{"id":5160,"date":"2024-03-24T17:37:44","date_gmt":"2024-03-24T16:37:44","guid":{"rendered":"https:\/\/ubc.uu.nl\/?page_id=5160"},"modified":"2026-06-23T14:22:38","modified_gmt":"2026-06-23T12:22:38","slug":"high-performance-computing","status":"publish","type":"page","link":"https:\/\/ubc.uu.nl\/high-performance-computing\/","title":{"rendered":"High Performance Computing"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"5160\" class=\"elementor elementor-5160\" data-elementor-post-type=\"page\">\n\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-88f2776 elementor-section-height-min-height elementor-section-content-middle elementor-section-boxed elementor-section-height-default elementor-section-items-middle\" data-id=\"88f2776\" data-element_type=\"section\" data-e-type=\"section\" data-settings=\"{&quot;background_background&quot;:&quot;classic&quot;}\">\n\t\t\t\t\t\t\t<div class=\"elementor-background-overlay\"><\/div>\n\t\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-d696243 animated-slow elementor-invisible\" data-id=\"d696243\" data-element_type=\"column\" data-e-type=\"column\" data-settings=\"{&quot;animation&quot;:&quot;fadeInLeft&quot;}\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-5c7ef60 elementor-widget__width-initial elementor-widget-mobile__width-initial elementor-widget elementor-widget-heading\" data-id=\"5c7ef60\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h1 class=\"elementor-heading-title elementor-size-default\">Utrecht Bioinformatics Center<\/br>\nInfrastructure<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-dcd40ea elementor-align-left elementor-widget elementor-widget-button\" data-id=\"dcd40ea\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"button.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<div class=\"elementor-button-wrapper\">\n\t\t\t\t\t<a class=\"elementor-button elementor-button-link elementor-size-sm elementor-animation-grow\" href=\"https:\/\/hpcusers.op.umcutrecht.nl\/xwiki\/bin\/view\/Main\/?\" target=\"_blank\">\n\t\t\t\t\t\t<span class=\"elementor-button-content-wrapper\">\n\t\t\t\t\t\t\t\t\t<span class=\"elementor-button-text\">Read more<\/span>\n\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/a>\n\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-54503c3 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"54503c3\" data-element_type=\"section\" data-e-type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-5fc4105\" data-id=\"5fc4105\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-8537751 elementor-widget elementor-widget-heading\" data-id=\"8537751\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">High Performance Computing<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-7c93054 elementor-widget__width-initial elementor-widget-tablet__width-initial elementor-widget elementor-widget-text-editor\" data-id=\"7c93054\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\tThe high performance compute (HPC) facility, as part of the Utrecht Bioinformatics Center (UBC) offers extensive computing possibilities for all researchers of the\u00a0<strong><a style=\"color: #22428b;\">Utrecht Science Park<\/a><\/strong>. From a large UU starting grand, the HPC has grown with the support of the community to the largest cluster on the campus, allowing both small and very large groups to run their computing. There are over 50 PI groups and 750 users registrered and generally over 50 different users active each day. These groups vary between disciplines, from life sciences to linguistics.\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-ea15903 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"ea15903\" data-element_type=\"section\" data-e-type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-3506729\" data-id=\"3506729\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-1ce0c78 elementor-widget elementor-widget-heading\" data-id=\"1ce0c78\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">Facts &amp; Figures<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3185e4f elementor-icon-list--layout-traditional elementor-list-item-link-full_width elementor-widget elementor-widget-icon-list\" data-id=\"3185e4f\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-list.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul class=\"elementor-icon-list-items\">\n\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-dna\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">The cluster consists of a collection of compute servers (&gt;2000 CPUcores, 30 GPUs, 20 TB ram), 1.7 PB high performance storage and 1.1 PB archive storage running on CentOS Linux.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-dna\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">It is controlled by the SLURM batch-wise queueing system with a few head nodes and data transfer nodes.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-dna\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Data storage is separated between PI groups.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-dna\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">We provide a central GUIX software management system, notebook services and containersupport.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-dna\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Two full time staff members are available to maintain, innovate and support this essential research resource.<\/span>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t<\/ul>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-7844523 elementor-widget elementor-widget-heading\" data-id=\"7844523\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">Costs<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-0af4d68 elementor-widget__width-initial elementor-widget-tablet__width-initial elementor-widget elementor-widget-text-editor\" data-id=\"0af4d68\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>To ensure future sustainability, users can participate after a free trial by buying virtual shares to cover their compute demand (in 2020: \u20ac1200,-\/50k CPUhrs; \u20ac1150\/5k GPUhrs; \u20ac180\/TB high-perf storage\/yr; \u20ac45,-\/TB archive storage\/yr).<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t<div class=\"elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-97ca201\" data-id=\"97ca201\" data-element_type=\"column\" data-e-type=\"column\" data-settings=\"{&quot;background_background&quot;:&quot;classic&quot;}\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-0cddce7 elementor-widget elementor-widget-image\" data-id=\"0cddce7\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img fetchpriority=\"high\" decoding=\"async\" width=\"1280\" height=\"720\" src=\"https:\/\/ubc.uu.nl\/wp-content\/uploads\/2017\/08\/UBC17_hq720.jpg\" class=\"attachment-full size-full wp-image-1515\" alt=\"\" srcset=\"https:\/\/ubc.uu.nl\/wp-content\/uploads\/2017\/08\/UBC17_hq720.jpg 1280w, https:\/\/ubc.uu.nl\/wp-content\/uploads\/2017\/08\/UBC17_hq720-300x169.jpg 300w, https:\/\/ubc.uu.nl\/wp-content\/uploads\/2017\/08\/UBC17_hq720-768x432.jpg 768w, https:\/\/ubc.uu.nl\/wp-content\/uploads\/2017\/08\/UBC17_hq720-1024x576.jpg 1024w, https:\/\/ubc.uu.nl\/wp-content\/uploads\/2017\/08\/UBC17_hq720-700x394.jpg 700w, https:\/\/ubc.uu.nl\/wp-content\/uploads\/2017\/08\/UBC17_hq720-539x303.jpg 539w\" sizes=\"(max-width: 1280px) 100vw, 1280px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-a2c56dd elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"a2c56dd\" data-element_type=\"section\" data-e-type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-6063e32\" data-id=\"6063e32\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-2ee164b elementor-widget elementor-widget-heading\" data-id=\"2ee164b\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">Trial usage:<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-71e25ea elementor-widget__width-initial elementor-widget elementor-widget-text-editor\" data-id=\"71e25ea\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<div class=\"wpb_column vc_column_container vc_col-sm-12\"><div class=\"vc_column-inner\"><div class=\"wpb_wrapper\"><div class=\"wpb_text_column wpb_content_element \"><div class=\"wpb_wrapper\"><p>The HPC is for and by the community, and for this reason we want to have an extremely low threshold to start using the HPC facility for researchers on the Utrecht Life Science Campus. Before people join the HPC community with paid accounts which helps ensure the sustainability of this service, there is an option to run in a trial configuration without costs to see if the HPC works for you. This trial account can be compared with \u00bc share (so ~12.5 kCPUhrs, ~1.6 kGPUhrs, 250GB storage) and is valid for one year, but ad-hoc projects can always be discussed. Each PI can start a trial account only once. Just as for regular accounts, there are limits to the extend users can reserve resources for their jobs. All trial users share the limits of 1 regular account.<\/p><\/div><\/div><\/div><\/div><\/div>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c002623 elementor-testimonial--mobile-align-left elementor-testimonial--skin-default elementor-testimonial--layout-image_inline elementor-testimonial--align-center elementor-arrows-yes elementor-pagination-type-bullets elementor-widget elementor-widget-testimonial-carousel\" data-id=\"c002623\" data-element_type=\"widget\" data-e-type=\"widget\" data-settings=\"{&quot;show_arrows&quot;:&quot;yes&quot;,&quot;pagination&quot;:&quot;bullets&quot;,&quot;speed&quot;:500,&quot;autoplay&quot;:&quot;yes&quot;,&quot;autoplay_speed&quot;:5000,&quot;loop&quot;:&quot;yes&quot;,&quot;pause_on_hover&quot;:&quot;yes&quot;,&quot;pause_on_interaction&quot;:&quot;yes&quot;,&quot;space_between&quot;:{&quot;unit&quot;:&quot;px&quot;,&quot;size&quot;:10,&quot;sizes&quot;:[]},&quot;space_between_tablet&quot;:{&quot;unit&quot;:&quot;px&quot;,&quot;size&quot;:10,&quot;sizes&quot;:[]},&quot;space_between_mobile&quot;:{&quot;unit&quot;:&quot;px&quot;,&quot;size&quot;:10,&quot;sizes&quot;:[]}}\" data-widget_type=\"testimonial-carousel.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<div class=\"elementor-swiper\">\n\t\t\t\t\t<div class=\"elementor-main-swiper swiper\" role=\"region\" aria-roledescription=\"carousel\" aria-label=\"Slides\">\n\t\t\t\t<div class=\"swiper-wrapper\">\n\t\t\t\t\t\t\t\t\t\t\t<div class=\"swiper-slide\" role=\"group\" aria-roledescription=\"slide\">\n\t\t\t\t\t\t\t\t\t<div class=\"elementor-testimonial\">\n\t\t\t\t\t\t\t<div class=\"elementor-testimonial__content\">\n\t\t\t\t\t<div class=\"elementor-testimonial__text\">\n\t\t\t\t\t\tThe HPC provides the neurogenetics group with a powerful tool to analyse large genomics datasets using a suite of compute heavy approaches most notably deep learning and various mixed linear models.\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t\t<div class=\"elementor-testimonial__footer\">\n\t\t\t\t\t\t\t\t\t<div class=\"elementor-testimonial__image\">\n\t\t\t\t\t\t<img decoding=\"async\" src=\"https:\/\/ubc.uu.nl\/wp-content\/uploads\/2015\/01\/cropped-veldink.png\" alt=\"Jan H. Veldink\">\n\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<cite class=\"elementor-testimonial__cite\"><span class=\"elementor-testimonial__name\">Jan H. Veldink<\/span><span class=\"elementor-testimonial__title\">Professor of Neurology and Neurogenetics, <\/br> Department of Neurology,<\/br>  University Medical Center Utrecht Brain Center,<\/br> Utrecht University<\/span><\/cite>\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-ee3efab elementor-widget__width-initial elementor-widget elementor-widget-text-editor\" data-id=\"ee3efab\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>More information:\u00a0<strong><a style=\"color: #22428b;\" href=\"https:\/\/hpcusers.op.umcutrecht.nl\/xwiki\/bin\/view\/Main\/\">HPC facility wiki*<\/a><\/strong><br \/>Contact:\u00a0<strong><a style=\"color: #22428b;\" href=\"mailto:i.nijman@umcutrecht.nl\">Ies Nijman<\/a><\/strong><\/p><p>* Only available on\u00a0<span class=\"ui-provider cif cig bcv cih cii cij cik cil cim cin cio cip ciq cir cis cit ciu civ ciw cix ciy ciz cja cjb cjc cjd cje cjf cjg cjh cji cjj cjk cjl cjm ContentPasted0\" dir=\"ltr\">managed networks of the collaborating institutes<\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>Utrecht Bioinformatics Center Infrastructure Read more High Performance Computing The high performance compute (HPC) facility, as part of the Utrecht Bioinformatics Center (UBC) offers extensive computing possibilities for all researchers of the\u00a0Utrecht Science Park. From a large UU starting grand, the HPC has grown with the support of the community to the largest cluster on [&hellip;]<\/p>\n","protected":false},"author":95,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"elementor_header_footer","meta":{"_acf_changed":false,"_angie_page":false,"footnotes":""},"class_list":["post-5160","page","type-page","status-publish","hentry"],"acf":[],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/pages\/5160","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/users\/95"}],"replies":[{"embeddable":true,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/comments?post=5160"}],"version-history":[{"count":19,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/pages\/5160\/revisions"}],"predecessor-version":[{"id":6721,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/pages\/5160\/revisions\/6721"}],"wp:attachment":[{"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/media?parent=5160"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}