CALMIP : HIGH PERFORMANCE COMPUTING
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1 CALMIP : HIGH PERFORMANCE COMPUTING Nicolas.renon@univ-tlse3.fr Emmanuel.courcelle@inp-toulouse.fr CALMIP (UMS 3667) Espace Clément Ader
2 CALMIP :Toulouse University Computing Center q Start in 1994 : 17 Labs. share computing resources q Support of University of Toulouse (6 Universities+ CNRS) q Purposes : q Promote High Performance Computing q training in parallel computing, code optimisation q Exchanges experiences (Thematic Days) q Access to a Competitive computing system q Purchase a system q Achieving performance/»easy to use»/stable q Support Users q Basics q Developping parallel code Page 2
3 CALMIP : a medium/meso size computing Center European O(10) PF National O(1) PF Mesocentre O(100) TF Labs. Mesocentre CALMIP : ü Propinquity ü Production (reliable ressources) ü Multi scientific topic TF = TeraFlop/s (10 12 flop/s) PF = PetaFlop/s (10 15 flop/s) Flop/s = Floating Operation per second Page 3
4 HPC in Europe (Partnership for Advanced Computing in Europe) Sweden Finland Archer 1.3 PFLOP Nederlands CURIE 9PFLOP JUQUEEN 5PFLOP HAZEL HEN SUPERMUC 5PFLOP 3PFLOP Czech Piz Daint 19 PFLOP Poland MareNostrum 6,2 PF MARCONI 6PFLOP PF = PetaFlop/s (10 15 flop/s)
5 CALMIP : CPU hours needs Evolution demande H_CPU/nombre_projets Heures CPU nombre projets Total demandes Total projets Années Page 5
6 CALMIP : CPU hours needs % per Scientific Topics. (+45 Labs) Theoretical Physics 4% Hour CPU needs per scientific topics Engineer Science 3% Matter Science 24% Fluid Mechanics 30% Quantum Chemistry 12% Life Science 10% Numerical Algorithm and Method 1% Universe Science 16% Page 6
7 CALMIP COMPUTING CAPACITY EVOLUTION CALMIP : Supercomputer Evolution # 500 x 7 # 500 # TFlops x TFlops 38,5 TFlops x 3,75 1,5 TFlops 400 GFlops SOLEIL1 SOLEIL2 HYPERION HYPERION+ EOS 68 CPU 136 Go RAM 512 CPU 512 Go RAM CPU 14 To RAM 3 500CPU 14 To RAAM CPU 39 To RAM
8 TOP 500 List # = 93 PF 15 MW 2,2 MW Moore s Law # = 10 PF 12 MW Page 8
9 Ø Shered Memory Machine (or SMP : Symetric Multi-Processing) Memory interconnect Application Parallelism: OpenMP!$OMP DO PARALLEL cores 0 1 limited #cores do i = 1, n a(i) = real(i) ; end do Ø Distributed Memory Machine!$OMP END DO Memory interconnect cores interconnexion interconnexion 0 1 n n+1 Application Parallelism: MPI (Message Passing Interface) more complexity ++ n large, almost unlimited #cores
10 CALMIP & Atomic and Molecular Computation Codes in Matter Science, Quantum Chemistry q 4HE-DFT (OpenMP) q LAMMPS (MPI, GPU) q ADF (MPI) q ABINIT (MPI) q AMBER (MPI, GPU) q bigdft (MPI GPU) q DeMon (demon-nano) (MPI) q DIRAC (MPI) q CPMD (MPI+OpenMP) q CP2K (MPI+OpenMP) q GAMESS (MPI) q GAUSSIAN (OpenMP) q GROMACS (MPI+OpenMP, GPU) q MOLCAS q MOLPRO q NWCHEM (MPI) q NAMD (MPI, GPU) q ORCA (MPI) q QMC=chem (Custom) q QUANTUM ESPRESSO (MPI+OpenMP) q SIESTA (MPI) q VASP (MPI+OpenMP, GPU) q WIEN2K (MPI, Custom) q Today focus on : 4HE-DFT Page 10
11 HIGH PERFORMANCE COMPUTING EOS COMPUTING SYSTEM Frontales de connexion : 4 x (20-cores,128 GB RAM) Cluster distribué BULLx DLC : cores nodes Intel Ivybridge 2,8 Ghz 10-cores 64 GB RAM / nœud Interconnection : Infiniband FDR Nœud large mémoire : 128 cores - 2 TB RAM Intel Haswell-EX 2,2 Ghz 16-cores - Page web associée Solution de visualisation à distance : 2 nœuds (20-cores, 128 GB RAM) Cartes Nvidia Quadro 6000
12 Supercomputer EOS : Architecture Interconnect Interconnexion infiniband FDR interconnexion Compute node (SMP) Compute node (SMP) Compute node (SMP) Memory 64Go SHARED 64Go SHARED 64Go SHARED 20 cores Cache Cache Cache Cache Cache Cache Intel Ivybridge processeur or socket = 10 cores and 25 Mo de cache
13 HIGH PERFORMANCE COMPUTING HANDS ON : CONNEXION TO FRONTAL NODE Connexion «Secure Shell» (ssh) Linux / macos ssh X {login}@eos Frontals nodes : 4 x (20-cores,128 GB RAM) Windows Client ssh with serveur X (Putty/Xming, MobaXterm) - Page web associée
14 HIGH PERFORMANCE COMPUTING LAUNCH COMPUTATIONS : BATCH SCHEDULER Connexion ssh X {login}@eos Frontales de connexion : 4 x (20-cores,128 GB RAM) Launch through the batch scheduler (SLURM) sbatch mon_job Distributed Memory Cluster BULLx DLC (12240 cores nodes) Processeurs Intel Ivybridge 2,8 Ghz 10-cores 64 GB RAM / nœud Interconnection : Infiniband FDR Topologie : full fat-tree
15 HIGH PERFORMANCE COMPUTING SLURM COMMANDS : BASICS Launch job sbatch mon_job Stop job scancel $SLURM_JOBID The list of jobs for $USER squeue u $USER - Page web associée
16 HIGH PERFORMANCE COMPUTING LAUNCH AN OPENMP CODE Shared Memory parallelism (multithreading) : #!/bin/bash #SBATCH --job-name=script_utilisationeos #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=5 #SBATCH --time=0-01:00:00 export OMP_NUM_THREADS=5 Specify # cores (example : 5) OpenMP variable specify the number of threads (should be the same as # cores above) srun./mon_appli.exe - Page web associée
17 MESOCENTER CALMIP
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