, ClusterVision and [http://www.clustervision.com/eNews/Nov2012/Headlines/Dell Dell] have engaged in a strategic alliance, and BCM is currently very often the [http://www.brightcomputing.com/News-Bright-Computing-Collaborates-with-Dell-for-Genomic-Analysis.php default cluster manager software in Dell-based clusters].<br /> <br /> ''' IMPORTANT - DO NOT TAKE THESE GRAPHS SERIOUSLY - THEY ARE NOT BASED ON RESERVED RESOURCES BUT USED RESOURCES, SO ARE USELESS FOR TELLING IF ANUNNA IS EMPTY! '''<br /> <br /> == Logging into Bright Cluster Manager Portal ==<br /> <br /> Logging into the BCM Portal can be done through a web browser. The address for the portal is:<br /> https://portal.anunna.wur.nl/userportal<br /> <br /> [[File:BCM_loggin.png|thumb|left|500px]]<br /> {{-}}<br /> <br /> == Using the Bright Cluster Manager Portal ==<br /> Through the portal various parameters and statistics can be found. This includes the architecture of the cluster, including available nodes, queues (partitions) etc, as well as the availability and current use of resources.<br /> [[File:BCM.png|thumb|left|600px]]<br /> {{-}}<br /> <br /> == Further reading is provided through the BCM Portal ==<br /> The portal offers various links that can be of interest to users of Anunna.<br /> [[File:BCM_docs.png|thumb|left|600px]]<br /> {{-}}<br /> <br /> == See also ==<br /> * [[cluster | Cluster]]<br /> * [[SLURM_on_cluster | Submit jobs with Slurm]]<br /> <br /> == external links ==<br /> * [http://www.brightcomputing.com Official website of Bright Computing ]</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=BCM_on_Anunna&diff=1938 2019-02-19T18:10:17Z

<p>Vaend001: </p> <hr /> <div>Computing clusters are usually managed by [http://en.wikipedia.org/wiki/Cluster_manager cluster managing software]. Anunna uses the cluster management sofware from [http://www.brightcomputing.com Bright ]. BCM is currently is a popular choice for compute clusters of any size, including some very large ones. Bright is a spin-off from [http://www.clustervision.com ClusterVision], the company that aided in implementing the B4F cluster. Furthermore, ClusterVision and [http://www.clustervision.com/eNews/Nov2012/Headlines/Dell Dell] have engaged in a strategic alliance, and BCM is currently very often the [http://www.brightcomputing.com/News-Bright-Computing-Collaborates-with-Dell-for-Genomic-Analysis.php default cluster manager software in Dell-based clusters].<br /> <br /> ''' IMPORTANT - DO NOT TAKE THESE GRAPHS SERIOUSLY - THEY ARE NOT BASED ON RESERVED RESOURCES BUT USED RESOURCES, SO ARE USELESS FOR TELLING IF ANUNNA IS EMPTY! '''<br /> <br /> == Logging into Bright Cluster Manager Portal ==<br /> <br /> Logging into the BCM Portal can be done through a web browser. The address for the portal is:<br /> https://portal.anunna.wur.nl/userportal<br /> <br /> [[File:BCM_loggin.png|thumb|left|500px]]<br /> {{-}}<br /> <br /> == Using the Bright Cluster Manager Portal ==<br /> Through the portal various parameters and statistics can be found. This includes the architecture of the cluster, including available nodes, queues (partitions) etc, as well as the availability and current use of resources.<br /> [[File:BCM.png|thumb|left|600px]]<br /> {{-}}<br /> <br /> == Further reading is provided through the BCM Portal ==<br /> The portal offers various links that can be of interest to users of the B4F cluster.<br /> [[File:BCM_docs.png|thumb|left|600px]]<br /> {{-}}<br /> <br /> == See also ==<br /> * [[cluster | Cluster]]<br /> * [[SLURM_on_cluster | Submit jobs with Slurm]]<br /> <br /> == external links ==<br /> * [http://www.brightcomputing.com Official website of Bright Computing ]</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=BCM_on_Anunna&diff=1937 2019-02-19T18:08:14Z

<p>Vaend001: </p> <hr /> <div>Computing clusters are usually managed by [http://en.wikipedia.org/wiki/Cluster_manager cluster managing software]. The B4F cluster uses the cluster management sofware from [http://www.brightcomputing.com Bright ]. BCM is currently is a popular choice for compute clusters of any size, including some very large ones. Bright is a spin-off from [http://www.clustervision.com ClusterVision], the company that aided in implementing the B4F cluster. Furthermore, ClusterVision and [http://www.clustervision.com/eNews/Nov2012/Headlines/Dell Dell] have engaged in a strategic alliance, and BCM is currently very often the [http://www.brightcomputing.com/News-Bright-Computing-Collaborates-with-Dell-for-Genomic-Analysis.php default cluster manager software in Dell-based clusters].<br /> <br /> ''' IMPORTANT - DO NOT TAKE THESE GRAPHS SERIOUSLY - THEY ARE NOT BASED ON RESERVED RESOURCES BUT USED RESOURCES, SO ARE USELESS FOR TELLING IF ANUNNA IS EMPTY! '''<br /> <br /> == Logging into Bright Cluster Manager Portal ==<br /> <br /> Logging into the BCM Portal can be done through a web browser. The address for the portal is:<br /> https://portal.anunna.wur.nl/userportal<br /> <br /> [[File:BCM_loggin.png|thumb|left|500px]]<br /> {{-}}<br /> <br /> == Using the Bright Cluster Manager Portal ==<br /> Through the portal various parameters and statistics can be found. This includes the architecture of the cluster, including available nodes, queues (partitions) etc, as well as the availability and current use of resources.<br /> [[File:BCM.png|thumb|left|600px]]<br /> {{-}}<br /> <br /> == Further reading is provided through the BCM Portal ==<br /> The portal offers various links that can be of interest to users of the B4F cluster.<br /> [[File:BCM_docs.png|thumb|left|600px]]<br /> {{-}}<br /> <br /> == See also ==<br /> * [[B4F_cluster | B4F Cluster]]<br /> * [[SLURM_on_B4F_cluster | Submit jobs with Slurm]]<br /> <br /> == external links ==<br /> * [http://www.brightcomputing.com Official website of Bright Computing ]</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=BCM_on_Anunna&diff=1936 2019-02-19T18:05:49Z

<p>Vaend001: </p> <hr /> <div>Computing clusters are usually managed by [http://en.wikipedia.org/wiki/Cluster_manager cluster managing software]. The B4F cluster uses the cluster management sofware from [http://www.brightcomputing.com Bright ]. BCM is currently is a popular choice for compute clusters of any size, including some very large ones. Bright is a spin-off from [http://www.clustervision.com ClusterVision], the company that aided in implementing the B4F cluster. Furthermore, ClusterVision and [http://www.clustervision.com/eNews/Nov2012/Headlines/Dell Dell] have engaged in a strategic alliance, and BCM is currently very often the [http://www.brightcomputing.com/News-Bright-Computing-Collaborates-with-Dell-for-Genomic-Analysis.php default cluster manager software in Dell-based clusters].<br /> <br /> ''' IMPORTANT - DO NOT TAKE THESE GRAPHS SERIOUSLY - THEY ARE NOT BASED ON RESERVED RESOURCES BUT USED RESOURCES, SO ARE USELESS FOR TELLING IF ANUNNA IS EMPTY! '''<br /> <br /> == Logging into Bright Cluster Manager Portal ==<br /> <br /> Logging into the BCM Portal can be done through a web browser. The address for the portal is:<br /> https://portal.hpcagrogenomics.wur.nl/userportal<br /> <br /> [[File:BCM_loggin.png|thumb|left|500px]]<br /> {{-}}<br /> <br /> == Using the Bright Cluster Manager Portal ==<br /> Through the portal various parameters and statistics can be found. This includes the architecture of the cluster, including available nodes, queues (partitions) etc, as well as the availability and current use of resources.<br /> [[File:BCM.png|thumb|left|600px]]<br /> {{-}}<br /> <br /> == Further reading is provided through the BCM Portal ==<br /> The portal offers various links that can be of interest to users of the B4F cluster.<br /> [[File:BCM_docs.png|thumb|left|600px]]<br /> {{-}}<br /> <br /> == See also ==<br /> * [[B4F_cluster | B4F Cluster]]<br /> * [[SLURM_on_B4F_cluster | Submit jobs with Slurm]]<br /> <br /> == external links ==<br /> * [http://www.brightcomputing.com Official website of Bright Computing ]</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Main_Page&diff=1935 2019-02-19T17:47:43Z

<p>Vaend001: </p> <hr /> <div>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 &amp; 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. <br /> <br /> = Using Anunna =<br /> == Gaining access to Anunna==<br /> Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP].<br /> * [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]<br /> * [[Services | Alternative access methods, and extra features and services on Anunna]]<br /> * [[Filesystems | Accessible storage methods on Anunna]]<br /> <br /> == Access Policy ==<br /> [[Access_Policy | Main Article: Access Policy]]<br /> <br /> 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 CAT-AGRO or FB-ICT.<br /> <br /> = Events =<br /> * [[Courses]] that have happened and are happening<br /> * [[Downtime]] that will affect all users<br /> * [[Meetings]] that may affect the policies of Anunna<br /> <br /> = Other Software =<br /> <br /> == Cluster Management Software and Scheduler ==<br /> Anunna uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.<br /> * [[BCM_on_B4F_cluster | Monitor cluster status with BCM]]<br /> * [[SLURM_on_B4F_cluster | Submit jobs with Slurm]]<br /> * [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']]<br /> * [[SLURM_Compare | Rosetta Stone of Workload Managers]]<br /> <br /> == Installation of software by users ==<br /> <br /> * [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]<br /> * [[Setting local variables]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> * [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]<br /> * [[Installing WRF and WPS]]<br /> <br /> == Installed software ==<br /> <br /> * [[Globally_installed_software | Globally installed software]]<br /> * [[ABGC_modules | ABGC specific modules]]<br /> <br /> = Useful Notes = <br /> <br /> == Being in control of Environment parameters ==<br /> <br /> * [[Using_environment_modules | Using environment modules]]<br /> * [[Setting local variables]]<br /> * [[Setting_TMPDIR | Set a custom temporary directory location]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> <br /> == Controlling costs ==<br /> <br /> * [[SACCT | using SACCT to see your costs]]<br /> * [[get_my_bill | using the &quot;get_my_bill&quot; script to estimate costs]]<br /> <br /> == Management ==<br /> [[Anunna | Main Article: Anunna management]]<br /> <br /> Project Leader of Anunna is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:lith010 | Jan van Lith (Wageningen UR,FB-IT, Infrastructure)]], [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] and [[User:vaend001 | Catharina Vaendel(Wageningen UR,FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]].<br /> <br /> = Miscellaneous =<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[History_of_the_Cluster | Historical information on the startup of Anunna]]<br /> * [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]<br /> * [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]<br /> * [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]<br /> * [[Manual GitLab | GitLab: Create projects and add scripts]]<br /> * [[Monitoring_executions | Monitoring job execution]]<br /> * [[Shared_folders | Working with shared folders in the Lustre file system]]<br /> <br /> = See also =<br /> * [[Maintenance_and_Management | Maintenance and Management]]<br /> * [[BCData | BCData]]<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[About_ABGC | About ABGC]]<br /> * [[Computer_cluster | High Performance Computing @ABGC]]<br /> * [[Lustre_PFS_layout | Lustre Parallel File System layout]]<br /> <br /> = External links =<br /> {| width=&quot;90%&quot;<br /> |- valign=&quot;top&quot;<br /> | width=&quot;30%&quot; |<br /> * [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]<br /> * [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]<br /> * [http://www.cobb-vantress.com Cobb-Vantress homepage]<br /> <br /> | width=&quot;30%&quot; |<br /> * [https://www.crv4all.nl CRV homepage]<br /> * [http://www.hendrix-genetics.com Hendrix Genetics homepage]<br /> * [http://www.topigs.com TOPIGS homepage]<br /> | width=&quot;30%&quot; |<br /> * [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]<br /> * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]<br /> |}</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Maintenance_and_Management&diff=1934 2019-02-19T17:43:25Z

<p>Vaend001: </p> <hr /> <div>== Maintenance and Management ==<br /> <br /> The cluster is maintained for firmware and software updates on a six-monthly basis. Typically one downtime is scheduled in May, whilst the other is scheduled in November, in order to disrupt usage as little as possible.<br /> <br /> Any issues should be directed to the WUR IT Servicedesk:<br /> <br /> This can be done via the mail: servicedesk.it@wur.nl <br /> And it can be done via the telephone: +31 317 488888<br /> Please give your name and phonenumber and tell that your mail/call is about Anunna and give the company you are working for.<br /> When you call the servicedesk, give also your email address.<br /> <br /> == Previous Maintenance Windows ==<br /> <br /> === Maintenance May 24th 2017 ===<br /> This update moved Bright Cluster Manager to version 7.3, and SLURM to 16.08. Downtime was 8am to 8pm.<br /> <br /> === Maintenance November 16th 2016 ===<br /> This was a firmware update and OS update for the system. Downtime was 8am to 8pm.<br /> <br /> === Maintenance May 23rd-29th 2016 ===<br /> This update moved the OS from Scientific Linux 6 to Scientific Linux 7, and updated Bright Cluster manager to version 7.2. A week was taken to reconstruct the entire environment from scratch, thanks to assistance from Clustervision for this expedience.<br /> <br /> === Maintenance March 23rd 2016 ===<br /> There will be mainly firmware maintenance between 8h and 20h CET . Because network controller and storage controller firmware will be upgrades, all servers need to be rebooted and also will have network hick ups. So to prevent job and/or data corruption, Anunna will be shut down during this maintenance window. Running jobs will be killed!<br /> <br /> === Maintenance June 17th 2015 ===<br /> There will be mainly firmware maintenance between 8h and 20h CET . Because network controller and storage controller firmware will be upgrades, all servers need to be rebooted and also will have network hick ups. So to prevent job and/or data corruption, Anunna will be shut down during this maintenance window. Running jobs will be killed!<br /> <br /> === Maintenance November 26th 2014 ===<br /> There will be mainly firmware maintenance between 8h and 20h CET . Because network controller and storage controller firmware will be upgrades, all servers need to be rebooted and also will have network hick ups. So to prevent job and/or data corruption, Anunna will be shut down during this maintenance window. Running jobs will be killed!<br /> <br /> === Maintenance June 11th 2014 ===<br /> There will be mainly firmware maintenance between 8h and 13h CET . Because network controller and storage controller firmware will be upgrades, all servers need to be rebooted and also will have network hick ups. So to prevent job and/or data corruption, Anunna will be shut down during this maintenance window. Running jobs will be killed!</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Maintenance_and_Management&diff=1933 2019-02-19T17:42:17Z

<p>Vaend001: </p> <hr /> <div>== Maintenance and Management ==<br /> <br /> The cluster is maintained for firmware and software updates on a six-monthly basis. Typically one downtime is scheduled in May, whilst the other is scheduled in November, in order to disrupt usage as little as possible.<br /> <br /> Any issues should be directed to the WUR IT Servicedesk:<br /> <br /> This can be done via the mail: servicedesk.it@wur.nl <br /> And it can be done via the telephone: +31 317 488888<br /> Please give your name and phonenumber and tell that your mail/call is about Anunna and give the company you are working for.<br /> When you call the servicedesk, give also your email address.<br /> <br /> == Previous Maintenance Windows ==<br /> <br /> === Maintenance May 24th 2017 ===<br /> This update moved Bright Cluster Manager to version 7.3, and SLURM to 16.08. Downtime was 8am to 8pm.<br /> <br /> === Maintenance November 16th 2016 ===<br /> This was a firmware update and OS update for the system. Downtime was 8am to 8pm.<br /> <br /> === Maintenance May 23rd-29th 2016 ===<br /> This update moved the OS from Scientific Linux 6 to Scientific Linux 7, and updated Bright Cluster manager to version 7.2. A week was taken to reconstruct the entire environment from scratch, thanks to assistance from Clustervision for this expedience.<br /> <br /> === Maintenance March 23rd 2016 ===<br /> There will be mainly firmware maintenance between 8h and 20h CET . Because network controller and storage controller firmware will be upgrades, all servers need to be rebooted and also will have network hick ups. So to prevent job and/or data corruption, the HPC will be shut down during this maintenance window. Running jobs will be killed!<br /> <br /> === Maintenance June 17th 2015 ===<br /> There will be mainly firmware maintenance between 8h and 20h CET . Because network controller and storage controller firmware will be upgrades, all servers need to be rebooted and also will have network hick ups. So to prevent job and/or data corruption, the HPC will be shut down during this maintenance window. Running jobs will be killed!<br /> <br /> === Maintenance November 26th 2014 ===<br /> There will be mainly firmware maintenance between 8h and 20h CET . Because network controller and storage controller firmware will be upgrades, all servers need to be rebooted and also will have network hick ups. So to prevent job and/or data corruption, the HPC will be shut down during this maintenance window. Running jobs will be killed!<br /> <br /> === Maintenance June 11th 2014 ===<br /> There will be mainly firmware maintenance between 8h and 13h CET . Because network controller and storage controller firmware will be upgrades, all servers need to be rebooted and also will have network hick ups. So to prevent job and/or data corruption, the HPC will be shut down during this maintenance window. Running jobs will be killed!</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Meetings&diff=1932 2019-02-19T17:41:25Z

<p>Vaend001: </p> <hr /> <div>The Steering Committee meets once every quarter to discuss progress and direction for Anunna.</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Access_Policy&diff=1931 2019-02-19T17:30:46Z

<p>Vaend001: </p> <hr /> <div>Access policy is still a work in progress. In principle, all staff and students of the five main partners will have access to Anunna. Access needs to be granted actively (by creation of an account on the cluster by FB-IT reagdring non WUR accounts). 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. <br /> <br /> == Contact Persons ==<br /> A request to access the cluster needs to be directed to one of the following persons (please refer to appropriate partner):<br /> <br /> === WUR ===<br /> ==== ESG ====<br /> * Ronald Hutjes<br /> * Kees van den Dries<br /> <br /> ==== Bioinformatics ====<br /> * Dick de Ridder<br /> <br /> ==== PRI ====<br /> * Jens Allmer (formerly Gabino Sanches-Perez)<br /> <br /> ==== ABGC ====<br /> ===== Animal Breeding and Genetics =====<br /> * [[User:Hulze001 |Alex Hulzebosch]]<br /> * [[User:Megen002 | Hendrik-Jan Megens]]<br /> ===== Wageningen Livestock Research =====<br /> * Mario Calus<br /> * Ina Hulsegge<br /> <br /> === Cobb-Vantress ===<br /> * Wes Barris<br /> * Jun Chen<br /> === CRV ===<br /> * Frido Hamoen<br /> * Chris Schrooten<br /> === Hendrix Genetics === <br /> * Ton Dings<br /> * Abe Huisman<br /> * Addie Vereijken<br /> === Topigs ===<br /> * [[User:dongen01 | Henk van Dongen]]<br /> * Egiel Hanenbarg<br /> * Naomi Duijvensteijn<br /> <br /> == See also ==<br /> [[Main_Page | Main page]]</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=HPCwiki:About&diff=1930 2019-02-19T17:27:41Z

<p>Vaend001: </p> <hr /> <div>This Wiki is intended for members and affiliates of Anunna of Wageningen UR only.</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Filesystems&diff=1929 2019-02-19T17:26:50Z

<p>Vaend001: </p> <hr /> <div>Anunna currently has multiple filesystem mounts that are available cluster-wide:<br /> <br /> == Global ==<br /> * /home - This mount uses NFS to mount the home directories directly from nfs01. Each user has a 200G quota for this filesystem, as it is regularly backed up to tape, and can reliably be restored from up to a week's history.<br /> <br /> * /cm/shared - This mount provides a consistent set of binaries for the entire cluster.<br /> <br /> * /lustre - This large mount uses the Lustre filesystem to provide files from multiple redundant servers. Access is provided per group, thus:<br /> /lustre/[level]/[partner]/[unit]<br /> e.g.<br /> /lustre/backup/WUR/ABGC/<br /> It comprises of three major parts (and some minor):<br /> * /lustre/backup - In case of disaster, this data is stored a second time on a separate machine. Whilst this backup is purely in case of complete tragedy (such as some immense filesystem error, or multiple component failure), it can potentially be used to revert mistakes if you are very fast about reporting them. There is however no guarantee of this service.<br /> * /lustre/nobackup - This is the 'normal' filesystem for Lustre - no backups, just stored on the filesystem. Without having a backup needed, the cost of data here is not as much as under /lustre/backup, but in case of disaster cannot be recivered.<br /> * /lustre/scratch - Files here may be removed after some time if the filesystem gets too full (Typically 30 days). You should tidy up this data yourself once work is complete.<br /> * /lustre/shared - Same as /lustre/backup, except publicly available. This is where truly shared data lives that isn't assigned to a specific group.<br /> <br /> === Private shared directories ===<br /> If you are working with a group of users on a similar project, you might consider making a [[Shared_folders|Shared directory]] to coordinate. Information on how to do so is in the linked article.<br /> <br /> == Local ==<br /> Specific to certain machines are some other filesystems that are available to you:<br /> * /archive - an archive mount only accessible from the login nodes. Files here are sent to the Isilon for deeper storage. The cost of storing data here is much less than on the Lustre, but it cannot be used for compute work. This location is only available to WUR users. Files are able to be reverted via snapshot, and there is a separated backup, however this only comes in fortnightly (14 day) intervals.<br /> <br /> * /tmp - On each worker node there is a /tmp mount that can be used for temporary local caching. Be advised that you should clean this up, lest your files become a hindrance to other users. You can request a node with free space in your sbatch script like so:<br /> &lt;source lang='bash'&gt;<br /> #SBATCH --tmp=&lt;required space&gt;<br /> &lt;/source&gt;<br /> <br /> <br /> * /dev/shm - On each worker you may also create a virtual filesystem directly into memory, for extremely fast data access. Be advised that this will count against the memory used for your job, but it is also the fastest available filesystem if needed.<br /> <br /> <br /> == See also ==<br /> * [[B4F_cluster | B4F cluster]]<br /> <br /> == External links ==<br /> * [http://wiki.lustre.org/index.php/Main_Page Lustre website]</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Services&diff=1928 2019-02-19T17:24:55Z

<p>Vaend001: Edited HPC names to Anunna</p> <hr /> <div>Several additional services are also attached to Anunna's environment:<br /> <br /> * [https://wiki.anunna.wur.nl This wiki] is what you're looking at now.<br /> * [https://mail.anunna.wur.nl Mailman] is in charge of whichever mailing lists are organised for Anunna.<br /> * [https://galaxy.anunna.wur.nl Galaxy] is a point-and-click friendly way of running genomics pipelines, which offloads the workload onto Anunna.<br /> * [https://rstudio.anunna.wur.nl R Studio Server] is a web-accessible R interpreter.<br /> * [https://notebook.anunna.wur.nl Jupyterhub] , the Jupyter notebook server, is a web-accessible environment for many languages. Primarily Python, includes R, octave, Julia etc.</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Log_in_to_Anunna&diff=1927 2019-02-19T17:24:28Z

<p>Vaend001: </p> <hr /> <div>== Log on using ssh ==<br /> One can log into the [[B4F_cluster | B4F Cluster]] (more specifically the nfs server) using ssh (default port tcp 22). The address of the login server is:<br /> login.anunna.wur.nl<br /> <br /> You will be automatically redirected to the currently valid login server. To log on one has to use an ssh ([http://en.wikipedia.org/wiki/Secure_Shell secure shell]) client. Such client systems are always available from Linux or MacOS systems. For Windows an ssh-client may need to be installed. The most popular ssh-client for Windows is [http://www.chiark.greenend.org.uk/~sgtatham/putty/ PuTTY].<br /> <br /> Note that current access may be restricted to certain IP-ranges. Furthermore, ssh-protocols may be prohibited on systems where port 22 is unavailable due to firewall.<br /> <br /> The ssh-connection can also be configured to work [[ssh_without_password | without password]], which means that no password needs to be provided at each log-in or secure copy attempt.<br /> <br /> '''IMPORTANT: the Login server can only act as access point and is not to be used for any serious CPU or RAM intensive work.''' <br /> '''Anything requiring even moderate resources should be [[SLURM_on_B4F_cluster |scheduled using SLURM!]]'''<br /> <br /> === CLI from a Linux/MacOSX terminal ===<br /> A Command Line Interface ([http://en.wikipedia.org/wiki/Command-line_interface CLI]) ssh client is available from any Linux or MacOSX terminal. Secure shell (ssh) protocols require port 22 to be open. Should a connection be refused, the firewall settings of the system should be checked. Alternatively, local ICT regulations may prohibit the use of port 22. Wageningen UR FB-ICT for instance does not allow traffic through port 22 over WiFi to certain systems.<br /> <br /> &lt;source lang='bash'&gt;<br /> ssh [user name]@login.anunna.wur.nl<br /> &lt;/source&gt;<br /> <br /> === PuTTY on Windows ===<br /> Putty is a free, powerful, and widely used SSH client that runs on Windows.<br /> It is extremely useful for those people who have a computer running Windows<br /> on their desk but must remotely connect to a computer running UNIX/Linux.<br /> Putty is one of a set of utilities that all work together to provide<br /> convenient connectivity between Windows and UNIX/Linux environments.<br /> Some of these utilities include:<br /> <br /> * Putty -- the SSH client<br /> * Pageant -- the authentication agent used with Putty<br /> * Puttygen -- the RSA key generation utility<br /> * Pscp -- the SCP secure file copy utility<br /> <br /> Depending on your tasks, the above utilities are probably your minimum<br /> set of tools to make convenient connections and file transfers between a<br /> computer running Windows and a computer running UNIX/Linux.<br /> <br /> ==== Putty Configuration ====<br /> <br /> Putty is able to store the configuration or connection profiles for a<br /> number of remote UNIX/Linix clients. Each of profile can be created<br /> and later edited by Right-clicking on a putty window header and choosing<br /> &quot;New Session...&quot;. The minimum set of items that need to be configured for<br /> a given connection are:<br /> <br /> * Session<br /> ** Host Name [login.anunna.wur.nl]<br /> ** Saved Session name [your name for this connection]<br /> * Terminal<br /> ** Keyboard<br /> *** Backspace key -&gt; Control-H<br /> * Connection<br /> ** Data<br /> *** Auto-login username [your remote username]<br /> ** SSH<br /> *** Auth<br /> **** Private key file for authentication [pathname to your .ppk file]<br /> <br /> Obviously, there are many other useful things that can be configured and<br /> customized in Putty but the above list should be considered a minimum.<br /> Please note that after making any change to a putty session you must<br /> explicitly save your changes.<br /> <br /> ==== Creating an SSH Key Pair ====<br /> <br /> Puttygen is the utility used for creating both a .ppk file (private<br /> key) and the public authorized key information. Briefly, here are<br /> the steps needed to create a key pair:<br /> <br /> * Run (double-click) the Puttygen application<br /> * Click on &quot;Generate&quot;<br /> * Replace the comment with something meaningful -- maybe your name<br /> * Type in your passphrase (password) twice<br /> * Save the .ppk file in a secure location on your Windows computer<br /> * Use your mouse to copy the public key string then paste it into the ~/.ssh/authorized_keys file on the remote computer<br /> <br /> Note: The full pathname of this .ppk file is used in the last step of Putty<br /> configuration as described above.<br /> <br /> ==== Using Pageant as an Interface for Putty ====<br /> <br /> Pageant is a Putty helper program that is used for two main purposes:<br /> <br /> * Pageant is used to hold the passphrase to your key pair<br /> * Pageant is used as a convenience application to run a Putty session from any of your saved profiles<br /> <br /> There is no configuration needed in Pageant. You simply need to<br /> run this program at login. Any easy way to do this is to create a<br /> shortcut in your startup folder that points to the Pageant executable.<br /> Once this has been done, every time you log in you will see a little<br /> icon of a computer with a hat in your taskbar. The first step in using<br /> this is to right-click on it and select &quot;Add Key&quot;. Navigate to your<br /> .ppk file and select &quot;Open&quot;. It will prompt you for your passphrase.<br /> At this point your passphrase has been conveniently stored for you so<br /> that when you use Putty to connect to your various remote computers,<br /> you won't have to type in your passphrase over and over again.<br /> The next step is to right-click on the Pageant icon again and select<br /> one of your saved sessions. If you have done everything correctly<br /> you will be logged right in so that you no longer have to type your<br /> passphrase.<br /> <br /> == Log on to worker nodes ==<br /> <br /> In a complete emergency, it is then possible to log on to any of the worker nodes via the login node. Logging on to the worker nodes does not require password authentication, you should therefore not be prompted to provide a password. This is not normally allowed - be aware that running tasks outside of SLURM is prohibited, but so far there has not been any serious abuse of this. This is provided to allow you to get a little more insight in what your job is doing.<br /> <br /> &lt;source lang='bash'&gt;<br /> ssh [user name]@[node name]<br /> &lt;/source&gt;<br /> <br /> For instance:<br /> <br /> &lt;source lang='bash'&gt;<br /> ssh dummy001@node049<br /> &lt;/source&gt;<br /> <br /> Again, it is not permitted to run jobs outside the scheduling software (slurm). So logging on to a worker node is for analyses of running jobs only.<br /> <br /> == File transfer using ssh-based file transfer protocols ==<br /> === Copying files to/from the cluster: scp ===<br /> <br /> From any Posix-compliant system (Linux/MacOSX) terminal files and folder can be transferred to and from the cluster using an ssh-based file copying protocol called scp ([http://en.wikipedia.org/wiki/Secure_copy secure copy]). For instance, copying a folder containing several files from scomp1090/lx6 can be achieved like this:<br /> <br /> Syntax of the scp command requires from-to order:<br /> <br /> &lt;source lang='bash'&gt;<br /> scp &lt;source&gt; &lt;destination&gt;<br /> &lt;/source&gt;<br /> <br /> &lt;source lang='bash'&gt;<br /> scp -pr /home/WUR/[username]/folder_to_transfer [username]@login.anunna.wur.nl:/lustre/scratch/WUR/ABGC/<br /> &lt;/source&gt;<br /> <br /> This example assumes a user that is part of the ABGC user group. See the [[Lustre_PFS_layout | Lustre Parallel File System layout]] page for further details. The -p flag will preserve the file metadata such as timestamps. The -r flag allows for recursive copying. Further options can be found in the [http://en.wikipedia.org/wiki/Man_page man pages].<br /> <br /> &lt;source lang='bash'&gt;<br /> man scp<br /> &lt;/source&gt;<br /> <br /> === rsync ===<br /> The [http://en.wikipedia.org/wiki/Rsync rsync protocol], like the scp protocol, allow CLI-based copying of files. The rsync protocol, however, will only transfer those files between systems that have changed, i.e. it synchronises the files, hence the name. The rsync protocol is very well suited for making regular backups and file syncs between file systems. Like the scp command, syntax is in the from-to order.<br /> &lt;source lang='bash'&gt;<br /> rsync &lt;source&gt; &lt;destination&gt;<br /> &lt;/source&gt;<br /> e.g.:<br /> &lt;source lang='bash'&gt;<br /> rsync -av /home/WUR/[username]/folder_to_transfer [username]@login.anunna.wur.nl:/lustre/scratch/WUR/ABGC/<br /> &lt;/source&gt;<br /> The -a flag will preserve file metadata and allows for recursive copying, amongst others. The -v flag provides verbose output. Further options can be found in the [http://en.wikipedia.org/wiki/Man_page man pages].<br /> &lt;source lang='bash'&gt;<br /> man scp<br /> &lt;/source&gt;<br /> <br /> === WinSCP ===<br /> [http://en.wikipedia.org/wiki/WinSCP WinSCP] is a free and open source (S)FTP client for Microsoft Windows. By providing the hostname (login.anunna.wur.nl), your username, and password, using SFTP protocol and port 22, you can login. After login files can be transferred between a local system (PC) and the cluster.<br /> <br /> === FileZilla ===<br /> [http://en.wikipedia.org/wiki/Filezilla FileZilla] is a free and open source graphical (S)FTP client. It is available for Linux, MacOSX, and Windows. By providing the address, username, password and server type (Unix, see Site Manager;Advanced), files can be transferred between a local system and the cluster. Furthermore, the graphical interface allows for easy browsing of files on Anunna. Detailed instruction can be found on the [https://wiki.filezilla-project.org/Using FileZilla Wiki].<br /> <br /> === Samba/CIFS based protocols ===<br /> The Common Interface File System ([http://en.wikipedia.org/wiki/Cifs CIFS]) is commonly used in and between Windows systems for file sharing. It is only available to clients within WURnet. If you enter the following UNC path \\nfs01.anunna.wur.nl\[username] in your Windows client, it will list the available (authenticated) shares (your home directory).<br /> <br /> == See also ==<br /> * [[B4F_cluster | B4F Cluster]]<br /> * [[BCM_on_B4F_cluster | Monitor cluster status with BCM]]<br /> * [[SLURM_on_B4F_cluster | Submit jobs with Slurm]]<br /> * [[ssh_without_password | ssh without password]]<br /> <br /> == External links ==<br /> * [http://en.wikipedia.org/wiki/Secure_Shell secure shell on Wikipedia]<br /> * [http://www.chiark.greenend.org.uk/~sgtatham/putty/ PuTTY homepage]<br /> * [http://winscp.net/eng/index.php WinSCP homepage]<br /> * [https://filezilla-project.org FileZilla homepage]<br /> * [http://en.wikipedia.org/wiki/Cifs The Common Interface File System (CIFS) on Wikipedia]</div>

Vaend001 https://wiki.anunna.wur.nl/index.php?title=Main_Page&diff=1926 2019-02-19T17:16:03Z

<p>Vaend001: </p> <hr /> <div>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 &amp; 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. <br /> <br /> = Using Anunna =<br /> == Gaining access to Anunna==<br /> Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP].<br /> * [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]<br /> * [[Services | Alternative access methods, and extra features and services on Anunna]]<br /> * [[Filesystems | Accessible storage methods on Anunna]]<br /> <br /> == Access Policy ==<br /> [[Access_Policy | Main Article: Access Policy]]<br /> <br /> 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 CAT-AGRO or FB-ICT.<br /> <br /> = Events =<br /> * [[Courses]] that have happened and are happening<br /> * [[Downtime]] that will affect all users<br /> * [[Meetings]] that may affect the policies of the HPC<br /> <br /> = Other Software =<br /> <br /> == Cluster Management Software and Scheduler ==<br /> Anunna uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.<br /> * [[BCM_on_B4F_cluster | Monitor cluster status with BCM]]<br /> * [[SLURM_on_B4F_cluster | Submit jobs with Slurm]]<br /> * [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']]<br /> * [[SLURM_Compare | Rosetta Stone of Workload Managers]]<br /> <br /> == Installation of software by users ==<br /> <br /> * [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]<br /> * [[Setting local variables]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> * [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]<br /> * [[Installing WRF and WPS]]<br /> <br /> == Installed software ==<br /> <br /> * [[Globally_installed_software | Globally installed software]]<br /> * [[ABGC_modules | ABGC specific modules]]<br /> <br /> = Useful Notes = <br /> <br /> == Being in control of Environment parameters ==<br /> <br /> * [[Using_environment_modules | Using environment modules]]<br /> * [[Setting local variables]]<br /> * [[Setting_TMPDIR | Set a custom temporary directory location]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> <br /> == Controlling costs ==<br /> <br /> * [[SACCT | using SACCT to see your costs]]<br /> * [[get_my_bill | using the &quot;get_my_bill&quot; script to estimate costs]]<br /> <br /> == Management ==<br /> [[Anunna | Main Article: Anunna management]]<br /> <br /> Project Leader of Anunna is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:lith010 | Jan van Lith (Wageningen UR,FB-IT, Infrastructure)]], [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] and [[User:vaend001 | Catharina Vaendel(Wageningen UR,FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]].<br /> <br /> = Miscellaneous =<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[History_of_the_Cluster | Historical information on the startup of Anunna]]<br /> * [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]<br /> * [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]<br /> * [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]<br /> * [[Manual GitLab | GitLab: Create projects and add scripts]]<br /> * [[Monitoring_executions | Monitoring job execution]]<br /> * [[Shared_folders | Working with shared folders in the Lustre file system]]<br /> <br /> = See also =<br /> * [[Maintenance_and_Management | Maintenance and Management]]<br /> * [[BCData | BCData]]<br /> * [[Mailinglist | Electronic mail discussion lists]]<br /> * [[About_ABGC | About ABGC]]<br /> * [[Computer_cluster | High Performance Computing @ABGC]]<br /> * [[Lustre_PFS_layout | Lustre Parallel File System layout]]<br /> <br /> = External links =<br /> {| width=&quot;90%&quot;<br /> |- valign=&quot;top&quot;<br /> | width=&quot;30%&quot; |<br /> * [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]<br /> * [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]<br /> * [http://www.cobb-vantress.com Cobb-Vantress homepage]<br /> <br /> | width=&quot;30%&quot; |<br /> * [https://www.crv4all.nl CRV homepage]<br /> * [http://www.hendrix-genetics.com Hendrix Genetics homepage]<br /> * [http://www.topigs.com TOPIGS homepage]<br /> | width=&quot;30%&quot; |<br /> * [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]<br /> * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]<br /> |}</div>

Vaend001