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!/