High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ High%performance/compu1ng/ systems/at/LSU/ Michal/Brylinski/ Department/of/Biological/Sciences/ Center/for/Computa1on/&/Technology/ Louisiana/State/University/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Mature/HIV%1/capsid/structure/by/cryo%electron/ microscopy/and/all/atom/molecular/dynamics/ / Zhao/et!al./(2013)/Nature/497(7451),/643%6/ 64%million%atoms% High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Outline/ / ! Introduc1on/to/HPC/ / ! Overview/of/HPC/systems/at/LSU/ / ! Accounts,/alloca1ons,/policy,/etc./ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Intro/to/HPC/ A/supercomputer/is/a/computer/with/a/large/ computa1onal/ capacity./ As/ of/ 2015,/ supercomputers/perform/up/to/quadrillions/ of/floa1ng/point/opera1ons/per/second./ / quadrillion/=/1015/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Intro/to/HPC/ Top/supercomputer/speeds:/logscale/speed/ over/60/years/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Intro/to/HPC/ Titan/at/Oak/ Ridge/NL/ (10/Pflops)/ SuperMike8II%at/ LSU/(146/Tflops)/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Intro/to/HPC/ Compute/node/1/ Head/node/m! Compute/node/2/ Storage/node/1/ Storage/node/n! Special/nodes/ Network/ Head/node/1/ Compute/node/3/ Compute/node/4/ Compute/node/k! High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Intro/to/HPC/ Opera1ng/systems/on/supercomputers/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Overview/of/HPC/systems/ HPC@LSU:/ /SuperMike%II/ / / / / /SuperMIC/ / / / / /Shelob,/Philip,/Pandora/ / LONI: / / /QueenBee2/ / / / / /Eric/ / XSEDE: / / /Stampede/(TACC)/ / / / / /SuperMIC/(LSU)/ / / / / /Comet/(SDSC)/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Overview/of/HPC/systems/ SuperMike8II% 2%Head%nodes:% • • • • • • / Two/2.6/GHz/8%Core/Xeon/64%bit/Processors/ 64GB/1666MHz/RAM/ 500GB/HD/ 40/Gigabit/sec/Infiniband/network/interface/ 1/Gigabit/Ethernet/network/interface/ Red/Hat/Enterprise/Linux/6/ 382%Compute%nodes:% 50%Compute%nodes:% • Two/NVIDIA/M2090/GPUs/ / 8%Compute%nodes:% • 256GB/1666MHz/RAM/ • • • • • • Two/2.6/GHz/8%Core/Xeon/64%bit/Processors/ 32GB/1666MHz/RAM/ 500GB/HD/ 40/Gigabit/sec/Infiniband/network/interface/ 1/Gigabit/Ethernet/network/interface/ Red/Hat/Enterprise/Linux/6/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Overview/of/HPC/systems/ SuperMIC% 2%Head%nodes:% • • • • • • • / Two/2.8GHz/10%Core/Xeon/64%bit/Processors/ One/Intel/Xeon/Phi/or/one/NVIDIA/GPU/ 128GB/DDR3/1866MHz/RAM/ 1TB/HD/ 56/Gigabit/sec/Infiniband/network/interface/ 10/Gigabit/Ethernet/network/interface/ Red/Hat/Enterprise/Linux/6/ 360%Compute%nodes:% 20%Hybrid%compute%nodes:% • One/Intel/Xeon/Phi/7120P/ Coprocessor/ • One/NVIDIA/Tesla/K20X/6GB/GPU/ with/GPUDirect/Support/ • • • • • • • Two/2.8GHz/10%Core/Xeon/64%bit/Processors/ Two/Intel/Xeon/Phi/7120P/Coprocessors/ 64GB/DDR3/1866MHz/RAM/ 500GB/HD/ 56/Gigabit/sec/Infiniband/network/interface/ 1/Gigabit/Ethernet/network/interface/ Red/Hat/Enterprise/Linux/6/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Overview/of/HPC/systems/ QueenBee%2% 1%Head%node:% • Two/10%core/2.8/GHz/Xeon/processors/ • 128/GB/RAM/ • Two/1/TB/HDDs/ • 1/NVIDIA/K20X/GPU/ / 4%VisualizaSon%nodes:% • Two/NVIDIA/Tesla/K40/GPUs/ • 128/GB/memory/ / 4%Big%memory%nodes:% • Four/12%core/2.6/GHz/processors/ • 1.5/TB/memory///// 480%Compute%nodes:% • Two/10%core/2.8/GHz/Xeon/processors/ • 64/GB/RAM/ • 500/GB/HDD/ • 2/NVIDIA/Tesla/K20x/GPUs/ / 16%Compute%nodes:% • Two/10%core/2.8/GHz/Xeon/processors/ • 64/GB/RAM/ • 500/GB/HDD/ • 2/Intel/Xeon/Phi/7120Ps/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Overview/of/HPC/systems/ Stampede%at%TACC% • • • • • 10/Pflops/linux/cluster/based/on/6400+/Dell/PowerEdge/nodes/ 2/Intel/Xeon/E5/(Sandy/Bridge)/processors/per/node/ 1/or/2/Intel/Xeon/Phi/coprocessor(s)/per/node/ Aggregate/peak/performance/of/the/Xeon/processors/is/2+PF% Aggregate/peak/performance/of/Xeon/Phi/coprocessors/is/7+PF% High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Overview/of/HPC/systems/ Massively%parallel%accelerators% NVIDIA/Graphics/ Processors/(GPU)/ Intel/Many/Integrated/ Cores/(MIC)/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Overview/of/HPC/systems/ Massively%parallel%accelerators% Intel/Xeon/Phi/ GeauxDock:% Molecular/ docking/code/for/ structure%based/ drug/discovery/ GeauxDock/runs/over/50×/faster/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Overview/of/HPC/systems/ Massively%parallel%accelerators% NVIDIA/GPU/ GeauxDock:% Molecular/ docking/code/for/ structure%based/ drug/discovery/ GeauxDock/runs/over/200×/faster/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Overview/of/HPC/systems/ Queuing%system% mike.hpc.lsu.edu% ssh% ssh% mike1/ qsub% qsub% mike2/ qsub% ssh% storage1/ storage2! mike001/ mike002/ mike003/ mike004/ mike508! High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Overview/of/HPC/systems/ / Rules% Head%nodes: /edit,/copy,/move/files/ / / / / / /request/compu1ng/nodes/ / / / / / /running/applica1ons/NOT%OK% % Compute%nodes:/run/applica1ons/ / / / / / / /edit,/copy,/move/files/ / / / / / / /compress/data,/clean/up,/etc./ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Overview/of/HPC/systems/ Storage% / /home/username/ /network,/5GB/quota,/ / / / / / / / / /regular/backups/ / /work/username/ /network,/380TB,/files/ / / / / / / / / /stored/up/to/60/days/ / /var/scratch/ / /local,/240GB,/files/are/ / / / / / / / / /deleted/aier/the/job/is/ / / / / / / / / /completed/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Accounts,/alloca1ons,/policy,/etc./ HPC@LSU: /hkp://www.hpc.lsu.edu/ / LONI: / / /hkp://www.loni.org/ / XSEDE:/ / /hkps://www.xsede.org/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Accounts/ HPC@LSU:/ / • Available/to/LSU/students,/postdoctoral/researchers,/ faculty/and/research/associates/ • Non%LSU/collaborators/must/be/sponsored/by/a/LSU/ faculty/member/or/a/research/associate/ / LONI:/ / • Available/to/LONI/affiliates/and/collaborators/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Alloca1ons/ HPC@LSU%and%LONI:/ / • Startup/Alloca1ons/(<50,000/SUs)/ • Research/Alloca1ons/(>/50,000/SUs)/ 1%SU/(Service/Unit)/is/1/core/for/1/hour/ / For/example,/you/will/be/charged:/ / • 16/SUs/for/using/1/node/on/SuperMike%II/for/1/hour/ • 20/SUs/for/using/1/node/on/QueenBee2/for/1/hour/ / 1/SU/is/app./$0.05/// High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Alloca1ons/ HPC@LSU%and%LONI:/ / Startup/Alloca1ons/(<50,000/SUs,/good/for/1/year)/ / • Any/qualified/PI/may/submit/a/request/ • Simplified/procedure/(online/form,/provide/ jus1fica1on/and/intended/use,/no/formal/proposal/is/ required)/ • Limit/of/2/ac1ve/alloca1ons/per/PI/at/any/given/1me/ • Small/projects,/data/analysis,/prep/for/large/ alloca1ons,/etc./ • Awarded/throughout/the/year/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Alloca1ons/ HPC@LSU:/ / Research/Alloca1ons/(>50,000/SUs,/good/for/1/year)/ / • Any/qualified/PI/may/submit/a/request/ • Online/form,/a/formal/proposal/is/required/ • Requests/limited/to/3/million/SUs,/a/PI/may/have/a/ total/of/5/million/SUs/ac1ve/at/any/given/1me/ • Intended/for/large/projects/may/be/eligible/for/ renewal/ • A/summary/report/is/required/at/the/end/of/alloca1on/ • Awarded/at/the/beginning/of/every/calendar/quarter/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Alloca1ons/ LONI:/ / Research/Alloca1ons/(>50,000/SUs,/good/for/1/year)/ / • Any/qualified/PI/may/submit/a/request/ • Online/form,/a/formal/proposal/is/required/ • Requests/limited/to/4%million%SUs,/a/PI/may/have/a/ total/of/6%million%SUs%ac1ve/at/any/given/1me/ • Intended/for/large/projects/may/be/eligible/for/ renewal/ • A/summary/report/is/required/at/the/end/of/alloca1on/ • Awarded/at/the/beginning/of/every/calendar/quarter/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Alloca1ons/ HPC@LSU%and%LONI:/ / Storage/Alloca1ons/(good/for/6/months)/ / • • • • Any/qualified/PI/may/submit/a/request/ May/be/requested/via/the/alloca1on/process/ Limit/of/1/storage/alloca1ons/per/PI/ Require/either/online/form/or/a/formal/proposal,/ depending/on/the/size:/ o Small/(<100GB)/ o Medium/(100GB/–/1TB)/ o Large/(>1TB)/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Accounts,/alloca1ons,/policy,/etc./ HPC@LSU%and%LONI:/ / • Help/available/through/email/at/sys%[email protected]/ / • Website:/hkp://www.hpc.lsu.edu// • Training/ o Moodle/ o Weakly/sessions/ o Workshops/ / • Online/documenta1on,/user/guides,/tutorials,/etc./ • Plenty/of/soiware/already/available/ High%performance/compu1ng////////////////!3D!Cryo(EM!Workshop/ Best/of/luck/using/ HPC/resources/in/ your/research!/
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