Campus school 2014 at University of Ljubljana

from to (CET)
at Fakulteta za strojništvo and FIŠ Novo mesto ( II/5, IV/2 and P2 )
Aškerčeva 6 1000 Ljubljana SLOVENIA
Description Summer HPC week organized for undergraduate and graduate students at two locations simultaneously:
  1. University of Ljubljana,  Faculty of Mechanical Engineering, Aškerčeva 6, Ljubljana (ULFME)
  2. Faculty of Information studies, Ulica talcev 3, Novo Mesto (FIS)
Morning lectures and live demonstrations on HPC are prepared by ULFME and FIS and broadcasted from one site to other. In the afternoon hands-on trainings in computing classrooms are conveyed at each site with different excercises on HPCFS supercomputer. On Thursday there will be organized transport from Novo mesto to Ljubljana and back. See attached programme for details.
Participants will receive accounts on supercomputer HPCFS for hands-on from both sites.

Important notices for participants will be published on local WEB page (http://hpc.fs.uni-lj.si/cs14).
Material:
Support Email: events@hpc.fs.uni-lj.si Telephone: +38614771436
Go to day
  • Monday, 7 July 2014
    • 09:00 - 17:00 Linux
      - Introduction to Campus school and visit to HPC center,
      - Introduction to GNU/Linux, GUI environments
         Bash, AWK scripts, Modules, Introduction to compiling
         Programming languages in and devel environments in Linuxu
      
      Intro to HPC, HPC usage and NxClient remote desktop connection to HPCFS, Batch and job scheduler LSF and interactive usage of nodes, 
      Presentation of possible solutions of parallel programs by using OpenMP in MPI, Hello World parallel in C with OpenMP, Hello World with OpenMPI and running on  HPCFS.
      
      Conveners: Dr. Leon Kos (University of Ljubljana), Matjaž Šubelj (FS)
      Location: FS ( II/5 )
      Material: Unix shell link slides pdf filedown arrow
      • 13:00 Lunch 1h30'
    • 10:45 - 11:00 Coffe break each day ( FS and FIS ( II/4 and P2 ) )
      Coffee, water and cookies will be self served in Room II/4
    • 14:30 - 18:00 Introduction to LINUX
      Introduction to linux, programming, programming environments, Hands-on on HPCFS
      Convener: Dr. Biljana Mileva Boshkoska (FIS)
      Location: FIS ( P2 )
      Material: slides pdf file
    • 15:45 - 16:00 Tea break each day
      Coffee, tea, water and cookies  self served
  • Tuesday, 8 July 2014
    • 09:00 - 13:00 Introduction to HPC: Video from NM to LJ
      HPC introduction and basics in C language. 
      Introduction to MPI on HPCFS
      
      Predstavitev HPC:
       - kaj je HPC in zakaj se uporablja
       - kaj sestavlja superračunalnik
      Osnove MPI:
       - kaj je MPI in zakaj se uporablja
       - pošiljanje sporočil med procesi
       - tipi komunikacije
       - osnovne MPI v jeziku C
      Convener: Dr. Matjaž Depolli (IJS)
      Location: FIS and FS ( P2 and IV/2 )
      Material: slides pdf filedown arrow
    • 13:00 - 14:30 Lunch
    • 14:30 - 18:00 Hands-on HPC
      - spoznavanje z MPI
       - merjenje zmogljivosti
       - sinhrona komunikacija
       - skupinska komunikacija
      Convener: Dr. Matjaž Depolli (IJS)
      Location: FIS ( P2 )
      Material: slides pdf file
    • 14:30 - 17:00 HPC introduction: MPI tutorials on HPCFS
      Convener: Dr. Leon Kos (University of Ljubljana)
      Location: FS ( II/5 )
      Material: slides pdf filedown arrow
  • Wednesday, 9 July 2014
    • 09:00 - 11:30 HPC for applications (NM video to FS)
      - GPU applications (Abellium),
      - Analysis of monoamin oksidaze (Kemijski inštitut), 
      - Problem MAX-Klike (IJS, Depolli)
      
      Convener: Dr. Tadej Kanduč
      Location: Novo Mesto
      • 09:00 Uporaba GPU 45'
        - Predstavitev osnov programiranja grafičnih procesorjev s pomočjo tehnologije OpenCL
        - Demonstracija izbranih primerov uporabe
        Speaker: Alen Orbanić (Abelium)
        Material: Slides pdf file
      • 09:45 Max Klika 45'
         - O NP-polnem problemu iskanja največje klike v grafu
         - Dve vzporednosti v algoritmu
         - Implementacija za večjedrne računalnike
        Speaker: Dr. Matjaž Depolli (JSI)
        Material: Slides pdf file
      • 10:30 Molekularne simulacije 45'
        - molekularne simulacije hidratiranih proteinov
        - obravnava daljnosežne elektrostatike
        - razgradnja serotonina in dopamina
        
        V predavanju bom predstavil molekularne simulacije hidratiranih proteinov. Klasične molekulske simulacije so numerično reševanje enačb gibanja za atomska jedra. Seznanili se bomo z upoštevanjem efektov topila, začetnim pogojem, uravnoteženjem in analizo trajektorije. Posebno pozornost bomo posvetili obravnavi daljnosežne elektrostatike. Za nekatere aplikacije je potrebo kvantizirati enačbe gibanja z metodo integracije po poti, za obravnavo kemijske reaktivnosti pa je treba uporabiti multiskalni pristop QM/MM. Encimska reakcija je tipičen primer, ki zahteva multiskalno obravnavo. Kot primer bom prikazal razgradnjo serotonina in dopamina z encimoma monoamino oksidaza A in B. Diskutirali bomo relevanco biomolekularnih simulacij za načrtovanje zdravil.)
        Speaker: Dr. Janez Mavri (Kemijski institut)
        Material: Slides pdf file
      • 11:15 Coffee break 15'
    • 11:30 - 13:00 Simulations (video from LJ to FIS)
      Introduction to open source simulation programs in the area of Computational Fluid Dynamic (CFD - OpenFoam) and Structural Mechanics and Multiphysics (Elmer), 
      
      Convener: Dr. Leon Kos (University of Ljubljana)
      Location: FS ( IV/2 )
      Material: slides link
      • 11:40 OpenFOAM introduction 20'
        Speaker: Dr. Marijo Telenta (FS)
        Material: Slides pdf file
      • 12:00 Elmer introduction 1h0'
        Speaker: Andrej Vihtelič
        Material: Slides pdf file
    • 13:00 - 14:30 Lunch ( )
    • 14:30 - 19:00 Simulations on HPC (LJ): CFD practicals on HPCFS
      Elmer and OpenFOAM
      Conveners: Dr. Marijo Telenta (FS), Andrej Vihtelič
      Location: FS ( II/5 )
      Material: Elmer tutorials link notes unknown type file
    • 15:00 - 18:00 Hands-on HPC (NM)
      - Different HPC programming examples
      - Overview of tasks and second part of assignments for home-work
      
       - asinhrona komunikacija
       - spoznavanje z OpenMP
       - izziv za vse željne več programiranja
       - paralelizacija iskanja praštevil
      Conveners: Dr. Matjaž Depolli (IJS), Dr. Borut Lužar (FIŠ), Dr. Tadej Kanduč (FIŠ)
      Location: FIS ( P2 )
  • Thursday, 10 July 2014
    • 08:00 - 09:00 Transfer from NM to FS
      Bus transfer will be organized in front of FIŠ to Ljubljana and back
    • 09:00 - 10:00 HPCFS demos 1h0' ( FS ( II/5 ) )
      - Cluster Manament Utility
      - Lustre on ZFS performance $HOME, $WORK, $SCRATCH 
      - Unified Fabric Manager
      - Allinea DDT
      - Mathematica parallel setup
      Speaker: Dr. Leon Kos (University of Ljubljana)
    • 10:00 - 18:00 Python MPI
      - Python programming language introduction and parallel programming with MPI4Py library.
      - NumPy library and its relevance for HPC.
      - Simple MPI4Py message passing examples 
      - Upgraded  MPI4Py examples with problem assignments in groups 
      - Parallelization suggestions for further development
      Convener: Dr. Leon Kos (University of Ljubljana)
      Material: MPI4Py API reference link MPI4Py User manual link NumPy Tutorial link Python in High-Performance Computing pdf file Python introduction link
      • 13:00 EGPR demos 1h0'
      • 14:00 Lunch 1h30'
    • 18:00 - 19:00 Transfer from FS to NM
  • Friday, 11 July 2014
    • 09:00 - 10:30 Parallel algorithms (NM) video to LJ
      Introduction to development and analysis of parallel algorithms
      Introduction to HiPEAC summer school, Ljubljana
      Convener: Dr. Matjaž Depolli (IJS)
      Location: FIS and FS ( P2 and IV/2 )
      Material: slides pdf file
    • 10:30 - 10:45 Coffe break
    • 10:45 - 13:00 HPC, visualization and PRACE (LJ) video to NM
      - Introduction to PGAS programming languages X10, Chapel (Jure Pečar, Arctur) 
      - Cluster management with  HPC-PUPPET and EasyBlocks (Jure Pečar, Arctur)
      - Latest results from CloudFlow and Fortissimo projects (Tomi Ilijaš, Arctur)
      - Introduction to PRACE and access to TIER-1 and TIER-0 supercomputers (Leon Kos, ULFME)
      
      Conveners: Dr. Leon Kos (University of Ljubljana), Jurij Pečar (Arctur)
      Location: FS and FIS ( IV/2 and P2 )
      Material: slides pdf filedown arrow
    • 13:00 - 14:30 Lunch ( )
    • 14:30 - 19:00 Hands on Visualization tools
      - Visualization with GNUplot, Inkscape, LLNL VisIt, ParaView, Inkscape, OpenGL, WebGL,  ...
      Material: VisIt, Paraview and OpenGL tutorial link
    • 14:30 - 16:30 Hands On (FIS)
      Various exercises and analysis of student assignments
      - pregled rešenih izzivov
      - optimiranje programov
      Location: FIS ( P2 )
    • 16:30 - 17:00 Closing ceremony ( FS and FIS ( II/5 in P2 ) )