{"id":979,"date":"2021-03-29T16:28:10","date_gmt":"2021-03-29T16:28:10","guid":{"rendered":"http:\/\/wordpress.ubi.pt\/clusterdem\/?page_id=979"},"modified":"2026-07-25T01:56:28","modified_gmt":"2026-07-25T01:56:28","slug":"computation-section","status":"publish","type":"page","link":"https:\/\/clusterdem.ubi.pt\/?page_id=979","title":{"rendered":"Computational Resources"},"content":{"rendered":"\n<div class=\"wp-block-group alignfull has-text-color has-background is-layout-constrained wp-container-core-group-is-layout-00ebdded wp-block-group-is-layout-constrained\" style=\"background-color:#0b192c;color:#ffffff;padding-top:50px;padding-bottom:50px;padding-left:40px;padding-right:40px;font-family:system-ui,-apple-system,sans-serif;\">\n    <h1 class=\"wp-block-heading has-text-align-center\" style=\"font-size:32px;font-weight:700;margin:0;\">Computational Resources<\/h1>\n    <p class=\"has-text-align-center\" style=\"font-size:1.1rem;margin:10px auto 0 auto;opacity:0.8;max-width:700px;\">OCTOPUS500 High-Performance Computing Cluster Guidelines and Reference.<\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-group alignfull is-layout-constrained wp-container-core-group-is-layout-d6b9e94e wp-block-group-is-layout-constrained\" style=\"padding:40px 20px;font-family:system-ui,-apple-system,sans-serif;max-width:1000px;margin:0 auto;\">\n\n    <!-- INFRASTRUCTURE OVERVIEW -->\n    <div style=\"display:flex; flex-wrap:wrap; gap:30px; margin-bottom:40px; align-items:center;\">\n        <div style=\"flex:1; min-width:300px;\">\n            <p style=\"font-size:16px; line-height:1.6; color:#2d3748; margin:0 0 15px 0;\">\n                At ClusterDEM, we leverage advanced computational power to support our research in numerical modeling and simulation. Our <strong>mini HPC system, OCTOPUS500<\/strong>, provides robust parallel computing architecture tailored for heavy engineering solvers.\n            <\/p>\n            <div style=\"background:#f8fafc; border:1px solid #e2e8f0; border-left:4px solid #3182ce; padding:15px; border-radius:6px; font-size:14px; color:#2d3748;\">\n                \ud83d\udc19 <strong>OCTOPUS500 Specifications:<\/strong>\n                <ul style=\"margin:8px 0 0 20px; padding:0;\">\n                    <li style=\"margin-bottom:4px;\"><strong>Core Count:<\/strong> 768 Compute Cores<\/li>\n                    <li style=\"margin-bottom:4px;\"><strong>Memory capacity:<\/strong> 2TB of High-Speed RAM<\/li>\n                    <li style=\"margin-bottom:4px;\"><strong>Operating System:<\/strong> CentOS Platform<\/li>\n                    <li><strong>Cluster Build Layout:<\/strong> ROCKS Cluster Distribution<\/li>\n                <\/ul>\n            <\/div>\n        <\/div>\n        <div style=\"flex:0 0 320px; max-width:100%; margin:0 auto; text-align:center;\">\n            <img decoding=\"async\" src=\"https:\/\/clusterdem.ubi.pt\/wp-content\/uploads\/2018\/03\/transferir-11.png\" alt=\"OCTOPUS500 Cluster Infrastructure\" style=\"width:100%; height:auto; border-radius:8px; box-shadow:0 4px 6px -1px rgba(0,0,0,0.1); border:1px solid #cbd5e1;\">\n        <\/div>\n    <\/div>\n\n    <!-- RUNNING YOUR CASE SECTION -->\n    <h2 style=\"font-size:22px; font-weight:700; color:#0b192c; margin-bottom:15px; border-bottom:2px solid #e2e8f0; padding-bottom:6px;\">Running Your Case on OCTOPUS500<\/h2>\n    <p style=\"font-size:15px; color:#4a5568; margin-bottom:20px;\">To efficiently utilize the shared cluster environment, all researchers must adhere strictly to the core environment mappings defined below.<\/p>\n\n    <h3 style=\"font-size:16px; font-weight:700; color:#2d3748; margin-bottom:12px;\">Available Parallel Environments<\/h3>\n    <p style=\"font-size:14px; color:#4a5568; line-height:1.5; margin-bottom:15px;\">\n        OCTOPUS500 relies on parallel tracks structured as <code>mpiX<\/code>, where <code>X<\/code> marks the exact allocation allocation bounds of CPUs deployed per cluster node (scaling systematically from <strong>1 to 10<\/strong>). You must configure your script allocation slots as an exact multiple of <code>X<\/code>.\n    <\/p>\n\n    <!-- VALID VS INVALID MATRIX -->\n    <div style=\"display:flex; flex-wrap:wrap; gap:20px; margin-bottom:30px;\">\n        <div style=\"flex:1; min-width:280px; border:1px solid #c6f6d5; background:#f0fff4; padding:15px; border-radius:6px;\">\n            <span style=\"font-weight:700; color:#22543d; display:block; margin-bottom:6px;\">\u2705 Example (Valid Submission)<\/span>\n            <pre style=\"background:#ffffff; padding:10px; border-radius:4px; border:1px solid #b2f5ea; font-family:monospace; font-size:13px; margin:0; color:#234e52;\">-pe mpi5 25<\/pre>\n            <span style=\"font-size:12px; color:#2f855a; display:block; margin-top:6px;\">Launches a balanced track using 5 compute nodes with 5 CPUs mapping each.<\/span>\n        <\/div>\n        <div style=\"flex:1; min-width:280px; border:1px solid #fed7d7; background:#fff5f5; padding:15px; border-radius:6px;\">\n            <span style=\"font-weight:700; color:#742a2a; display:block; margin-bottom:6px;\">\u274c Invalid Setup Configurations<\/span>\n            <pre style=\"background:#ffffff; padding:10px; border-radius:4px; border:1px solid #feb2b2; font-family:monospace; font-size:13px; margin:0; color:#9b2c2c; line-height:1.4;\">-pe mpi5 22  # Incorrect: Not a multiple of 5\n-pe mpi2 5   # Incorrect: Not a multiple of 2<\/pre>\n        <\/div>\n    <\/div>\n\n    <!-- NODE SELECTION & GANGLIA -->\n    <div style=\"background:#f7fafc; border:1px solid #e2e8f0; border-radius:8px; padding:20px; margin-bottom:40px;\">\n        <h4 style=\"margin:0 0 6px 0; font-size:15px; color:#2d3748; font-weight:700;\">Cluster Node Selection<\/h4>\n        <p style=\"font-size:14px; color:#4a5568; margin-bottom:8px;\">Target specific hardware strings directly by passing the core node handle parameter:<\/p>\n        <pre style=\"background:#ffffff; padding:10px; border-radius:4px; border:1px solid #cbd5e1; font-family:monospace; font-size:13px; margin:0 0 15px 0; color:#2d3748;\">-l h=compute-0-x<\/pre>\n        <p style=\"font-size:13px; color:#4a5568; margin:0;\">Replace <code>x<\/code> with the specific target slot index identifier assigned to your tracking job.<\/p>\n        \n        <div style=\"margin-top:20px; background:#fffaf0; border:1px solid #feebc8; border-radius:6px; padding:15px; display:flex; gap:12px; align-items:center;\">\n            <span style=\"font-size:20px;\">\ud83d\udca1<\/span>\n            <span style=\"font-size:13.5px; color:#744210; line-height:1.4;\">\n                <strong>Resource Allocation Rule:<\/strong> Always check cluster computing overhead and tracking pipelines inside your network terminal prior to firing tasks: <a href=\"http:\/\/192.168.92.140\/ganglia\" target=\"_blank\" rel=\"noopener\" style=\"color:#dd6b20; font-weight:600; text-decoration:none;\">Open Ganglia Monitoring System Portal \u2197<\/a> (Accessible within the local UBI network domain limits).\n            <\/span>\n        <\/div>\n    <\/div>\n\n    <!-- JOB MANAGEMENT SECTION -->\n    <h2 style=\"font-size:22px; font-weight:700; color:#0b192c; margin-bottom:15px; border-bottom:2px solid #e2e8f0; padding-bottom:6px;\">Job Submission &amp; Management<\/h2>\n    \n    <h3 style=\"font-size:15px; font-weight:700; color:#2d3748; margin-bottom:8px;\">Submitting a Job<\/h3>\n    <p style=\"font-size:14px; color:#4a5568; margin-bottom:10px;\">Queue up compilation script arrays running the baseline scheduler submission handle:<\/p>\n    <pre style=\"background:#1a202c; color:#f7fafc; padding:12px 18px; border-radius:6px; font-family:monospace; font-size:13.5px; margin-bottom:15px; overflow-x:auto;\">qsub RUN.sh<\/pre>\n    <p style=\"font-size:14px; color:#4a5568; margin-bottom:25px;\">SGE engine environments will throw back an confirmation echo array identifying task parameters: <code style=\"background:#edf2f7; padding:2px 6px; border-radius:4px; font-size:13px; color:#2d3748;\">Your job 624556 (\"myjob.cmd\") has been submitted<\/code>.<\/p>\n\n    <!-- OPENFOAM SUBMISSION SCRIPT BLOCK -->\n    <h3 style=\"font-size:15px; font-weight:700; color:#2d3748; margin-bottom:8px;\">Example OpenFOAM Submission Script<\/h3>\n    <p style=\"font-size:14px; color:#4a5568; margin-bottom:10px;\">Deploy the boilerplate environment submission script below, ensuring modifications are passed inside target tracking cases.<\/p>\n    \n    <div style=\"background:#1a202c; border-radius:8px; padding:20px; margin-bottom:40px; box-shadow:inset 0 2px 4px rgba(0,0,0,0.14);\">\n        <pre style=\"margin:0; font-family:monospace; font-size:13px; color:#f7fafc; line-height:1.5; overflow-x:auto;\">#!\/bin\/bash\n#$ -S \/bin\/bash\n#$ -pe mpi5 10\n#$ -cwd\n#$ -N MySimulation\n#$ -o log\n#$ -e error.err\n#$ -p 0\n#$ -M youremail@ubi.pt\n#$ -m bea\n\n# Source environment parameters\n. $HOME\/OpenFOAM\/OpenFOAM-2.0.x\/etc\/bashrc\n\n# Arguments tracking configuration\nARGS=\"--mca btl ^openib --mca btl_tcp_if_include eth0\"\n\n# Execute solver runtime target\nSOLVER=clusterMHDFoam\nmpirun -np $NSLOTS $ARGS $SOLVER -parallel<\/pre>\n    <\/div>\n\n    <!-- COMMANDS REFERENCE DICTIONARY TABLE -->\n    <h2 style=\"font-size:22px; font-weight:700; color:#0b192c; margin-bottom:15px; border-bottom:2px solid #e2e8f0; padding-bottom:6px;\">SGE Commands Reference Guide<\/h2>\n    <p style=\"font-size:14px; color:#4a5568; margin-bottom:20px;\">Quick directory tracking standard Sun Grid Engine (SGE) system parameters:<\/p>\n\n    <table style=\"width:100%; border-collapse:collapse; font-size:14px; color:#2d3748; margin-bottom:30px; text-align:left;\">\n        <thead>\n            <tr style=\"background:#0b192c; color:#ffffff;\">\n                <th style=\"padding:12px; border:1px solid #0b192c;\">Command Syntax<\/th>\n                <th style=\"padding:12px; border:1px solid #0b192c;\">System Context Operation Description<\/th>\n            <\/tr>\n        <\/thead>\n        <tbody>\n            <tr style=\"background:#ffffff;\">\n                <td style=\"padding:10px; border:1px solid #e2e8f0;\"><code style=\"color:#b83280; font-weight:600;\">qsub RUN.sh<\/code><\/td>\n                <td style=\"padding:10px; border:1px solid #e2e8f0;\">Submit a pipeline batch script configuration down the scheduling path rows.<\/td>\n            <\/tr>\n            <tr style=\"background:#f7fafc;\">\n                <td style=\"padding:10px; border:1px solid #e2e8f0;\"><code style=\"color:#b83280; font-weight:600;\">qstat \/ qstat -u username<\/code><\/td>\n                <td style=\"padding:10px; border:1px solid #e2e8f0;\">Check computing queues runtime status indexes or filter specifically by user.<\/td>\n            <\/tr>\n            <tr style=\"background:#ffffff;\">\n                <td style=\"padding:10px; border:1px solid #e2e8f0;\"><code style=\"color:#b83280; font-weight:600;\">qhost \/ qhost -j \/ qhost -q<\/code><\/td>\n                <td style=\"padding:10px; border:1px solid #e2e8f0;\">Display architecture compute nodes details, metrics bounds, or active lines.<\/td>\n            <\/tr>\n            <tr style=\"background:#f7fafc;\">\n                <td style=\"padding:10px; border:1px solid #e2e8f0;\"><code style=\"color:#b83280; font-weight:600;\">qdel [job_id] \/ qdel -f [job_id]<\/code><\/td>\n                <td style=\"padding:10px; border:1px solid #e2e8f0;\">Cancel or explicitly pass force termination signals down running system nodes.<\/td>\n            <\/tr>\n            <tr style=\"background:#ffffff;\">\n                <td style=\"padding:10px; border:1px solid #e2e8f0;\"><code style=\"color:#b83280; font-weight:600;\">qhold [job_id]<\/code><\/td>\n                <td style=\"padding:10px; border:1px solid #e2e8f0;\">Hold a specific queued job array inside structural lines buffer boundaries.<\/td>\n            <\/tr>\n            <tr style=\"background:#f7fafc;\">\n                <td style=\"padding:10px; border:1px solid #e2e8f0;\"><code style=\"color:#b83280; font-weight:600;\">qrls [job_id]<\/code><\/td>\n                <td style=\"padding:10px; border:1px solid #e2e8f0;\">Release a held job instance framework allocation back to scheduling pipelines.<\/td>\n            <\/tr>\n        <\/tbody>\n    <\/table>\n    \n    <div style=\"background:#edf2f7; padding:12px 15px; border-radius:6px; font-size:13px; color:#4a5568;\">\n        \ud83d\udd0d Deeper diagnostics flags configuration can be parsed using manual documentation variables: <code style=\"background:#ffffff; padding:2px 6px; border-radius:4px; font-family:monospace; color:#2d3748;\">man qsub<\/code>.\n    <\/div>\n\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Computational Resources OCTOPUS500 High-Performance Computing Cluster Guidelines and Reference. At ClusterDEM, we leverage advanced computational power to support our research in numerical modeling and simulation. Our mini HPC system, OCTOPUS500, provides robust parallel computing architecture tailored for heavy engineering solvers. \ud83d\udc19 OCTOPUS500 Specifications: Core Count: 768 Compute Cores Memory capacity: 2TB of High-Speed RAM Operating [&hellip;]<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":13,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"disabled","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"set","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":""},"class_list":["post-979","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/clusterdem.ubi.pt\/index.php?rest_route=\/wp\/v2\/pages\/979","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/clusterdem.ubi.pt\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/clusterdem.ubi.pt\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/clusterdem.ubi.pt\/index.php?rest_route=\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/clusterdem.ubi.pt\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=979"}],"version-history":[{"count":11,"href":"https:\/\/clusterdem.ubi.pt\/index.php?rest_route=\/wp\/v2\/pages\/979\/revisions"}],"predecessor-version":[{"id":3249,"href":"https:\/\/clusterdem.ubi.pt\/index.php?rest_route=\/wp\/v2\/pages\/979\/revisions\/3249"}],"up":[{"embeddable":true,"href":"https:\/\/clusterdem.ubi.pt\/index.php?rest_route=\/wp\/v2\/pages\/13"}],"wp:attachment":[{"href":"https:\/\/clusterdem.ubi.pt\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=979"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}