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TWiki's HPC web https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC The HPC web of TWiki. TWiki is a Web-Based Collaboration Platform for the Enterprise. en-us Copyright 2021 by contributing authors TWiki Administrator [bioinf-holstege@lists.umcutrecht.nl] The contributing authors of TWiki TWiki Home - this site is powered by TWiki(R).HPC https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC https://wiki.bioinformatics.umcutrecht.nl/pub/TWiki/TWikiLogos/T-logo-140x40-t.gif SshCommandLine https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/SshCommandLine SSH configuration for Mac and Linux # goto your homedirectory cd # create a .ssh directory mkdir .ssh # goto .ssh directory cd ~/.ssh # create a ssh keypair ssh keygen... (last changed by ReneJanssen) 2021-04-09T08:12:00Z rjanssen SlurmScheduler https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/SlurmScheduler Slurm Starting in May 2019, we`re testing our new Slurm setup. Slurm is similar to GridEngine: it manages a cluster, distributing user jobs in (hopefully) a fair and... (last changed by ReneJanssen) 2021-02-16T10:34:26Z rjanssen SoftwareInstallation https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/SoftwareInstallation SoftwareInstallation Can I install my own software? The answer is: yes, (of course) you can. There is a group specific directory that is made available for this purpose... (last changed by ReneJanssen) 2020-08-10T15:22:35Z rjanssen SlurmLimits https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/SlurmLimits Resource Limits in Slurm Very short summary The resources that we put limits on are: CPU, memory, GPU. And runtime, sort of. Whom do we limit this to? Not to you... (last changed by MartinMarinus) 2020-05-26T09:54:21Z mmarinus PuTTy https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/PuTTy Configure Putty ssh client Download the Putty software : https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html Put in a directory on your local machine p... (last changed by MartinMarinus) 2020-05-06T11:09:01Z mmarinus MoBaXterm https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/MoBaXterm Mobaxterm Configuration HPC To use the HPC you must use a ssh client. An example of this software is the Mobaxterm for Windows.(https://mobaxterm.mobatek.net/) To... (last changed by MartinMarinus) 2020-05-06T11:08:26Z mmarinus HPCInTimesOfCovid19 https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/HPCInTimesOfCovid19 HPC In Times Of Covid 19 (Un)limited Service Like most of you, we`re working from home at the moment. We try to provide the same service as always, so feel free... (last changed by MartinMarinus) 2020-03-17T14:52:08Z mmarinus WebHome https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/WebHome Welcome to the High Performance Computing (HPC) Facility wiki The High performance Computing (HPC) facility is setup to provide high performance computing power to... (last changed by ReneJanssen) 2020-03-03T14:02:30Z rjanssen ContactDetails https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/ContactDetails ContactDetails Initial contact Initial intakes for new research groups and general information about the HPC facility are handled by Jeroen de Ridder. Please contact... (last changed by ReneJanssen) 2019-08-13T09:04:52Z rjanssen CromWellService https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/CromWellService Cromwell workflow management system Cromwell is a workflow management system geared towards scientific workflows. More information can be found online. It can function... (last changed by ReneJanssen) 2019-05-13T13:08:44Z rjanssen MyTest https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/MyTest Title Article text. Comments (last changed by ReneJanssen) 2019-05-13T09:47:23Z rjanssen ConditionsAndSupport https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/ConditionsAndSupport Conditions and Support Conditions In order to be able to use the HPC facility, you need to be affiliated with University Medical Center Utrecht, Utrecht University... (last changed by MartinMarinus) 2018-05-22T07:39:51Z mmarinus ParticipatingGroups https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/ParticipatingGroups ParticipatingGroups University Medical Center Utrecht Division Biomedical Genetics Edwin Cuppen, Medical Genetics David Egan, Cellbiology Wigard Kloosterman... (last changed by PatrickKemmeren) 2017-12-08T11:19:26Z patrick NewGateway https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/NewGateway New Gateway on hpcgw.op.umcutrecht.nl We installed a new gateway server in the HPC named hpcgw.op.umcutrecht.nl. The old server gw.op.umcutrecht.nl will soon be disabled... (last changed by ReneJanssen) 2017-09-14T08:05:16Z rjanssen PuttyTerm https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/PuttyTerm change configuration Putty ssh client Load the current configuration for the gateway Change the configuration and save (last changed by ReneJanssen) 2017-08-25T11:11:39Z rjanssen MakingSoftwareAvailableUsingLMOD https://wiki.bioinformatics.umcutrecht.nl/bin/view/HPC/MakingSoftwareAvailableUsingLMOD Howto create your own/group software modules Introduction Often a program requires particular environment variables in order to run. LMOD environment modules provide... (last changed by ReneJanssen) 2017-03-27T11:35:50Z rjanssen
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